From b396b6383bc89a56e6d37b291cc47a2622d02620 Mon Sep 17 00:00:00 2001 From: roalva1 Date: Mon, 4 May 2015 17:13:14 +0200 Subject: [PATCH 001/178] concatenate in one VCF some splitted vcfs whith bcftools --- lib/galaxy/datatypes/tabular.py | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index df571eb1120..1573fede07f 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -7,6 +7,10 @@ pkg_resources.require( "bx-python" ) import gzip import logging import os +import tempfile +import subprocess +import shutil + from cgi import escape from galaxy import util from galaxy.datatypes import data @@ -658,6 +662,25 @@ class Vcf( Tabular ): if line and line.startswith( '#' ): # Found header line, get sample names. dataset.metadata.sample_names = line.split()[ 9: ] + @staticmethod + def merge(split_files, output_file): + + tmp_dir = tempfile.mkdtemp() + stderr_name = tempfile.NamedTemporaryFile(dir=tmp_dir, prefix="bam_merge_stderr").name + command = ["bcftools", "concat"] + split_files + ["-o", output_file] + print command + proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) + exit_code = proc.wait() + # Did merge succeed? + stderr = open(stderr_name).read().strip() + if stderr: + if exit_code != 0: + shutil.rmtree(tmp_dir) # clean up + raise Exception, "Error merging VCF files: %s" % stderr + else: + print stderr + os.unlink(stderr_name) + os.rmdir(tmp_dir) # ------------- Dataproviders @dataproviders.decorators.dataprovider_factory( 'genomic-region', From d4fba962310ea8357516526a941df05572fa2a9e Mon Sep 17 00:00:00 2001 From: Eteri Date: Mon, 22 Jun 2015 14:56:41 +0200 Subject: [PATCH 002/178] graph visualization added --- .../plugins/visualizations/graphviz/README.md | 71 + .../graphviz/config/graphviz.xml | 15 + .../graphviz/static/css/style.css | 197 + .../graphviz/static/img/15xvbd5.png | Bin 0 -> 174 bytes .../graphviz/static/img/lite-blue-check.png | Bin 0 -> 3101 bytes .../graphviz/static/js/collapse.js | 215 + .../graphviz/static/js/cytoscape.min.js | 27 + .../graphviz/static/js/graphVis.js | 165 + .../graphviz/static/js/jquery.qtip.js | 3451 +++++++++++++++++ .../graphviz/static/js/tip_centerwindow.js | 104 + .../graphviz/static/js/tip_followscroll.js | 88 + .../graphviz/static/js/toolPanelFunctions.js | 631 +++ .../graphviz/static/js/wz_tooltip.js | 1301 +++++++ .../graphviz/templates/graphviz.mako | 171 + 14 files changed, 6436 insertions(+) create mode 100644 config/plugins/visualizations/graphviz/README.md create mode 100644 config/plugins/visualizations/graphviz/config/graphviz.xml create mode 100644 config/plugins/visualizations/graphviz/static/css/style.css create mode 100644 config/plugins/visualizations/graphviz/static/img/15xvbd5.png create mode 100644 config/plugins/visualizations/graphviz/static/img/lite-blue-check.png create mode 100644 config/plugins/visualizations/graphviz/static/js/collapse.js create mode 100644 config/plugins/visualizations/graphviz/static/js/cytoscape.min.js create mode 100644 config/plugins/visualizations/graphviz/static/js/graphVis.js create mode 100644 config/plugins/visualizations/graphviz/static/js/jquery.qtip.js create mode 100644 config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js create mode 100644 config/plugins/visualizations/graphviz/static/js/tip_followscroll.js create mode 100644 config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js create mode 100644 config/plugins/visualizations/graphviz/static/js/wz_tooltip.js create mode 100644 config/plugins/visualizations/graphviz/templates/graphviz.mako diff --git a/config/plugins/visualizations/graphviz/README.md b/config/plugins/visualizations/graphviz/README.md new file mode 100644 index 00000000000..c851f8a831e --- /dev/null +++ b/config/plugins/visualizations/graphviz/README.md @@ -0,0 +1,71 @@ +# Galaxy Graph Visualization Framework # + +The framework visualizes graphs and tries to provide functionality to easily manipulate them in Galaxy platform. +For graph construction and visualization [Cytoscape.js](http://js.cytoscape.org/) library is used. + +### Input formats ### + +As input files json or txt formats can be used. + +Examples: + +* json file + +``` +#!json + +{ + "nodes":[ + { + "id": 1, + }, + { + "id": 2, + } + ], + "links":[ + + { + "source":1, + "target":2, + } + ] +} + +``` + +* txt file with matrix notation + + +``` +#!python + +1 3 4 5 +2 4 6 +3 1 5 6 2 +4 3 +5 +6 +``` +Line "1 3 4 5" can be read as: source: node "1" , target: node "3" ("4","5") + + +### General Description ### + +The framework consists of 3 parts. On the left and right sides of the screen are 2 sliding panels. By default they are hidden. They can be opened by clicking the button on the upper part of each panel. The left panel is Tool Panel where user can choose different features to manipulate the graph. On the right panel all available node information (metadata) is displayed. +In between these panels is the main screen where the visualization is displayed. + + +### Features ### + +| Feature | Description | +| ------------- | ------------------------------ | +| Lazy loading | If the graph contains more than 50 nodes lazy loading will be performed. At first the framework will load only the root nodes(nodes that have no incoming edges) and their child nodes. The child nodes that can be expanded (contain other nodes) will have bigger size. To load the rest of the graph *Expand* feature must be used on the expandable nodes. It's working only if the graph has at least one root node | +| Delete | Deletes selected nodes and edges. Can be performed by using corresponding button or shortcut key 'd' | +| Restore | Restores the deleted nodes and edges form the very last deletion performed | +| Collapse | Collapse feature can be performed on the selected node which has outgoing edges. It hides all outgoing (child) nodes and edges of the selected node. Useful for compact view. Can be performed by using corresponding button or shortcut key 'c'. To uncollapse the node *Expand* or *Restore Structure* can be used | +|Expand| Expand feature can be used to load more nodes in case if lazy loading was used or to uncollapse collapsed nodes.Can be performed by using corresponding button or shortcut key 'e' | +|Metadata | Node metadata is always displayed on the right panel | +|Child/parent dependencies| To see incoming/outgoing nodes and edges of the selected node enable (check) corresponding feature on the left panel | +|Labels| Node and edge labels can be shown/hidden by enabling/disabling corresponding option on the left Panel | +|Export PNG| It is possible to export the visualization of the graph as a png picture. To perform the action click on the corresponding button | \ No newline at end of file diff --git a/config/plugins/visualizations/graphviz/config/graphviz.xml b/config/plugins/visualizations/graphviz/config/graphviz.xml new file mode 100644 index 00000000000..1a51da4c699 --- /dev/null +++ b/config/plugins/visualizations/graphviz/config/graphviz.xml @@ -0,0 +1,15 @@ + + + + + + HistoryDatasetAssociation + data.Text + dataset_id + + + + dataset_id + + + diff --git a/config/plugins/visualizations/graphviz/static/css/style.css b/config/plugins/visualizations/graphviz/static/css/style.css new file mode 100644 index 00000000000..61d7eaba86e --- /dev/null +++ b/config/plugins/visualizations/graphviz/static/css/style.css @@ -0,0 +1,197 @@ + + +#cy { + height: 100%; + width: 100%; + position: absolute; + top: 0; +} +p { +text-align:center; +} + + +.panel { + + width:245px; + float:left; + height: 650px; + background:#d9dada; + position:relative; + left:-250px; + top: -10px; + font-family: Arial, "Helvetica Neue", Helvetica, sans-serif; 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i--) { + + cy.style() + .selector('.collapsedNode' + i) + .css({ + 'opacity': 0.8, + 'background-color': '#888888', + 'line-color': '#ddd', + 'target-arrow-color': '#ddd' + }) + .update(); + + cy.style() + .selector('.superNode') + .css({ + 'opacity': 0.8, + 'background-color': '#888888', // + 'border-width': 0 + }) + .update(); + + cy.remove('.virtualEdges' + i); + + cy.nodes().removeClass('superNode'); + cy.nodes().removeClass('collapsedNode' + i); + cy.edges().removeClass('collapsedNode' + i); + cy.edges().removeClass('virtualEdges' + i); + + } +} + + + +// counts the number of collapsed nodes for the given superNode +function countCollapse(nd) { + + if (nd.hasClass('superNode')) { + Tip('contains ' + nd.data().colNum + ' node(s)', PADDING, 10); + } else if (nd.hasClass('toBeExpaned')) { + + var eles = allcy.nodes(); + var selectedNodeId = nd.id(); + selectedNodeId = selectedNodeId.replace(/[^0-9\.]+/g, ""); + + var nodeCount = eles[selectedNodeId].outdegree(); + Tip('contains ' + nodeCount + ' node(s)', PADDING, 10); + + } else { + Tip('contains 0 node(s)', PADDING, 10); + } +} diff --git a/config/plugins/visualizations/graphviz/static/js/cytoscape.min.js b/config/plugins/visualizations/graphviz/static/js/cytoscape.min.js new file mode 100644 index 00000000000..c285cf77dbf --- /dev/null +++ b/config/plugins/visualizations/graphviz/static/js/cytoscape.min.js @@ -0,0 +1,27 @@ +/*! + * This file is part of Cytoscape.js 2.4.0. + * + * Cytoscape.js is free software: you can redistribute it and/or modify it + * under the terms of the GNU Lesser General Public License as published by the Free + * Software Foundation, either version 3 of the License, or (at your option) any + * later version. + * + * Cytoscape.js is distributed in the hope that it will be useful, but WITHOUT + * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS + * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more + * details. + * + * You should have received a copy of the GNU Lesser General Public License along with + * Cytoscape.js. 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b=t.parse(y,m);b?(f.push({name:y,val:m}),n()):(e.util.error("Skipping property: Invalid property definition in: "+s),n())}else e.util.error("Skipping property: Invalid property name in: "+s),n()}if(v){i();break}t.selector(d);for(var w=0;w1?", "+JSON.stringify(r):"")+" );"," "," resolve = origResolve;"," resolve( res.length > 0 ? res : ret );","}"].join("\n"))}};e.fn.thread({reduce:o({name:"reduce"}),reduceRight:o({name:"reduceRight"}),map:o({name:"map"})});var s=e.thdfn;s.promise=s.run,s.terminate=s.halt=s.stop,s.include=s.require,e.worker=e.Worker=e.Thread,e.fn.thread({on:e.define.on(),one:e.define.on({unbindSelfOnTrigger:!0}),off:e.define.off(),trigger:e.define.trigger()}),e.define.eventAliasesOn(e.thdfn)}(cytoscape,"undefined"==typeof window?null:window),function(e,t){"use strict";e.Fabric=function(t){if(!(this instanceof e.Fabric))return new e.Fabric(t);this._private={pass:[]};var r=4;e.is.number(t),t="undefined"!=typeof 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i=e.fabfn;i.promise=i.run,i.terminate=i.halt=i.stop,i.include=i.require,e.fn.fabric({on:e.define.on(),one:e.define.on({unbindSelfOnTrigger:!0}),off:e.define.off(),trigger:e.define.trigger()}),e.define.eventAliasesOn(e.fabfn)}(cytoscape,"undefined"==typeof window?null:window),function(e,t){"use strict";var r=e.is.touch(),i={},n=e.util.copy(i);e.defaults=function(t){i=e.util.extend({},n,t)},e.fn.core=function(t,r){for(var i in t){var n=t[i];e.Core.prototype[i]=n}},e.Core=function(n){if(!(this instanceof e.Core))return new e.Core(n);var a=this;n=e.util.extend({},i,n);var o=n.container,s=o?o._cyreg:null;if(s=s||{},s&&s.cy){if(o)for(;o.firstChild;)o.removeChild(o.firstChild);s.cy.notify({type:"destroy"}),s={}}var l=s.readies=s.readies||[];o&&(o._cyreg=s),s.cy=a;var u=void 0!==t&&void 0!==o&&!n.headless,c=n;c.layout=e.util.extend({name:u?"grid":"null"},c.layout),c.renderer=e.util.extend({name:u?"canvas":"null"},c.renderer);var d=function(e,t,r){return void 0!==t?t:void 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r,i=this;if(e.is.elementOrCollection(t)){var n=t;if(n._private.cy===i)r=n.restore();else{for(var a=[],o=0;oo;o++){var d=u[o],h=l[d];if(e.is.array(h))for(var p=0,v=h.length;v>p;p++){var f=h[p];f.group=d,a.push(f)}}r=new e.Collection(i,a)}else{var f=t;r=new e.Element(i,f).collection()}return r},remove:function(t){if(e.is.elementOrCollection(t))t=t;else if(e.is.string(t)){var r=t;t=this.$(r)}return t.remove()},load:function(i,n,a){function o(){s.one("layoutready",function(e){s.notifications(!0),s.trigger(e),s.notify({type:"load",collection:s.elements()}),s.one("load",n),s.trigger("load")}).one("layoutstop",function(){s.one("done",a),s.trigger("done")});var t=e.util.extend({},s._private.options.layout);t.eles=s.$(),s.layout(t)}var s=this;s.notifications(!1);var l=s.elements();return l.length>0&&l.remove(),null!=i&&(e.is.plainObject(i)||e.is.array(i))&&s.add(i),t?r(o):o(),this}})}(cytoscape,"undefined"==typeof window?null:window),function(e,t){"use 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d=l._private.pan,h={x:d.x,y:d.y},p=l._private.zoom;r.started=!0,r.startTime=Date.now(),r.startPosition=u,r.startStyle=c,r.startPan=h,r.startZoom=p}function a(t,r,i,n){var a,u=l._private.style,c=r.properties,d=r.params,h=r.startTime,p=!n;if(a=0===r.duration?1:Math.min(1,(i-h)/r.duration),0>a?a=0:a>1&&(a=1),null==c.delay){var v=r.startPosition,f=c.position,g=t._private.position;f&&p&&(o(v.x,f.x)&&(g.x=s(v.x,f.x,a)),o(v.y,f.y)&&(g.y=s(v.y,f.y,a)));var y=r.startPan,m=c.pan,x=t._private.pan,b=null!=m&&n;b&&(o(y.x,m.x)&&(x.x=s(y.x,m.x,a)),o(y.y,m.y)&&(x.y=s(y.y,m.y,a)),t.trigger("pan"));var w=r.startZoom,_=c.zoom,E=null!=_&&n;E&&(o(w,_)&&(t._private.zoom=s(w,_,a)),t.trigger("zoom")),(b||E)&&t.trigger("viewport");var S=c.style||c.css;if(S&&p)for(var D=0;D=1&&(r.done=!0),a}function o(t,r){return null==t||null==r?!1:e.is.number(t)&&e.is.number(r)?!0:t&&r?!0:!1}function s(t,r,i){0>i?i=0:i>1&&(i=1);var n,a;if(n=null!=t.pxValue||null!=t.value?null!=t.pxValue?t.pxValue:t.value:t,a=null!=r.pxValue||null!=r.value?null!=r.pxValue?r.pxValue:r.value:r,e.is.number(n)&&e.is.number(a))return n+(a-n)*i;if(e.is.number(n[0])&&e.is.number(a[0])){var o=n,s=a,l=function(e,t){var r=t-e,n=e;return Math.round(i*r+n)},u=l(o[0],s[0]),c=l(o[1],s[1]),d=l(o[2],s[2]);return[u,c,d]}return void 0}var l=this;l.styleEnabled()&&t&&r()}})}(cytoscape,"undefined"==typeof window?null:window),function(e){"use strict";e.fn.core({data:e.define.data({field:"data",bindingEvent:"data",allowBinding:!0,allowSetting:!0,settingEvent:"data",settingTriggersEvent:!0,triggerFnName:"trigger",allowGetting:!0}),removeData:e.define.removeData({field:"data",event:"data",triggerFnName:"trigger",triggerEvent:!0}),scratch:e.define.data({field:"scratch",allowBinding:!1,allowSetting:!0,settingTriggersEvent:!1,allowGetting:!0}),removeScratch:e.define.removeData({field:"scratch",triggerEvent:!1})})}(cytoscape),function(e){"use 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`"+r+"` found; did you include its JS file?");t.eles=null!=t.eles?t.eles:this.$(),e.is.string(t.eles)&&(t.eles=this.$(t.eles));var n=new i(e.util.extend({},t,{cy:this}));return e.is.plainObject(n._private)||(n._private={}),n._private.cy=this,n._private.listeners=[],n}}),e.corefn.createLayout=e.corefn.makeLayout}(cytoscape),function(e){"use strict";e.fn.core({notify:function(e){if(this._private.batchingNotify){var t=this._private.batchNotifyEles,r=this._private.batchNotifyTypes;if(e.collection)for(var i=0;i0&&l>0&&!isNaN(i.w)&&!isNaN(i.h)&&i.w>0&&i.h>0){o=Math.min((s-2*r)/i.w,(l-2*r)/i.h),o=o>this._private.maxZoom?this._private.maxZoom:o,o=othis._private.maxZoom?this._private.maxZoom:i,i=ir.maxZoom||!r.zoomingEnabled?o=!0:(r.zoom=l,a.push("zoom"))}if(n&&(!o||!t.cancelOnFailedZoom)&&r.panningEnabled){var u=t.pan;e.is.number(u.x)&&(r.pan.x=u.x,s=!1),e.is.number(u.y)&&(r.pan.y=u.y,s=!1),s||a.push("pan")}return a.length>0&&(a.push("viewport"),this.trigger(a.join(" 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e=this.width(),t=this.height();return{x1:0,y1:0,x2:e,y2:t,w:e,h:t}}}),e.corefn.centre=e.corefn.center,e.corefn.autolockNodes=e.corefn.autolock,e.corefn.autoungrabifyNodes=e.corefn.autoungrabify}(cytoscape),function(e){"use strict";e.fn.collection=e.fn.eles=function(t,r){for(var i in t){var n=t[i];e.Collection.prototype[i]=n}};var t={prefix:{nodes:"n",edges:"e"},id:{nodes:0,edges:0},generate:function(t,r,i){var n=e.is.element(r)?r._private:r,a=n.group,o=null!=i?i:this.prefix[a]+this.id[a];if(t.getElementById(o).empty())this.id[a]++;else for(;!t.getElementById(o).empty();)o=this.prefix[a]+ ++this.id[a];return o}};e.Element=function(t,r,i){if(!(this instanceof e.Element))return new e.Element(t,r,i);var n=this;if(i=void 0===i||i?!0:!1,void 0===t||void 0===r||!e.is.core(t))return void e.util.error("An element must have a core reference and parameters set");if("nodes"!==r.group&&"edges"!==r.group)return void e.util.error("An element must be of type `nodes` or `edges`; you specified `"+r.group+"`");if(this.length=1,this[0]=this,this._private={cy:t,single:!0,data:r.data||{},position:r.position||{},autoWidth:void 0,autoHeight:void 0,listeners:[],group:r.group,style:{},rstyle:{},styleCxts:[],removed:!0,selected:r.selected?!0:!1,selectable:void 0===r.selectable?!0:r.selectable?!0:!1,locked:r.locked?!0:!1,grabbed:!1,grabbable:void 0===r.grabbable?!0:r.grabbable?!0:!1,active:!1,classes:{},animation:{current:[],queue:[]},rscratch:{},scratch:r.scratch||{},edges:[],children:[]},r.renderedPosition){var a=r.renderedPosition,o=t.pan(),s=t.zoom();this._private.position={x:(a.x-o.x)/s,y:(a.y-o.y)/s}}if(e.is.string(r.classes))for(var l=r.classes.split(/\s+/),u=0,c=l.length;c>u;u++){var d=l[u];d&&""!==d&&(n._private.classes[d]=!0)}r.css&&t.style().applyBypass(this,r.css),(void 0===i||i)&&this.restore()},e.Collection=function(r,i,n){if(!(this instanceof e.Collection))return new e.Collection(r,i);if(void 0===r||!e.is.core(r))return void e.util.error("A collection must have a 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r=this._private.cy,i=this._private.ids[t];return i?i:e.Collection(r)},e.elesfn.json=function(){var t=this.element();if(null==t)return void 0;var r=t._private,i=e.util.copy({data:r.data,position:r.position,group:r.group,bypass:r.bypass,removed:r.removed,selected:r.selected,selectable:r.selectable,locked:r.locked,grabbed:r.grabbed,grabbable:r.grabbable,classes:""}),n=[];for(var a in r.classes)r.classes[a]&&n.push(a);for(var o=0;od;d++){var p=i[d];p.isNode()?(s.push(p),u++):(l.push(p),c++)}o=s.concat(l);for(var d=0,h=o.length;h>d;d++){var p=o[d];if(p.removed()){var v=p._private,f=v.data;if(void 0===f.id)f.id=t.generate(a,p);else{if(e.is.emptyString(f.id)||!e.is.string(f.id)){e.util.error("Can not create element with invalid string ID `"+f.id+"`");continue}if(0!==a.getElementById(f.id).length){e.util.error("Can not create second element with ID `"+f.id+"`");continue}}var g=f.id;if(p.isEdge()){for(var y=p,m=["source","target"],x=m.length,b=!1,w=0;x>w;w++){var _=m[w],E=f[_];null==E||""===E?(e.util.error("Can not create edge `"+g+"` with unspecified "+_),b=!0):a.getElementById(E).empty()&&(e.util.error("Can not create edge `"+g+"` with nonexistant "+_+" `"+E+"`"),b=!0)}if(b)continue;var S=a.getElementById(f.source),D=a.getElementById(f.target);S._private.edges.push(y),D._private.edges.push(y),y._private.source=S,y._private.target=D}v.ids={},v.ids[g]=p,v.removed=!1,a.addToPool(p),n.push(p)}}for(var d=0;u>d;d++){var k=o[d],f=k._private.data,P=k._private.data.parent,C=null!=P;if(C){var T=a.getElementById(P);if(T.empty())f.parent=void 0;else{for(var M=!1,N=T;!N.empty();){if(k.same(N)){M=!0,f.parent=void 0;break}N=N.parent()}M||(T[0]._private.children.push(k),k._private.parent=T[0],a._private.hasCompoundNodes=!0)}}}if(n=new e.Collection(a,n),n.length>0){var B=n.add(n.connectedNodes()).add(n.parent());B.updateStyle(r),r?n.rtrigger("add"):n.trigger("add")}return i},e.elesfn.removed=function(){var e=this[0];return e&&e._private.removed},e.elesfn.inside=function(){var e=this[0];return e&&!e._private.removed},e.elesfn.remove=function(t){function r(e){for(var t=e._private.edges,r=0;rh;h++){var v=s[h];n(v)}for(var h=0;h0&&(t&&this.cy().notify({type:"remove",collection:x}),x.trigger("remove"));for(var b={},h=0;h0,a=t.getElementById(i).length>0;if(n||a){var o=this.jsons();this.remove();for(var s=0;s0;if(c){var o=this.jsons(),d=this.descendants(),h=d.merge(d.add(this).connectedEdges());this.remove();for(var s=0;su||!n)&&(o=u,n=l)}return{edge:n,dist:o}};f.size()>0;){var y=f.pop(),m=y.value,x=y.id,b=a.getElementById(x);if(u[x]=m,m===Math.Infinite)break;for(var w=b.neighborhood().intersect(d),p=0;p0)for(i.unshift(r);l[n.id()];){var o=l[n.id()];i.unshift(o.edge),i.unshift(o.node),n=o.node}return new e.Collection(a,i)}}}}),e.elesfn.bfs=e.elesfn.breadthFirstSearch,e.elesfn.dfs=e.elesfn.depthFirstSearch,e.elesfn.stdBfs=e.elesfn.stdBreadthFirstSearch,e.elesfn.stdDfs=e.elesfn.stdDepthFirstSearch}(cytoscape),function(e){"use strict";e.fn.eles({aStar:function(t){t=t||{};var r=function(e,t,i,a){if(e==t)return a.push(n.getElementById(t)),a;if(t in i){var o=i[t],s=p[t];return a.push(n.getElementById(t)),a.push(n.getElementById(s)),r(e,o,i,a)}return void 0},i=function(e,t){if(0===e.length)return void 0;for(var r=0,i=t[e[0]],n=1;na&&(i=a,r=n)}return r},n=this._private.cy;if(null==t||null==t.root)return void 0;var a=e.is.string(t.root)?this.filter(t.root)[0]:t.root[0];if(null==t.goal)return void 0;var o=e.is.string(t.goal)?this.filter(t.goal)[0]:t.goal[0];if(null!=t.heuristic&&e.is.fn(t.heuristic))var s=t.heuristic;else var s=function(){return 0};if(null!=t.weight&&e.is.fn(t.weight))var l=t.weight;else var l=function(e){return 1};if(null!=t.directed)var u=t.directed;else var u=!1;var c=[],d=[a.id()],h={},p={},v={},f={};v[a.id()]=0,f[a.id()]=s(a);for(var g=this.edges().stdFilter(function(e){return!e.isLoop()}),y=this.nodes(),m=0;d.length>0;){var x=i(d,f),b=n.getElementById(d[x]);if(m++,b.id()==o.id()){var w=r(a.id(),o.id(),h,[]);return w.reverse(),{found:!0,distance:v[b.id()],path:new e.Collection(n,w),steps:m}}c.push(b.id()),d.splice(x,1);var _=b.connectedEdges();u&&(_=_.stdFilter(function(e){return e.data("source")===b.id()})),_=_.intersect(g);for(var E=0;E<_.length;E++){var S=_[E],D=S.connectedNodes().stdFilter(function(e){return e.id()!==b.id()}).intersect(y);if(-1==c.indexOf(D.id())){var k=v[b.id()]+l.apply(S,[S]);-1!=d.indexOf(D.id())?ku;u++)l[o[u].id()]=u;for(var c=[],u=0;s>u;u++){for(var d=new Array(s),h=0;s>h;h++)d[h]=u==h?0:1/0;c.push(d)}var p=[],v=[],f=function(e){for(var t=0;s>t;t++){for(var r=new Array(s),i=0;s>i;i++)r[i]=void 0;e.push(r)}};f(p),f(v);for(var u=0;um&&(c[g][y]=m,p[g][y]=y,v[g][y]=a[u])}if(!n)for(var u=0;um&&(c[g][y]=m,p[g][y]=y,v[g][y]=a[u])}for(var x=0;s>x;x++)for(var u=0;s>u;u++)for(var h=0;s>h;h++)c[u][x]+c[x][h]u;u++)b.push(o[u].id());var w={distance:function(t,i){if(e.is.string(t))var n=r.filter(t)[0].id();else var n=t.id();if(e.is.string(i))var a=r.filter(i)[0].id();else var a=i.id();return c[l[n]][l[a]]},path:function(t,i){var n=function(e,t,i,n,a){if(e===t)return r.getElementById(n[e]);if(void 0===i[e][t])return void 0;for(var o=[r.getElementById(n[e])],s=e;e!==t;){s=e,e=i[e][t];var l=a[s][e];o.push(l),o.push(r.getElementById(n[e]))}return o};if(e.is.string(t))var a=r.filter(t)[0].id();else var a=t.id();if(e.is.string(i))var o=r.filter(i)[0].id();else var o=i.id();var s=n(l[a],l[o],p,b,v);return new e.Collection(r,s)}};return w},bellmanFord:function(t){if(t=t||{},null!=t.weight&&e.is.fn(t.weight))var r=t.weight;else var r=function(e){return 1};if(null!=t.directed)var i=t.directed;else var i=!1;if(null==t.root)return void e.util.error("options.root 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t[e[1]]===o&&t[e[2]]===s?!1:t[e[1]]===s&&t[e[2]]===o?!1:!0}),u=0;u=n)return t;var o=Math.floor(Math.random()*t.length),s=r(o,e,t);return i(e,s,n-1,a)},n=this._private.cy,a=this.edges().stdFilter(function(e){return!e.isLoop()}),o=this.nodes(),s=o.length,l=a.length,u=Math.ceil(Math.pow(Math.log(s)/Math.LN2,2)),c=Math.floor(s/Math.sqrt(2));if(2>s)return void e.util.error("At least 2 nodes are required for KargerSteing algorithm!");for(var d={},h=0;s>h;h++)d[o[h].id()]=h;for(var p=[],h=0;l>h;h++){var v=a[h];p.push([h,d[v.source().id()],d[v.target().id()]])}for(var f,g=1/0,y=[],h=0;s>h;h++)y.push(h);for(var m=0;u>=m;m++){var x=y.slice(0),b=i(x,p,s,c),w=x.slice(0),_=i(x,b,c,2),E=i(w,b,c,2);_.length<=E.length&&_.lengthi;i++)r+=e[i];for(var i=0;t>i;i++)e[i]=e[i]/r};if(null!=t&&null!=t.dampingfactor)var i=t.dampingFactor;else var i=.8;if(null!=t&&null!=t.precision)var n=t.precision;else var n=1e-6;if(null!=t&&null!=t.iterations)var a=t.iterations;else var a=200;if(null!=t&&null!=t.weight&&e.is.fn(t.weight))var o=t.weight;else var o=function(e){return 1};for(var s=this._private.cy,l=this.edges().stdFilter(function(e){return!e.isLoop()}),u=this.nodes(),c=u.length,d=l.length,h={},p=0;c>p;p++)h[u[p].id()]=p;for(var v=[],f=[],g=(1-i)/c,p=0;c>p;p++){for(var y=[],m=0;c>m;m++)y.push(0);v.push(y),f.push(0)}for(var p=0;d>p;p++){var x=l[p],b=h[x.source().id()],w=h[x.target().id()],_=o.apply(x,[x]);v[w][b]+=_,f[b]+=_}for(var E=1/c+g,m=0;c>m;m++)if(0===f[m])for(var p=0;c>p;p++)v[p][m]=E;else for(var p=0;c>p;p++)v[p][m]=v[p][m]/f[m]+g;for(var S,D=[],k=[],p=0;c>p;p++)D.push(1),k.push(0);for(var P=0;a>P;P++){for(var C=k.slice(0),p=0;c>p;p++)for(var m=0;c>m;m++)C[p]+=v[p][m]*D[m];r(C),S=D,D=C;for(var T=0,p=0;c>p;p++)T+=Math.pow(S[p]-D[p],2);if(n>T)break}var M={rank:function(t){if(e.is.string(t))var r=s.filter(t)[0].id();else var r=t.id();return D[h[r]]}};return M},degreeCentralityNormalized:function(t){if(t=t||{},null!=t.directed)var r=t.directed;else var r=!1;var i=this.nodes(),n=i.length;if(r){for(var a={},o={},s=0,l=0,u=0;n>u;u++){var c=i[u],d=this.degreeCentrality(e.util.extend({},t,{root:c}));su;u++){var c=i[u],d=this.degreeCentrality(e.util.extend({},t,{root:c}));pi&&(i=s),r[n[o].id()]=s}return{closeness:function(t){if(e.is.string(t))var t=cy.filter(t)[0].id();else var t=t.id();return r[t]/i}}},closenessCentrality:function(t){if(t=t||{},null==t.root)return void e.util.error("options.root required");if(e.is.string(t.root))var r=this.filter(t.root)[0];else var r=t.root[0];if(null!=t.weight&&e.is.fn(t.weight))var i=t.weight;else var i=function(){return 1};if(null!=t.directed&&e.is.bool(t.directed))var n=t.directed;else var n=!1;for(var a=this.dijkstra({root:r,weight:i,directed:n}),o=0,s=this.nodes(),l=0;l0;){var y=g.pop();h.push(y),l[y].forEach(i?function(e){if(o.$("#"+y).edgesTo(e).length>0)var t=o.$("#"+y).edgesTo(e)[0];else var t=e.edgesTo("#"+y)[0];var 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e.Collection(r._private.cy,i).updateStyle(),r.trigger("class"),r},flashClass:function(e,t){var r=this;if(null==t)t=250;else if(0===t)return r;return r.addClass(e),setTimeout(function(){r.removeClass(e)},t),r}})}(cytoscape),function(e){"use strict";e.fn.eles({allAre:function(e){return this.filter(e).length===this.length},is:function(e){return this.filter(e).length>0},some:function(e,t){for(var r=0;r0},allAreNeighbors:function(e){return e=this.cy().collection(e),this.neighborhood().intersect(e).length===e.length}}),e.elesfn.allAreNeighbours=e.elesfn.allAreNeighbors}(cytoscape),function(e){"use strict";e.fn.eles({parent:function(t){for(var r=[],i=this._private.cy,n=0;n0&&r.push(o)}return new e.Collection(i,r,{unique:!0}).filter(t)},parents:function(t){for(var r=[],i=this.parent();i.nonempty();){for(var n=0;n0?this.add(s):this;r?l.trigger("position"):l.rtrigger("position")}return this},silentPositions:function(e){return this.positions(e,!0)},updateCompoundBounds:function(){function 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i=e.elesfn;i.attr=i.data,i.removeAttr=i.removeData,i.modelPosition=i.point=i.position,i.modelPositions=i.points=i.positions,i.renderedPoint=i.renderedPosition,i.relativePoint=i.relativePosition,i.boundingbox=i.boundingBox,i.renderedBoundingbox=i.renderedBoundingBox}(cytoscape),function(e){"use strict";function t(e){return function(t){var r=this;if(void 0===t&&(t=!0),0!==r.length&&r.isNode()&&!r.removed()){for(var i=0,n=r[0],a=n._private.edges,o=0;oe}),maxDegree:r("degree",function(e,t){return e>t}),minIndegree:r("indegree",function(e,t){return t>e}),maxIndegree:r("indegree",function(e,t){return e>t}),minOutdegree:r("outdegree",function(e,t){return t>e}),maxOutdegree:r("outdegree",function(e,t){return e>t})}),e.fn.eles({totalDegree:function(e){for(var t=0,r=this.nodes(),i=0;i1&&!n){var a=this.length-1,o=this[a];this[a]=void 0,this[i]=o,t.indexes[o.id()]=i}return this.length--,this},unmerge:function(t){var r=this._private.cy;if(!t)return this;if(e.is.string(t)){var 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w=d["haystack-radius"].value,_=w/2,E=m._private.position,S=m.width(),D=m.height(),k=y._private.position,P=y.width(),C=y.height(),T=k.x+c.source.x*P*_,M=k.y+c.source.y*C*_,N=E.x+c.target.x*S*_,B=E.y+c.target.y*D*_;(x=e.math.inLineVicinity(r,i,T,M,N,B,g))&&b()&&f+p>e.math.sqDistanceToFiniteLine(r,i,T,M,N,B)&&u.push(o)}else"straight"===c.edgeType?(x=e.math.inLineVicinity(r,i,c.startX,c.startY,c.endX,c.endY,g))&&b()&&f+p>e.math.sqDistanceToFiniteLine(r,i,c.startX,c.startY,c.endX,c.endY)&&u.push(o):"bezier"===c.edgeType&&(x=e.math.inBezierVicinity(r,i,c.startX,c.startY,c.cp2x,c.cp2y,c.endX,c.endY,f))&&b()&&f+p>e.math.sqDistanceToQuadraticBezier(r,i,c.startX,c.startY,c.cp2x,c.cp2y,c.endX,c.endY)&&u.push(o);if(x&&b()&&0===u.length||u[u.length-1]!==o){var 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t=this.lastZOrderCachedNodes,r=this.lastZOrderCachedEdges,i=this.getCachedNodes(),n=this.getCachedEdges(),a=[];if(!e&&t&&r&&t===i&&r===n)a=this.cachedZSortedEles;else{for(var o=0;oo){for(var h=u.split(/\s+/),p="",v=0;v=m?p+=f+" ":(s.push(p),p=f+" ")}p.match(/^\s+$/)||s.push(p)}else s.push(u)}n.labelWrapCachedLines=s,n.labelWrapCachedText=r=s.join("\n"),n.labelWrapKey=n.labelKey}return r},r.calculateLabelDimensions=function(e,t,r){var i=this,n=e._private.style,a=n["font-style"].strValue,o=n["font-size"].pxValue+"px",s=n["font-family"].strValue,l=n["font-weight"].strValue,u=e._private.labelKey;r&&(u+="$@$"+r);var c=i.labelDimCache||(i.labelDimCache={});if(c[u])return c[u];var d=this.labelCalcDiv;d||(d=this.labelCalcDiv=document.createElement("div"),document.body.appendChild(d));var h=d.style;return 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B=E.intersectLine(y.x,y.y,x,b,m.x,m.y,D/2),O=S.intersectLine(m.x,m.y,w,_,y.x,y.y,k/2),z={x1:B[0],x2:O[0],y1:B[1],y2:O[1]},I=O[1]-B[1],L=O[0]-B[0],R=Math.sqrt(L*L+I*I),V={x:L,y:I},A={x:V.x/R,y:V.y/R};P={x:-A.y,y:A.x},(S.checkPoint(B[0],B[1],k/2,w,_,m.x,m.y)||E.checkPoint(O[0],O[1],D/2,x,b,y.x,y.y))&&(P={},C=!0)}for(var c,X,u=0;uze,Le=e.math.distance({x:X.cp2x,y:X.cp2y},{x:X.endX,y:X.endY}),Re=Oe>Le;if("bezier"===X.edgeType){var Ve=!1;if(Pe||Ce||Ie){Ve=!0;var Ae={x:X.cp2x-y.x,y:X.cp2y-y.y},Xe=Math.sqrt(Ae.x*Ae.x+Ae.y*Ae.y),Fe={x:Ae.x/Xe,y:Ae.y/Xe},Ye=Math.max(x,b),qe={x:X.cp2x+2*Fe.x*Ye,y:X.cp2y+2*Fe.y*Ye},je=E.intersectLine(y.x,y.y,x,b,qe.x,qe.y,D/2);Ie?(X.cp2x=X.cp2x+Fe.x*(Oe-ze),X.cp2y=X.cp2y+Fe.y*(Oe-ze)):(X.cp2x=je[0]+Fe.x*Oe,X.cp2y=je[1]+Fe.y*Oe)}if(Te||Me||Re){Ve=!0;var Ae={x:X.cp2x-m.x,y:X.cp2y-m.y},Xe=Math.sqrt(Ae.x*Ae.x+Ae.y*Ae.y),Fe={x:Ae.x/Xe,y:Ae.y/Xe},Ye=Math.max(x,b),qe={x:X.cp2x+2*Fe.x*Ye,y:X.cp2y+2*Fe.y*Ye},$e=S.intersectLine(m.x,m.y,w,_,qe.x,qe.y,k/2);Re?(X.cp2x=X.cp2x+Fe.x*(Oe-Le),X.cp2y=X.cp2y+Fe.y*(Oe-Le)):(X.cp2x=$e[0]+Fe.x*Oe,X.cp2y=$e[1]+Fe.y*Oe)}Ve&&this.findEndpoints(c)}else"straight"===X.edgeType&&(X.midX=(G+ne)/2,X.midY=(J+oe)/2);this.projectBezier(c),this.recalculateEdgeLabelProjection(c)}}}for(var u=0;uS*k+D*P)n.straightEdgeTooShort=!0;else{var _=n;this.drawStyledEdge(r,e,[_.startX,_.startY,_.endX,_.endY],g,f),n.straightEdgeTooShort=!1}}else{var _=n;this.drawStyledEdge(r,e,[_.startX,_.startY,_.cp2x,_.cp2y,_.endX,_.endY],g,f)}"haystack"===n.edgeType?this.drawArrowheads(e,r,i):n.noArrowPlacement!==!0&&void 0!==n.startX&&this.drawArrowheads(e,r,i),this.shadowStyle(e,"transparent",0)}}},r.drawStyledEdge=function(e,r,i,n,a){var o,s=e._private.rscratch,l=r,u=!1,c=t.usePaths();if(c){for(var d=i,h=s.pathCacheKey&&d.length===s.pathCacheKey.length,p=h,v=0;p&&vu?y+=Math.PI/2:y=-(Math.PI/2+y);var m=this.getArrowWidth(a),x=t.arrowShapes[o];if(h){var b=m+"$"+o+"$"+y+"$"+s+"$"+l;p.arrowPathCacheKey=p.arrowPathCacheKey||{},p.arrowPathCache=p.arrowPathCache||{};var w=p.arrowPathCacheKey[r]===b;w?(d=i=p.arrowPathCache[r],v=!0):(d=i=new Path2D,p.arrowPathCacheKey[r]=b,p.arrowPathCache[r]=d)}i.beginPath&&i.beginPath(),v||x.draw(i,m,y,g),!x.leavePathOpen&&i.closePath&&i.closePath(),i=f,("filled"===n||"both"===n)&&(h?i.fill(d):i.fill()),("hollow"===n||"both"===n)&&(i.lineWidth=x.matchEdgeWidth?a:1,i.lineJoin="miter",h?i.stroke(d):i.stroke())}}(cytoscape),function(e){"use strict";var t=e("renderer","canvas"),r=t.prototype;r.getCachedImage=function(e,t){var r=this,i=r.imageCache=r.imageCache||{};if(i[e]&&i[e].image)return i[e].image;var n=i[e]=i[e]||{},a=n.image=new Image;return a.addEventListener("load",t),a.src=e,a},r.drawInscribedImage=function(e,r,i){var n=this,a=i._private.position.x,o=i._private.position.y,s=i._private.style,l=s["background-fit"].value,u=s["background-position-x"],c=s["background-position-y"],d=s["background-repeat"].value,h=i.width(),p=i.height(),v=i._private.rscratch,f=s["background-clip"].value,g="node"===f,y=s["background-image-opacity"].value,m=r.width,x=r.height;if(0!==m&&0!==x){var b=s["background-width"];"auto"!==b.value&&(m="%"===b.units?b.value/100*h:b.pxValue);var w=s["background-height"];if("auto"!==w.value&&(x="%"===w.units?w.value/100*p:w.pxValue),0!==m&&0!==x){if("contain"===l){var _=Math.min(h/m,p/x);m*=_,x*=_}else if("cover"===l){var _=Math.max(h/m,p/x);m*=_,x*=_}var E=a-h/2;E+="%"===u.units?(h-m)*u.value/100:u.pxValue;var S=o-p/2;S+="%"===c.units?(p-x)*c.value/100:c.pxValue,v.pathCache&&(E-=a,S-=o,a=0,o=0);var D=e.globalAlpha;if(e.globalAlpha=y,"no-repeat"===d)g&&(e.save(),v.pathCache?e.clip(v.pathCache):(t.nodeShapes[n.getNodeShape(i)].drawPath(e,a,o,h,p),e.clip())),e.drawImage(r,0,0,r.width,r.height,E,S,m,x),g&&e.restore();else{var k=e.createPattern(r,d);e.fillStyle=k,t.nodeShapes[n.getNodeShape(i)].drawPath(e,a,o,h,p),e.translate(E,S),e.fill(),e.translate(-E,-S)}e.globalAlpha=D}}}}(cytoscape),function(e){"use strict";function t(e,t,r,i,n,a){var a=a||5;e.beginPath(),e.moveTo(t+a,r),e.lineTo(t+i-a,r),e.quadraticCurveTo(t+i,r,t+i,r+a),e.lineTo(t+i,r+n-a),e.quadraticCurveTo(t+i,r+n,t+i-a,r+n),e.lineTo(t+a,r+n),e.quadraticCurveTo(t,r+n,t,r+n-a),e.lineTo(t,r+a),e.quadraticCurveTo(t,r,t+a,r),e.closePath(),e.fill()}var r=e("renderer","canvas"),i=r.prototype;i.drawEdgeText=function(t,r){var i=r._private.style.content.strValue;if(!(!i||i.match(/^\s+$/)||this.hideEdgesOnViewport&&(this.dragData.didDrag||this.pinching||this.hoverData.dragging||this.data.wheel||this.swipePanning))){var n=r._private.style["font-size"].pxValue*r.cy().zoom(),a=r._private.style["min-zoomed-font-size"].pxValue;if(!(a>n)){t.textAlign="center",t.textBaseline="middle";var o=r._private.rscratch;if(e.is.number(o.labelX)&&e.is.number(o.labelY)){var s,l,u,c=r._private.style,d="autorotate"===c["edge-text-rotation"].strValue;if(d){switch(o.edgeType){case"haystack":l=o.haystackPts[2]-o.haystackPts[0],u=o.haystackPts[3]-o.haystackPts[1];break;default:l=o.endX-o.startX,u=o.endY-o.startY}s=Math.atan(u/l),t.translate(o.labelX,o.labelY),t.rotate(s),this.drawText(t,r,0,0),t.rotate(-s),t.translate(-o.labelX,-o.labelY)}else this.drawText(t,r,o.labelX,o.labelY)}}}},i.drawNodeText=function(t,r){var i=r._private.style.content.strValue;if(i&&!i.match(/^\s+$/)){var n=r._private.style["font-size"].pxValue*r.cy().zoom(),a=r._private.style["min-zoomed-font-size"].pxValue;if(!(a>n)){ +var o=r._private.style["text-halign"].strValue,s=r._private.style["text-valign"].strValue,l=r._private.rscratch;if(e.is.number(l.labelX)&&e.is.number(l.labelY)){switch(o){case"left":t.textAlign="right";break;case"right":t.textAlign="left";break;default:t.textAlign="center"}switch(s){case"top":t.textBaseline="bottom";break;case"bottom":t.textBaseline="top";break;default:t.textBaseline="middle"}this.drawText(t,r,l.labelX,l.labelY)}}}},i.getFontCache=function(e){var t;this.fontCaches=this.fontCaches||[];for(var r=0;r0)&&p>0){var v=o["text-border-width"].pxValue,f=4+v/2;r.isNode()&&("top"==h?n-=f:"bottom"==h&&(n+=f),"left"==d?i-=f:"right"==d&&(i+=f));var g=s.labelWidth,y=s.labelHeight,m=i;d&&("center"==d?m-=g/2:"left"==d&&(m-=g));var x=n;if(r.isNode()?"top"==h?x-=y:"center"==h&&(x-=y/2):x-=y/2,"autorotate"===o["edge-text-rotation"].strValue?(n=0,g+=4,m=i-g/2,x=n-y/2):(m-=f,x-=f,y+=2*f,g+=2*f),o["text-background-color"]){var b=e.fillStyle,w=o["text-background-color"].value;e.fillStyle="rgba("+w[0]+","+w[1]+","+w[2]+","+p*u+")";var _=o["text-background-shape"].strValue;"roundrectangle"==_?t(e,m,x,g,y,2):e.fillRect(m,x,g,y),e.fillStyle=b}if(v>0){var E=e.strokeStyle,S=e.lineWidth,D=o["text-border-color"].value,k=o["text-border-style"].value;if(e.strokeStyle="rgba("+D[0]+","+D[1]+","+D[2]+","+p*u+")",e.lineWidth=v,e.setLineDash)switch(k){case"dotted":e.setLineDash([1,1]);break;case"dashed":e.setLineDash([4,2]);break;case"double":e.lineWidth=v/4,e.setLineDash([]);break;case"solid":e.setLineDash([])}if(e.strokeRect(m,x,g,y),"double"===k){var P=v/2;e.strokeRect(m+P,x+P,g-2*P,y-2*P)}e.setLineDash&&e.setLineDash([]),e.lineWidth=S,e.strokeStyle=E}}var C=2*o["text-outline-width"].pxValue;if(C>0&&(e.lineWidth=C),"wrap"===o["text-wrap"].value){var T=l.labelWrapCachedLines,M=s.labelHeight/T.length;switch(h){case"top":n-=(T.length-1)*M;break;case"bottom":break;default:case"center":n-=(T.length-1)*M/2}for(var N=0;N0&&e.strokeText(T[N],i,n),e.fillText(T[N],i,n),n+=M}else C>0&&e.strokeText(c,i,n),e.fillText(c,i,n);this.shadowStyle(e,"transparent",0)}}}}(cytoscape),function(e){"use strict";var t=e("renderer","canvas"),r=t.prototype;r.drawNode=function(e,r,i){var n,a,o,s=this,l=r._private.style,u=r._private.rscratch,c=r._private,d=t.usePaths(),h=e,p=!1,v=l["overlay-padding"].pxValue,f=l["overlay-opacity"].value,g=l["overlay-color"].value;if(!i||0!==f){var y=r.effectiveOpacity();if(0!==y)if(n=this.getNodeWidth(r),a=this.getNodeHeight(r),e.lineWidth=l["border-width"].pxValue,void 0!==i&&i)f>0&&(this.fillStyle(e,g[0],g[1],g[2],f),t.nodeShapes.roundrectangle.drawPath(e,r._private.position.x,r._private.position.y,n+2*v,a+2*v),e.fill());else{var m,x=l["background-image"].value[2]||l["background-image"].value[1];if(void 0!==x){m=this.getCachedImage(x,function(){s.data.canvasNeedsRedraw[t.NODE]=!0,s.data.canvasNeedsRedraw[t.DRAG]=!0,s.drawingImage=!0,s.redraw()});var b=c.backgrounding;c.backgrounding=!m.complete,b!==c.backgrounding&&r.updateStyle(!1)}var w=l["background-color"].value,_=l["border-color"].value,E=l["border-style"].value;this.fillStyle(e,w[0],w[1],w[2],l["background-opacity"].value*l.opacity.value*y),this.strokeStyle(e,_[0],_[1],_[2],l["border-opacity"].value*l.opacity.value*y);var S=l["shadow-blur"].pxValue,D=l["shadow-opacity"].value,k=l["shadow-color"].value,P=l["shadow-offset-x"].pxValue,C=l["shadow-offset-y"].pxValue;if(this.shadowStyle(e,k,D,S,P,C),e.lineJoin="miter",e.setLineDash)switch(E){case"dotted":e.setLineDash([1,1]);break;case"dashed":e.setLineDash([4,2]);break;case"solid":case"double":e.setLineDash([])}var T=l.shape.strValue,M=r._private.position;if(d){var N=T+"$"+n+"$"+a;e.translate(M.x,M.y),u.pathCacheKey===N?(o=e=u.pathCache,p=!0):(o=e=new Path2D,u.pathCacheKey=N,u.pathCache=o)}if(!p){var B=M;d&&(B={x:0,y:0}),t.nodeShapes[this.getNodeShape(r)].drawPath(e,B.x,B.y,n,a)}e=h,d?e.fill(o):e.fill(),this.shadowStyle(e,"transparent",0),void 0!==x&&m.complete&&this.drawInscribedImage(e,m,r);var O=l["background-blacken"].value,z=l["border-width"].pxValue;if(this.hasPie(r)&&(this.drawPie(e,r),(0!==O||0!==z)&&(d||t.nodeShapes[this.getNodeShape(r)].drawPath(e,M.x,M.y,n,a))),O>0?(this.fillStyle(e,0,0,0,O),d?e.fill(o):e.fill()):0>O&&(this.fillStyle(e,255,255,255,-O),d?e.fill(o):e.fill()),z>0&&(d?e.stroke(o):e.stroke(),"double"===E)){e.lineWidth=l["border-width"].pxValue/3;var I=e.globalCompositeOperation;e.globalCompositeOperation="destination-out",d?e.stroke(o):e.stroke(),e.globalCompositeOperation=I}d&&e.translate(-M.x,-M.y),e.setLineDash&&e.setLineDash([])}}},r.hasPie=function(e){return e=e[0],e._private.hasPie},r.drawPie=function(r,i){i=i[0];var n=i._private.style["pie-size"],a=this.getNodeWidth(i),o=this.getNodeHeight(i),s=i._private.position.x,l=i._private.position.y,u=Math.min(a,o)/2,c=0,d=t.usePaths();d&&(s=0,l=0),"%"===n.units?u=u*n.value/100:void 0!==n.pxValue&&(u=n.pxValue/2);for(var h=1;h<=e.style.pieBackgroundN;h++){var p=i._private.style["pie-"+h+"-background-size"].value,v=i._private.style["pie-"+h+"-background-color"].value,f=i._private.style["pie-"+h+"-background-opacity"].value,g=p/100,y=1.5*Math.PI+2*Math.PI*c,m=2*Math.PI*g,x=y+m;0===p||c>=1||c+g>1||(r.beginPath(),r.moveTo(s,l),r.arc(s,l,u,y,x),r.closePath(),this.fillStyle(r,v[0],v[1],v[2],f),r.fill(),c+=g)}}}(cytoscape),function(e){"use strict";var t=e("renderer","canvas"),r=t,i=t.prototype;i.getPixelRatio=function(){var e=this.data.contexts[0];if(null!=this.forcedPixelRatio)return this.forcedPixelRatio;var t=e.backingStorePixelRatio||e.webkitBackingStorePixelRatio||e.mozBackingStorePixelRatio||e.msBackingStorePixelRatio||e.oBackingStorePixelRatio||e.backingStorePixelRatio||1;return(window.devicePixelRatio||1)/t},i.paintCache=function(e){for(var t,r=this.paintCaches=this.paintCaches||[],i=!0,n=0;n0?(e.shadowBlur=i*o,e.shadowColor="rgba("+t[0]+","+t[1]+","+t[2]+","+r+")",e.shadowOffsetX=n*o,e.shadowOffsetY=a*o):(e.shadowBlur=0,e.shadowColor="transparent")},i.matchCanvasSize=function(e){var i=this.data,n=e.clientWidth,a=e.clientHeight,o=this.getPixelRatio(),s=this.motionBlurPxRatio;(e===this.data.bufferCanvases[r.MOTIONBLUR_BUFFER_NODE]||e===this.data.bufferCanvases[r.MOTIONBLUR_BUFFER_DRAG])&&(o=s);var l,u=n*o,c=a*o;if(u!==this.canvasWidth||c!==this.canvasHeight){this.fontCaches=null;var d=i.canvasContainer;d.style.width=n+"px",d.style.height=a+"px";for(var h=0;h=o&&(l=i.bufferCanvases[t.TEXTURE_BUFFER],this.textureMult=2,l.width=u*this.textureMult,l.height=c*this.textureMult),this.canvasWidth=u,this.canvasHeight=c}},i.renderTo=function(e,t,r,i){this.redraw({forcedContext:e,forcedZoom:t,forcedPan:r,drawAllLayers:!0,forcedPxRatio:i})},i.timeToRender=function(){return this.redrawTotalTime/this.redrawCount},t.minRedrawLimit=1e3/60,t.maxRedrawLimit=1e3,t.motionBlurDelay=100,i.redraw=function(i){function n(){function i(e,t,r,i,n){var a=e.globalCompositeOperation;e.globalCompositeOperation="destination-out",c.fillStyle(e,255,255,255,c.motionBlurTransparency),e.fillRect(t,r,i,n),e.globalCompositeOperation=a}function n(e,t){var n,s,d,h;/*!r.fullQualityMb &&*/c.clearingMotionBlur||e!==p.bufferContexts[r.MOTIONBLUR_BUFFER_NODE]&&e!==p.bufferContexts[r.MOTIONBLUR_BUFFER_DRAG]?(n=P,s=D,d=c.canvasWidth,h=c.canvasHeight):(n={x:k.x*y,y:k.y*y},s=S*y,d=c.canvasWidth*y,h=c.canvasHeight*y),e.setTransform(1,0,0,1,0,0),"motionBlur"===t?i(e,0,0,d,h):a||void 0!==t&&!t||e.clearRect(0,0,d,h),o||(e.translate(n.x,n.y),e.scale(s,s)),u&&e.translate(u.x,u.y),l&&e.scale(l,l)}function b(e,t){for(var r=e.eles,i=0;i0&&(I.strokeStyle="rgba("+E["selection-box-border-color"].value[0]+","+E["selection-box-border-color"].value[1]+","+E["selection-box-border-color"].value[2]+","+E["selection-box-opacity"].value+")",I.strokeRect(p.select[0],p.select[1],p.select[2]-p.select[0],p.select[3]-p.select[1]))}if(p.bgActivePosistion&&!c.hoverData.selecting){var S=p.cy.zoom(),K=p.bgActivePosistion;I.fillStyle="rgba("+E["active-bg-color"].value[0]+","+E["active-bg-color"].value[1]+","+E["active-bg-color"].value[2]+","+E["active-bg-opacity"].value+")",I.beginPath(),I.arc(K.x,K.y,E["active-bg-size"].pxValue/S,0,2*Math.PI),I.fill()}var J=c.averageRedrawTime;if(c.showFps&&J){J=Math.round(J);var Q=Math.round(1e3/J);I.setTransform(1,0,0,1,0,0),I.fillStyle="rgba(255, 0, 0, 0.75)",I.strokeStyle="rgba(255, 0, 0, 0.75)",I.lineWidth=1,I.fillText("1 frame = "+J+" ms = "+Q+" 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0===c.redrawTotalTime&&(c.redrawTotalTime=0),c.redrawTotalTime+=oe-C,c.lastRedrawTime=oe-C,c.averageRedrawTime=c.averageRedrawTime/2+(oe-C)/2,c.currentlyDrawing=!1,c.prevViewport=T,c.clearingMotionBlur&&(c.clearingMotionBlur=!1,c.motionBlurCleared=!0,c.motionBlur=!0),g&&(c.motionBlurTimeout=setTimeout(function(){c.motionBlurTimeout=null,c.clearedForMotionBlur[r.NODE]=!1,c.clearedForMotionBlur[r.DRAG]=!1,c.motionBlur=!1,c.clearingMotionBlur=!f,c.mbFrames=0,v[r.NODE]=!0,v[r.DRAG]=!0,c.redraw()},t.motionBlurDelay)),c.drawingImage=!1}i=i||{};var a=i.forcedContext,o=i.drawAllLayers,s=i.drawOnlyNodeLayer,l=i.forcedZoom,u=i.forcedPan,c=this,d=void 0===i.forcedPxRatio?this.getPixelRatio():i.forcedPxRatio,h=c.data.cy,p=c.data,v=p.canvasNeedsRedraw,f=c.textureOnViewport&&!a&&(c.pinching||c.hoverData.dragging||c.swipePanning||c.data.wheelZooming),g=void 0!==i.motionBlur?i.motionBlur:c.motionBlur,y=c.motionBlurPxRatio,m=h.hasCompoundNodes(),x=c.hoverData.draggingEles,b=c.hoverData.selecting||c.touchData.selecting?!0:!1;g=g&&!a&&c.motionBlurEnabled&&!b;var w=g;!a&&c.motionBlurTimeout&&clearTimeout(c.motionBlurTimeout),!a&&this.redrawTimeout&&clearTimeout(this.redrawTimeout),this.redrawTimeout=null,void 0===this.averageRedrawTime&&(this.averageRedrawTime=0);var _=t.minRedrawLimit,E=t.maxRedrawLimit,S=this.averageRedrawTime;S=_>S?_:S,S=E>S?S:E,void 0===this.lastDrawTime&&(this.lastDrawTime=0);var D=Date.now(),k=D-this.lastDrawTime,P=k>=S;if(!a&&!c.clearingMotionBlur){if(!P||this.currentlyDrawing)return void(this.redrawTimeout=setTimeout(function(){c.redraw()},S));this.lastDrawTime=D,this.currentlyDrawing=!0}g&&(null==c.mbFrames&&(c.mbFrames=0),c.drawingImage||c.mbFrames++,c.mbFrames<3&&(w=!1),c.mbFrames>c.minMbLowQualFrames&&(c.motionBlurPxRatio=c.mbPxRBlurry)),c.clearingMotionBlur&&(c.motionBlurPxRatio=1);var C=Date.now();a?n():e.util.requestAnimationFrame(n),a||c.initrender||(c.initrender=!0,h.trigger("initrender")),a||h.triggerOnRender()}}(cytoscape),function(e){"use strict";var t=e("renderer","canvas"),r=t.prototype;r.drawPolygonPath=function(e,t,r,i,n,a){var o=i/2,s=n/2;e.beginPath&&e.beginPath(),e.moveTo(t+o*a[0],r+s*a[1]);for(var l=1;l0&&o>0)if(d.clearRect(0,0,a,o),t.bg&&(d.fillStyle=t.bg,d.rect(0,0,a,o),d.fill()),d.globalCompositeOperation="source-over",t.full)this.redraw({forcedContext:d,drawAllLayers:!0,forcedZoom:s,forcedPan:{x:-n.x1*s,y:-n.y1*s},forcedPxRatio:1});else{var h=i.pan(),p={x:h.x*s,y:h.y*s},v=i.zoom()*s;this.redraw({forcedContext:d,drawAllLayers:!0,forcedZoom:v,forcedPan:p,forcedPxRatio:1})}return c},r.png=function(e){return this.bufferCanvasImage(e).toDataURL("image/png")},r.jpg=function(e){return this.bufferCanvasImage(e).toDataURL("image/jpeg")}}(cytoscape),function(e){"use strict";var t=e("renderer","canvas"),r=t,i=r.prototype;i.registerBinding=function(e,t,r,i){this.bindings.push({target:e,event:t,handler:r,useCapture:i}),e.addEventListener(t,r,i)},i.nodeIsDraggable=function(e){return 0!==e._private.style.opacity.value&&"visible"==e._private.style.visibility.value&&"element"==e._private.style.display.value&&!e.locked()&&e.grabbable()?!0:!1},i.load=function(){var t=this,i=function(e){var r;if(e.addToList&&t.data.cy.hasCompoundNodes()){if(!e.addToList.hasId){e.addToList.hasId={};for(var i=0;is[0]&&i.clientXs[1]&&i.clientY=r.panOrBoxSelectDelay)&&!t.hoverData.selecting&&P>=t.tapThreshold2&&h.panningEnabled()&&h.userPanningEnabled())t.hoverData.dragging=!0,t.hoverData.selecting=!1,t.hoverData.justStartedPan=!0,f[4]=0;else{if(h.boxSelectionEnabled()&&!t.hoverData.dragging&&Math.pow(f[2]-f[0],2)+Math.pow(f[3]-f[1],2)>7&&f[4]&&(clearTimeout(t.bgActiveTimeout),t.data.bgActivePosistion=void 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e.Event(i,{type:"mouseup",cyPosition:{x:s[0],y:s[1]}})).trigger(new e.Event(i,{type:"tapend",cyPosition:{x:s[0],y:s[1]}})).trigger(new e.Event(i,{type:"vmouseup",cyPosition:{x:s[0],y:s[1]}})),Math.pow(l[2]-l[0],2)+Math.pow(l[3]-l[1],2)!==0||t.dragData.didDrag||t.hoverData.dragged||(null!=u?u.trigger(new e.Event(i,{type:"click",cyPosition:{x:s[0],y:s[1]}})).trigger(new e.Event(i,{type:"tap",cyPosition:{x:s[0],y:s[1]}})).trigger(new e.Event(i,{type:"vclick",cyPosition:{x:s[0],y:s[1]}})):null==u&&a.trigger(new e.Event(i,{type:"click",cyPosition:{x:s[0],y:s[1]}})).trigger(new e.Event(i,{type:"tap",cyPosition:{x:s[0],y:s[1]}})).trigger(new e.Event(i,{type:"vclick",cyPosition:{x:s[0],y:s[1]}}))),u!=d||t.dragData.didDrag||null!=u&&u._private.selectable&&(t.hoverData.dragging||("additive"===a.selectionType()||h?u.selected()?u.unselect():u.select():h||(a.$(":selected").unmerge(u).unselect(),u.select())),p[r.NODE]=!0),t.hoverData.selecting&&a.boxSelectionEnabled()&&Math.pow(l[2]-l[0],2)+Math.pow(l[3]-l[1],2)>7&&l[4]){var g=[],y=t.getAllInBox(l[0],l[1],l[2],l[3]);p[r.SELECT_BOX]=!0,y.length>0&&(p[r.NODE]=!0);for(var m=0;m=0&&w>=d&&p>=0&&w>=p&&h>=0&&_>=h&&v>=0&&_>=v;var T=n.pan(),M=n.zoom();f=S(d,h,p,v),g=D(d,h,p,v),y=[(d+p)/2,(h+v)/2],m=[(y[0]-T.x)/M,(y[1]-T.y)/M];var N=200,B=N*N;if(B>g&&!i.touches[2]){var O=t.findNearestElement(l[0],l[1],!0),z=t.findNearestElement(l[2],l[3],!0);return O&&O.isNode()?(O.activate().trigger(new e.Event(i,{type:"cxttapstart",cyPosition:{x:l[0],y:l[1]}})),t.touchData.start=O):z&&z.isNode()?(z.activate().trigger(new e.Event(i,{type:"cxttapstart",cyPosition:{x:l[0],y:l[1]}})),t.touchData.start=z):(n.trigger(new e.Event(i,{type:"cxttapstart",cyPosition:{x:l[0],y:l[1]}})),t.touchData.start=null),t.touchData.start&&(t.touchData.start._private.grabbed=!1),t.touchData.cxt=!0,t.touchData.cxtDragged=!1,t.data.bgActivePosistion=void 0,void t.redraw()}}if(i.touches[2]);else if(i.touches[1]);else if(i.touches[0]){var I=t.findNearestElement(l[0],l[1],!0);if(null!=I){if(I.activate(),t.touchData.start=I,I.isNode()&&t.nodeIsDraggable(I)){var L=t.dragData.touchDragEles=[];if(c[r.NODE]=!0,c[r.DRAG]=!0,I.selected())for(var R=n.$(function(){return this.isNode()&&this.selected()}),V=0;V=q||V>=F){t.touchData.cxt=!1,t.touchData.start&&(t.touchData.start.unactivate(),t.touchData.start=null),t.data.bgActivePosistion=void 0,y[r.SELECT_BOX]=!0;var j=new e.Event(i,{type:"cxttapend",cyPosition:{x:l[0],y:l[1]}});t.touchData.start?t.touchData.start.trigger(j):s.trigger(j)}}if(o&&t.touchData.cxt){var j=new e.Event(i,{type:"cxtdrag",cyPosition:{x:l[0],y:l[1]}});t.data.bgActivePosistion=void 0,y[r.SELECT_BOX]=!0,t.touchData.start?t.touchData.start.trigger(j):s.trigger(j),t.touchData.start&&(t.touchData.start._private.grabbed=!1),t.touchData.cxtDragged=!0;var $=t.findNearestElement(l[0],l[1],!0);t.touchData.cxtOver&&$===t.touchData.cxtOver||(t.touchData.cxtOver&&t.touchData.cxtOver.trigger(new e.Event(i,{type:"cxtdragout",cyPosition:{x:l[0],y:l[1]}})),t.touchData.cxtOver=$,$&&$.trigger(new e.Event(i,{type:"cxtdragover",cyPosition:{x:l[0],y:l[1]}})))}else if(o&&i.touches[2]&&s.boxSelectionEnabled())t.data.bgActivePosistion=void 0,clearTimeout(this.threeFingerSelectTimeout),this.lastThreeTouch=+new Date,t.touchData.selecting=!0,y[r.SELECT_BOX]=!0,n&&0!==n.length&&void 0!==n[0]?(n[2]=(l[0]+l[2]+l[4])/3,n[3]=(l[1]+l[3]+l[5])/3):(n[0]=(l[0]+l[2]+l[4])/3,n[1]=(l[1]+l[3]+l[5])/3,n[2]=(l[0]+l[2]+l[4])/3+1,n[3]=(l[1]+l[3]+l[5])/3+1),n[4]=1,t.touchData.selecting=!0,t.redraw();else if(o&&i.touches[1]&&s.zoomingEnabled()&&s.panningEnabled()&&s.userZoomingEnabled()&&s.userPanningEnabled()){t.data.bgActivePosistion=void 0,y[r.SELECT_BOX]=!0;var W=t.dragData.touchDragEles;if(W){y[r.DRAG]=!0;for(var H=0;H=t.tapThreshold2){for(var W=t.dragData.touchDragEles,ce=0;ce4&&(t.touchData.singleTouchMoved=!0);if(o&&(null==le||le.isEdge())&&s.panningEnabled()&&s.userPanningEnabled()){t.swipePanning?s.panBy({x:_[0]*c,y:_[1]*c}):O>=t.tapThreshold2&&(t.swipePanning=!0,s.panBy({x:C*c,y:M*c})),le&&(le.unactivate(),t.data.bgActivePosistion||(t.data.bgActivePosistion={x:l[0],y:l[1]}),y[r.SELECT_BOX]=!0,t.touchData.start=null);var w=t.projectIntoViewport(i.touches[0].clientX,i.touches[0].clientY);l[0]=w[0],l[1]=w[1]}}for(var k=0;k0?h[r.NODE]=!0:t.redraw()}var b=!1;if(null!=n&&(n._private.active=!1,b=!0,n.unactivate()),i.touches[2])t.data.bgActivePosistion=void 0,h[r.SELECT_BOX]=!0;else if(i.touches[1]);else if(i.touches[0]);else if(!i.touches[0]){if(t.data.bgActivePosistion=void 0,h[r.SELECT_BOX]=!0,null!=n){n._private.grabbed&&(n._private.grabbed=!1,n.trigger("free"),n._private.rscratch.inDragLayer=!1);for(var w=n._private.edges,_=0;_d;d++)h[4*d]=p[2*d],h[4*d+1]=p[2*d+1],h[4*d+2]=v[2*d],h[4*d+3]=v[2*d+1];h=e.math.fitPolygonToSquare(h),t("star",h),t("vee",[-1,-1,0,-.333,1,-1,0,1]),t("rhomboid",[-1,-1,.333,-1,1,1,-.333,1])}(cytoscape),function(e){"use strict";function t(t){this._private={},this._private.options=e.util.extend({},r,t)}var r={animate:!0,maxSimulationTime:4e3,fit:!0,padding:30,boundingBox:void 0,ungrabifyWhileSimulating:!1,ready:void 0,stop:void 0,repulsion:void 0,stiffness:void 0,friction:void 0,gravity:!0,fps:void 0,precision:void 0,nodeMass:void 0,edgeLength:void 0,stepSize:.1,stableEnergy:function(e){var t=e;return t.max<=.5||t.mean<=.3},infinite:!1};t.prototype.run=function(){var t=this,r=this._private.options;return e.util.require("arbor",function(i){function n(e,t){return null==t?void 0:"function"==typeof t?t.apply(e,[e._private.data,{nodes:u.length,edges:c.length,element:e}]):t}function a(e){if(!e.isFullAutoParent()){var t=e._private.data.id,i=n(e,r.nodeMass),a=e._private.locked,o=e.position(),s=p.fromScreen({x:o.x,y:o.y});e.scratch().arbor=p.addNode(t,{element:e,mass:i,fixed:a,x:a?s.x:void 0,y:a?s.y:void 0})}}function o(e){var t=e.source().id(),i=e.target().id(),a=n(e,r.edgeLength);e.scratch().arbor=p.addEdge(t,i,{length:a})}var s=r.cy,l=r.eles,u=l.nodes().not(":parent"),c=l.edges(),d=e.util.makeBoundingBox(r.boundingBox?r.boundingBox:{x1:0,y1:0,w:s.width(),h:s.height()}),h=!1;if(t.trigger({type:"layoutstart",layout:t}),void 0!==r.liveUpdate&&(r.animate=r.liveUpdate),s.nodes().size()<=1)return r.fit&&s.reset(),s.nodes().position({x:Math.round((d.x1+d.x2)/2),y:Math.round((d.y1+d.y2)/2)}),t.one("layoutready",r.ready),t.trigger({type:"layoutready",layout:t}),t.one("layoutstop",r.stop),void t.trigger({type:"layoutstop",layout:t});var p=t._private.system=i.ParticleSystem();p.parameters({repulsion:r.repulsion,stiffness:r.stiffness,friction:r.friction,gravity:r.gravity,fps:r.fps,dt:r.dt,precision:r.precision}),r.animate&&r.fit&&s.fit(d,r.padding);var v,f=250,g=!1,y=+new Date,m={init:function(e){},redraw:function(){var e=p.energy();if(!r.infinite&&null!=r.stableEnergy&&null!=e&&e.n>0&&r.stableEnergy(e))return void t.stop();r.infinite||f==1/0||(clearTimeout(v),v=setTimeout(D,f));var i=s.collection();p.eachNode(function(e,t){var r=e.data,n=r.element;null!=n&&(n.locked()||n.grabbed()||(n.silentPosition({x:d.x1+t.x,y:d.y1+t.y}),i.merge(n)))}),r.animate&&i.length>0&&(h=!0,i.rtrigger("position"),r.fit&&s.fit(r.padding),y=+new Date,h=!1),g||(g=!0,t.one("layoutready",r.ready),t.trigger({type:"layoutready",layout:t}))}};p.renderer=m,p.screenSize(d.w,d.h),p.screenPadding(r.padding,r.padding,r.padding,r.padding),p.screenStep(r.stepSize);var x;u.on("grab free position",x=function(e){if(!h){var t=this.position(),n=p.fromScreen(t);if(n){var a=i.Point(n.x,n.y),o=r.padding;switch(d.x1+o<=t.x&&t.x<=d.x2-o&&d.y1+o<=t.y&&t.y<=d.y2-o&&(this.scratch().arbor.p=a),e.type){case"grab":this.scratch().arbor.fixed=!0;break;case"free":this.scratch().arbor.fixed=!1}}}});var b;u.on("lock unlock",b=function(e){node.scratch().arbor.fixed=node.locked()});var w;l.on("remove",w=function(e){});var _;s.on("add","*",_=function(){});var E;s.on("resize",E=function(){if(null==r.boundingBox&&null!=t._private.system){var e=s.width(),i=s.height();p.screenSize(e,i)}}),u.each(function(e,t){a(t)}),c.each(function(e,t){o(t)});var S=u.filter(":grabbable");r.ungrabifyWhileSimulating&&S.ungrabify();var D=t._private.doneHandler=function(){t._private.doneHandler=null,r.animate||(r.fit&&s.reset(),u.rtrigger("position")),u.off("grab free position",x),u.off("lock unlock",b),l.off("remove",w),s.off("add","*",_),s.off("resize",E),r.ungrabifyWhileSimulating&&S.grabify(),t.one("layoutstop",r.stop),t.trigger({type:"layoutstop",layout:t})};p.start(),!r.infinite&&null!=r.maxSimulationTime&&r.maxSimulationTime>0&&r.maxSimulationTime!==1/0&&setTimeout(function(){t.stop()},r.maxSimulationTime)}),this},t.prototype.stop=function(){return null!=this._private.system&&this._private.system.stop(),this._private.doneHandler&&this._private.doneHandler(),this},e("layout","arbor",t)}(cytoscape),function(e){"use strict";function t(t){this.options=e.util.extend({},r,t)}var r={fit:!0,directed:!1,padding:30,circle:!1,spacingFactor:1.75,boundingBox:void 0,avoidOverlap:!0,roots:void 0,maximalAdjustments:0,animate:!1,animationDuration:500,ready:void 0,stop:void 0};t.prototype.run=function(){var t,r=this.options,i=r,n=r.cy,a=i.eles,o=a.nodes().not(":parent"),s=a,l=e.util.makeBoundingBox(i.boundingBox?i.boundingBox:{x1:0,y1:0,w:n.width(),h:n.height()});if(e.is.elementOrCollection(i.roots))t=i.roots;else if(e.is.array(i.roots)){for(var u=[],c=0;c0;){var f=n.collection();a.bfs({roots:v[0],visit:function(e,t,r,i,n){f=f.add(r)},directed:!1}),v=v.not(f),p.push(f)}t=n.collection();for(var c=0;cP;){for(var C=D.shift(),T=C.neighborhood().nodes(),M=!1,c=0;cc;c++)for(var N=x[c],R=N.length,V=0;R>V;V++){var h=N[V],A=h._private.scratch.breadthfirst,X=O(h);X&&(A.intEle=X,L.push(h))}for(var c=0;cx.length-1;)x.push([]);x[Y].push(h),A.depth=Y,A.index=x[Y].length-1}B()}var q=0;if(i.avoidOverlap){for(var c=0;cu||0===t)&&(i+=l/c,n++)}return n=Math.max(1,n),i/=n,0===n&&(i=void 0),W[e.id()]=i,i},Z=function(e,t){var r=H(e),i=H(t);return r-i},U=0;3>U;U++){for(var c=0;c0&&x[0].length<=3?c/2:0),h=2*Math.PI/x[n].length*a;return 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0,userConstIter:void 0,allConstIter:void 0,infinite:!1};t.prototype.run=function(){var t=this,r=this.options;return e.util.require("cola",function(i){var n=r.cy,a=r.eles,o=a.nodes(),s=a.edges(),l=!1,u=e.util.makeBoundingBox(r.boundingBox?r.boundingBox:{x1:0,y1:0,w:n.width(),h:n.height()}),c=function(t,r){if(e.is.fn(t)){var i=t;return i.apply(r,[r])}return t},d=function(){for(var t={min:1/0,max:-(1/0)},i={min:1/0,max:-(1/0)},a=0;ar&&!e;r++)e=e||n();return e};if(r.animate){var o=function(){a()||e.util.requestAnimationFrame(o)};e.util.requestAnimationFrame(o)}else for(;!n(););},on:function(e,t){},drag:function(){}});t.adaptor=g;var y=o.filter(":grabbable");r.ungrabifyWhileSimulating&&y.ungrabify();var m;o.on("grab free position",m=function(t){var r=this,i=r._private.scratch.cola,n=r._private.position;switch(r.grabbed()?(i.x=n.x-u.x1,i.y=n.y-u.y1,g.dragstart(i)):e.is.number(i.x)&&e.is.number(i.y)&&(n.x=i.x+u.x1,n.y=i.y+u.y1),t.type){case"grab":g.dragstart(i),g.resume();break;case"free":g.dragend(i)}});var x;o.on("lock unlock",x=function(e){var t=this,r=t._private.scratch.cola;t.locked()?g.dragstart(r):g.dragend(r)});var b=o.stdFilter(function(e){return!e.isParent()});if(g.nodes(b.map(function(e,t){var i=c(r.nodeSpacing,e),n=e.position(),a=e._private.scratch.cola={x:r.randomize?Math.round(Math.random()*u.w):n.x,y:r.randomize?Math.round(Math.random()*u.h):n.y,width:e.outerWidth()+2*i,height:e.outerHeight()+2*i,index:t};return a})),r.alignment){var w=[],_=[];b.forEach(function(e){var t=c(r.alignment,e),i=e._private.scratch.cola,n=i.index;t&&(null!=t.x&&w.push({node:n,offset:t.x}),null!=t.y&&_.push({node:n,offset:t.y}))});var E=[];w.length>0&&E.push({type:"alignment",axis:"x",offsets:w}),_.length>0&&E.push({type:"alignment",axis:"y",offsets:_}),g.constraints(E)}g.groups(o.stdFilter(function(e){return e.isParent()}).map(function(e,t){return e._private.scratch.cola={index:t,leaves:e.descendants().stdFilter(function(e){return!e.isParent()}).map(function(e){return e[0]._private.scratch.cola.index})},e}).map(function(e){return e._private.scratch.cola.groups=e.descendants().stdFilter(function(e){return e.isParent()}).map(function(e){return e._private.scratch.cola.index}),e._private.scratch.cola}));var S,D;null!=r.edgeLength?(S=r.edgeLength,D="linkDistance"):null!=r.edgeSymDiffLength?(S=r.edgeSymDiffLength,D="symmetricDiffLinkLengths"):null!=r.edgeJaccardLength?(S=r.edgeJaccardLength,D="jaccardLinkLengths"):(S=100,D="linkDistance");var k=function(e){return e.calcLength};if(g.links(s.stdFilter(function(e){return!e.source().isParent()&&!e.target().isParent()}).map(function(e,t){var r=e._private.scratch.cola={source:e.source()[0]._private.scratch.cola.index,target:e.target()[0]._private.scratch.cola.index};return null!=S&&(r.calcLength=c(S,e)),r})),g.size([u.w,u.h]),null!=S&&g[D](k),r.flow){var P,C="y",T=50;e.is.string(r.flow)?P={axis:r.flow,minSeparation:T}:e.is.number(r.flow)?P={axis:C,minSeparation:r.flow}:e.is.plainObject(r.flow)?(P=r.flow,P.axis=P.axis||C,P.minSeparation=null!=P.minSeparation?P.minSeparation:T):P={axis:C,minSeparation:T},g.flowLayout(P.axis,P.minSeparation)}g.avoidOverlaps(r.avoidOverlap).handleDisconnected(r.handleDisconnected).start(r.unconstrIter,r.userConstIter,r.allConstIter),t.trigger({type:"layoutstart",layout:t}),r.infinite||setTimeout(function(){g.stop()},r.maxSimulationTime)}),this},t.prototype.stop=function(){return this.adaptor&&(this.manuallyStopped=!0,this.adaptor.stop()),this},e("layout","cola",t)}(cytoscape),function(e){"use strict";function t(t){this.options=e.util.extend({},r,t)}var r={fit:!0,padding:30,startAngle:1.5*Math.PI,counterclockwise:!1,minNodeSpacing:10,boundingBox:void 0,avoidOverlap:!0,height:void 0,width:void 0,concentric:function(e){return e.degree()},levelWidth:function(e){return e.maxDegree()/4},animate:!1,animationDuration:500,ready:void 0,stop:void 0};t.prototype.run=function(){for(var t=this.options,r=t,i=t.cy,n=r.eles,a=n.nodes().not(":parent"),o=e.util.makeBoundingBox(r.boundingBox?r.boundingBox:{x1:0,y1:0,w:i.width(),h:i.height()}),s={x:o.x1+o.w/2,y:o.y1+o.h/2},l=[],u=r.startAngle,c=0,d=0;d0){var m=Math.abs(g[0].value-y.value);m>=v&&(g=[],f.push(g))}g.push(y)}var x={},b=0,w=c+r.minNodeSpacing;if(!r.avoidOverlap){var _=f.length>0&&f[0].length>1,E=Math.min(o.w,o.h)/2-w,S=E/(f.length+_?1:0);w=Math.min(w,S)}for(var d=0;d1&&r.avoidOverlap){var P=Math.cos(k)-Math.cos(0),C=Math.sin(k)-Math.sin(0),T=Math.sqrt(w*w/(P*P+C*C));b=Math.max(T,b)}for(var M=0;M=d;){var g=c[d++],y=s.idToIndex[g],m=s.layoutNodes[y],x=m.children;if(x.length>0){s.graphSet.push(x);for(var l=0;li.count?0:i.graph},o=function(e,t,r,i){var n=i.graphSet[r];if(-1<$.inArray(e,n)&&-1<$.inArray(t,n))return{count:2,graph:r};for(var a=0,s=0;so;o++)for(var s=e.layoutNodes[e.idToIndex[n[o]]],l=o+1;a>l;l++){var u=e.layoutNodes[e.idToIndex[n[l]]];h(s,u,e,t,r)}},h=function(e,t,r,i,n){var a=t.positionX-e.positionX,o=t.positionY-e.positionY;if(0!==a||0!==o){var s=v(e,t,a,o);if(s>0)var l=n.nodeOverlap*s,u=Math.sqrt(a*a+o*o),c=l*a/u,d=l*o/u;else var h=p(e,a,o),f=p(t,-1*a,-1*o),g=f.x-h.x,y=f.y-h.y,m=g*g+y*y,u=Math.sqrt(m),l=n.nodeRepulsion/m,c=l*g/u,d=l*y/u;e.offsetX-=c,e.offsetY-=d,t.offsetX+=c,t.offsetY+=d}},p=function(e,t,r){var i=e.positionX,n=e.positionY,a=e.height,o=e.width,s=r/t,l=a/o,u={};do{if(0===t&&r>0){u.x=i,u.y=n+a/2;break}if(0===t&&0>r){u.x=i,u.y=n+a/2;break}if(t>0&&s>=-1*l&&l>=s){u.x=i+o/2,u.y=n+o*r/2/t;break}if(0>t&&s>=-1*l&&l>=s){u.x=i-o/2,u.y=n-o*r/2/t;break}if(r>0&&(-1*l>=s||s>=l)){u.x=i+a*t/2/r,u.y=n+a/2;break}if(0>r&&(-1*l>=s||s>=l)){u.x=i-a*t/2/r,u.y=n-a/2;break}}while(!1);return u},v=function(e,t,r,i){if(r>0)var n=e.maxX-t.minX;else var n=t.maxX-e.minX;if(i>0)var a=e.maxY-t.minY;else var a=t.maxY-e.minY;return n>=0&&a>=0?Math.sqrt(n*n+a*a):0},f=function(e,t,r){for(var i=0;ic;c++){var d=e.layoutNodes[e.idToIndex[n[c]]],h=o-d.positionX,p=s-d.positionY,v=Math.sqrt(h*h+p*p);if(v>1){var f=r.gravity*h/v,g=r.gravity*p/v;d.offsetX+=f,d.offsetY+=g}}}},y=function(e,t,r){var i=[],n=0,a=-1;for(i.push.apply(i,e.graphSet[0]),a+=e.graphSet[0].length;a>=n;){var o=i[n++],s=e.idToIndex[o],l=e.layoutNodes[s],u=l.children;if(0r)var n={x:r*e/i,y:r*t/i};else var n={x:e,y:t};return n},b=function(e,t){var r=e.parentId;if(null!=r){var i=t.layoutNodes[t.idToIndex[r]],n=!1;return(null==i.maxX||e.maxX+i.padRight>i.maxX)&&(i.maxX=e.maxX+i.padRight,n=!0),(null==i.minX||e.minX-i.padLefti.maxY)&&(i.maxY=e.maxY+i.padBottom,n=!0),(null==i.minY||e.minY-i.padTops){var p=d(),v=h();(p-1)*v>=s?d(p-1):(v-1)*p>=s&&h(v-1)}else for(;s>c*u;){var p=d(),v=h();(v+1)*p>=s?h(v+1):d(p+1)}var f=o.w/c,g=o.h/u;if(r.avoidOverlap)for(var y=0;y=c&&(D=0,S++)},P={},y=0;yu&&(u=Math.max(.05,Math.min(.1,l/Math.sqrt(n*s/S.length)*.5)));for(var R=t(N.edges),V=0>=R,A=0,X=0;!V;){++A;for(var F=0;4>=F;++F){P.recycle(N),N=P.compute(S,C),B=N.cells;for(var M=0;M=Y?V=!0:(Y>=R||A>=4)&&(X>=c?V=!0:(n+=n*u,s+=s*u,C={xl:0,xr:n,yt:0,yb:s},++X,A=0)),R=Y,h(),p()}return h(),e}).then(function(e){var r=e.vertices;s(e);var i=e.startTime,a=new Date;console.info("Layout on "+r.length+" nodes took "+(a-i)+" ms"),t.one("layoutstop",n.stop),n.animate||t.trigger("layoutready"),t.trigger("layoutstop"),_.stop()})}),this},t.prototype.stop=function(){},e("layout","spread",t)}(cytoscape),function(e){"use strict";function t(t){this.options=e.util.extend(!0,{},r,t)}var r={animate:!0,maxSimulationTime:4e3,ungrabifyWhileSimulating:!1,fit:!0,padding:30,boundingBox:void 0,random:!1,infinite:!1,ready:void 0,stop:void 0,stiffness:400,repulsion:400,damping:.5};t.prototype.run=function(){var t=this,r=this,i=this.options;return e.util.require("Springy",function(n){function a(e){var t=e.scratch("springy").model.id,r=w.layout.nodePoints[t].p,i=e.position(),n=null!=i.x&&null!=i.y?y(e.position()):{x:4*Math.random()-2,y:4*Math.random()-2};r.x=n.x,r.y=n.y}function o(){r.stopped=!1,i.ungrabifyWhileSimulating&&E.ungrabify(),w.start()}var s=!1,l=i.cy;t.trigger({type:"layoutstart",layout:t});var u=i.eles,c=u.nodes().not(":parent"),d=u.edges(),h=e.util.makeBoundingBox(i.boundingBox?i.boundingBox:{x1:0,y1:0,w:l.width(),h:l.height()}),p=new n.Graph;c.each(function(e,t){t.scratch("springy",{model:p.newNode({element:t})})}),d.each(function(e,t){var r=t.source().scratch("springy").model,i=t.target().scratch("springy").model;t.scratch("springy",{model:p.newEdge(r,i,{element:t})})});var v=window.sim=new n.Layout.ForceDirected(p,i.stiffness,i.repulsion,i.damping);i.infinite&&(v.minEnergyThreshold=-(1/0));var f=v.getBoundingBox(),g=function(e){f=v.getBoundingBox();var t=f.topright.subtract(f.bottomleft),r=e.subtract(f.bottomleft).divide(t.x).x*h.w+h.x1,i=e.subtract(f.bottomleft).divide(t.y).y*h.h+h.x1;return new n.Vector(r,i)},y=function(e){f=v.getBoundingBox();var t=f.topright.subtract(f.bottomleft),r=(e.x-h.x1)/h.w*t.x+f.bottomleft.x,i=(e.y-h.y1)/h.h*t.y+f.bottomleft.y;return new n.Vector(r,i)},m=l.collection(),x=l.nodes().size(),b=1,w=new n.Renderer(v,function(){r.stopped||m.length>0&&i.animate&&(s=!0,m.rtrigger("position"),i.fit&&l.fit(i.padding),m=l.collection(),s=!1)},function(e,t,r){},function(e,n){if(!r.stopped){var a=g(n),o=e.data.element;o.locked()||o.grabbed()||(o._private.position={x:a.x,y:a.y},m.merge(o)),b==x&&(t.one("layoutready",i.ready),t.trigger({type:"layoutready",layout:t})),b++}});c.each(function(e,t){i.random||a(t)});var _;c.on("position",_=function(){s||a(this)});var E=c.filter(":grabbable");r.stopSystem=function(){r.stopped=!0,p.filterNodes(function(){return!1}),i.ungrabifyWhileSimulating&&E.grabify(),i.fit&&l.fit(i.padding),c.off("drag position",_),t.one("layoutstop",i.stop),t.trigger({type:"layoutstop",layout:t}),r.stopSystem=null},o(),i.infinite||setTimeout(function(){r.stop()},i.maxSimulationTime)}),this},t.prototype.stop=function(){return null!=this.stopSystem&&this.stopSystem(),this},e("layout","springy",t)}(cytoscape),function(e){"use strict";function t(e){this.options=e}t.prototype.recalculateRenderedStyle=function(){},t.prototype.notify=function(){},e("renderer","null",t)}(cytoscape); \ No newline at end of file diff --git a/config/plugins/visualizations/graphviz/static/js/graphVis.js b/config/plugins/visualizations/graphviz/static/js/graphVis.js new file mode 100644 index 00000000000..f89e3d39ad0 --- /dev/null +++ b/config/plugins/visualizations/graphviz/static/js/graphVis.js @@ -0,0 +1,165 @@ + var showNodeLabel; + var showEdgeLabel; + var showOut; + var showIn; + var demoNodes = []; + var demoEdges = []; + var shape; + var allcy; + var cy; + + + + $(function() { // on dom ready + + + $("body").css("overflow-x", "hidden"); //// remove horizontal scrollbar + + + }); // END on dom ready + +// shape of the graph + $("select option:selected").each(function() { + shape = $(this).val(); + + }); + + ///////// create graph + function createGraph(data) { + + allcy = cytoscape({ + headless: true, + }); + + cy = cytoscape({ + + container: document.getElementById('cy'), + + layout: { + name: shape + //avoidOverlap: true, + //padding: 10 + }, + hideEdgesOnViewport: true, + hideLabelsOnViewport: true, + motionBlur: true, + textureOnViewport: true, + + ready: function() { + + window.cy = this; + cy.nodes().on("click", function(e) { + + showNodeInfo(e.cyTarget); + + }); + }, + style: cytoscape.stylesheet() + .selector('node') + .css({ + 'content': showNodeLabel, + 'text-valign': 'center', + 'background-color': '#888888', + 'opacity': 0.8 + + }) + .selector('edge') + .css({ + 'curve-style': 'unbundled-bezier', + 'target-arrow-shape': 'triangle', + 'width': 4, + 'line-color': '#ddd', + 'target-arrow-color': '#ddd', + 'content': showEdgeLabel + + + }) + .selector(':selected') + .css({ + 'background-color': '#FE2E64', + 'line-color': '#FE2E64', + 'target-arrow-color': '#FE2E64', + 'source-arrow-color': '#FE2E64', + 'opacity': 1 + }) + .selector('core') + .css({ + 'outside-texture-bg-color': 'white' + + }) + }); + allcy.load(data); + +// if graph contains more than 50 nodes load only root nodes + if (allcy.nodes().length > 50 && allcy.nodes().roots().length != 0 ) { + + var toAdd = allcy.nodes().roots().closedNeighborhood(); + allcy.nodes().roots().addClass("roots"); + + showNodesToExpand(toAdd); + cy.add(toAdd); + cy.load(cy.elements('*').jsons()); + + cy.style() + .selector('.toBeExpaned') + .css({ + + 'width': 50, + 'height': 50 + }) + .update(); + + } else { + + cy.add(data); + cy.load(cy.elements('*').jsons()); + } + cy.boxSelectionEnabled(true); + + + checkBoxes(); + + + } // END create graph + + + //// parse function for matrix data + function parseAndCreate(demoNodes, demoEdges) { + var data = { + nodes: demoNodes, + edges: demoEdges + }; + createGraph(data); + } + + + ///// parsing function for json: for link/egde and "" issues + function parseJson(dataToParse) { + + if (dataToParse.links == null) { + + var links = dataToParse.edges; + } else { + var links = dataToParse.links; + dataToParse.edges = links; + + } + + var nodes = dataToParse.nodes; + + for (var i = 0; i < nodes.length; i++) { + + dataToParse.nodes[i].data = nodes[i]; + dataToParse.nodes[i].data.id = '"' + nodes[i].id + '"'; + } + + + for (var i = 0; i < links.length; i++) { + + dataToParse.edges[i].data = links[i]; + dataToParse.edges[i].data.source = '"' + links[i].source + '"'; + dataToParse.edges[i].data.target = '"' + links[i].target + '"'; + } + + createGraph(dataToParse); + } \ No newline at end of file diff --git a/config/plugins/visualizations/graphviz/static/js/jquery.qtip.js b/config/plugins/visualizations/graphviz/static/js/jquery.qtip.js new file mode 100644 index 00000000000..67473e1b7c4 --- /dev/null +++ b/config/plugins/visualizations/graphviz/static/js/jquery.qtip.js @@ -0,0 +1,3451 @@ +/* + * qTip2 - Pretty powerful tooltips - v2.2.1 + * http://qtip2.com + * + * Copyright (c) 2014 + * Released under the MIT licenses + * http://jquery.org/license + * + * Date: Sat Sep 6 2014 11:12 GMT+0100+0100 + * Plugins: tips modal viewport svg imagemap ie6 + * Styles: core basic css3 + */ +/*global window: false, jQuery: false, console: false, define: false */ + +/* Cache window, document, undefined */ +(function( window, document, undefined ) { + +// Uses AMD or browser globals to create a jQuery plugin. +(function( factory ) { + "use strict"; + if(typeof define === 'function' && define.amd) { + define(['jquery'], factory); + } + else if(jQuery && !jQuery.fn.qtip) { + factory(jQuery); + } +} +(function($) { + "use strict"; // Enable ECMAScript "strict" operation for this function. See more: http://ejohn.org/blog/ecmascript-5-strict-mode-json-and-more/ +;// Munge the primitives - Paul Irish tip +var TRUE = true, +FALSE = false, +NULL = null, + +// Common variables +X = 'x', Y = 'y', +WIDTH = 'width', +HEIGHT = 'height', + +// Positioning sides +TOP = 'top', +LEFT = 'left', +BOTTOM = 'bottom', +RIGHT = 'right', +CENTER = 'center', + +// Position adjustment types +FLIP = 'flip', +FLIPINVERT = 'flipinvert', +SHIFT = 'shift', + +// Shortcut vars +QTIP, PROTOTYPE, CORNER, CHECKS, +PLUGINS = {}, +NAMESPACE = 'qtip', +ATTR_HAS = 'data-hasqtip', +ATTR_ID = 'data-qtip-id', +WIDGET = ['ui-widget', 'ui-tooltip'], +SELECTOR = '.'+NAMESPACE, +INACTIVE_EVENTS = 'click dblclick mousedown mouseup mousemove mouseleave mouseenter'.split(' '), + +CLASS_FIXED = NAMESPACE+'-fixed', +CLASS_DEFAULT = NAMESPACE + '-default', +CLASS_FOCUS = NAMESPACE + '-focus', +CLASS_HOVER = NAMESPACE + '-hover', +CLASS_DISABLED = NAMESPACE+'-disabled', + +replaceSuffix = '_replacedByqTip', +oldtitle = 'oldtitle', +trackingBound, + +// Browser detection +BROWSER = { + /* + * IE version detection + * + * Adapted from: http://ajaxian.com/archives/attack-of-the-ie-conditional-comment + * Credit to James Padolsey for the original implemntation! + */ + ie: (function(){ + for ( + var v = 4, i = document.createElement("div"); + (i.innerHTML = "") && i.getElementsByTagName("i")[0]; + v+=1 + ) {} + return v > 4 ? v : NaN; + }()), + + /* + * iOS version detection + */ + iOS: parseFloat( + ('' + (/CPU.*OS ([0-9_]{1,5})|(CPU like).*AppleWebKit.*Mobile/i.exec(navigator.userAgent) || [0,''])[1]) + .replace('undefined', '3_2').replace('_', '.').replace('_', '') + ) || FALSE +}; +;function QTip(target, options, id, attr) { + // Elements and ID + this.id = id; + this.target = target; + this.tooltip = NULL; + this.elements = { target: target }; + + // Internal constructs + this._id = NAMESPACE + '-' + id; + this.timers = { img: {} }; + this.options = options; + this.plugins = {}; + + // Cache object + this.cache = { + event: {}, + target: $(), + disabled: FALSE, + attr: attr, + onTooltip: FALSE, + lastClass: '' + }; + + // Set the initial flags + this.rendered = this.destroyed = this.disabled = this.waiting = + this.hiddenDuringWait = this.positioning = this.triggering = FALSE; +} +PROTOTYPE = QTip.prototype; + +PROTOTYPE._when = function(deferreds) { + return $.when.apply($, deferreds); +}; + +PROTOTYPE.render = function(show) { + if(this.rendered || this.destroyed) { return this; } // If tooltip has already been rendered, exit + + var self = this, + options = this.options, + cache = this.cache, + elements = this.elements, + text = options.content.text, + title = options.content.title, + button = options.content.button, + posOptions = options.position, + namespace = '.'+this._id+' ', + deferreds = [], + tooltip; + + // Add ARIA attributes to target + $.attr(this.target[0], 'aria-describedby', this._id); + + // Create public position object that tracks current position corners + cache.posClass = this._createPosClass( + (this.position = { my: posOptions.my, at: posOptions.at }).my + ); + + // Create tooltip element + this.tooltip = elements.tooltip = tooltip = $('
', { + 'id': this._id, + 'class': [ NAMESPACE, CLASS_DEFAULT, options.style.classes, cache.posClass ].join(' '), + 'width': options.style.width || '', + 'height': options.style.height || '', + 'tracking': posOptions.target === 'mouse' && posOptions.adjust.mouse, + + /* ARIA specific attributes */ + 'role': 'alert', + 'aria-live': 'polite', + 'aria-atomic': FALSE, + 'aria-describedby': this._id + '-content', + 'aria-hidden': TRUE + }) + .toggleClass(CLASS_DISABLED, this.disabled) + .attr(ATTR_ID, this.id) + .data(NAMESPACE, this) + .appendTo(posOptions.container) + .append( + // Create content element + elements.content = $('
', { + 'class': NAMESPACE + '-content', + 'id': this._id + '-content', + 'aria-atomic': TRUE + }) + ); + + // Set rendered flag and prevent redundant reposition calls for now + this.rendered = -1; + this.positioning = TRUE; + + // Create title... + if(title) { + this._createTitle(); + + // Update title only if its not a callback (called in toggle if so) + if(!$.isFunction(title)) { + deferreds.push( this._updateTitle(title, FALSE) ); + } + } + + // Create button + if(button) { this._createButton(); } + + // Set proper rendered flag and update content if not a callback function (called in toggle) + if(!$.isFunction(text)) { + deferreds.push( this._updateContent(text, FALSE) ); + } + this.rendered = TRUE; + + // Setup widget classes + this._setWidget(); + + // Initialize 'render' plugins + $.each(PLUGINS, function(name) { + var instance; + if(this.initialize === 'render' && (instance = this(self))) { + self.plugins[name] = instance; + } + }); + + // Unassign initial events and assign proper events + this._unassignEvents(); + this._assignEvents(); + + // When deferreds have completed + this._when(deferreds).then(function() { + // tooltiprender event + self._trigger('render'); + + // Reset flags + self.positioning = FALSE; + + // Show tooltip if not hidden during wait period + if(!self.hiddenDuringWait && (options.show.ready || show)) { + self.toggle(TRUE, cache.event, FALSE); + } + self.hiddenDuringWait = FALSE; + }); + + // Expose API + QTIP.api[this.id] = this; + + return this; +}; + +PROTOTYPE.destroy = function(immediate) { + // Set flag the signify destroy is taking place to plugins + // and ensure it only gets destroyed once! + if(this.destroyed) { return this.target; } + + function process() { + if(this.destroyed) { return; } + this.destroyed = TRUE; + + var target = this.target, + title = target.attr(oldtitle), + timer; + + // Destroy tooltip if rendered + if(this.rendered) { + this.tooltip.stop(1,0).find('*').remove().end().remove(); + } + + // Destroy all plugins + $.each(this.plugins, function(name) { + this.destroy && this.destroy(); + }); + + // Clear timers + for(timer in this.timers) { + clearTimeout(this.timers[timer]); + } + + // Remove api object and ARIA attributes + target.removeData(NAMESPACE) + .removeAttr(ATTR_ID) + .removeAttr(ATTR_HAS) + .removeAttr('aria-describedby'); + + // Reset old title attribute if removed + if(this.options.suppress && title) { + target.attr('title', title).removeAttr(oldtitle); + } + + // Remove qTip events associated with this API + this._unassignEvents(); + + // Remove ID from used id objects, and delete object references + // for better garbage collection and leak protection + this.options = this.elements = this.cache = this.timers = + this.plugins = this.mouse = NULL; + + // Delete epoxsed API object + delete QTIP.api[this.id]; + } + + // If an immediate destory is needed + if((immediate !== TRUE || this.triggering === 'hide') && this.rendered) { + this.tooltip.one('tooltiphidden', $.proxy(process, this)); + !this.triggering && this.hide(); + } + + // If we're not in the process of hiding... process + else { process.call(this); } + + return this.target; +}; +;function invalidOpt(a) { + return a === NULL || $.type(a) !== 'object'; +} + +function invalidContent(c) { + return !( $.isFunction(c) || (c && c.attr) || c.length || ($.type(c) === 'object' && (c.jquery || c.then) )); +} + +// Option object sanitizer +function sanitizeOptions(opts) { + var content, text, ajax, once; + + if(invalidOpt(opts)) { return FALSE; } + + if(invalidOpt(opts.metadata)) { + opts.metadata = { type: opts.metadata }; + } + + if('content' in opts) { + content = opts.content; + + if(invalidOpt(content) || content.jquery || content.done) { + content = opts.content = { + text: (text = invalidContent(content) ? FALSE : content) + }; + } + else { text = content.text; } + + // DEPRECATED - Old content.ajax plugin functionality + // Converts it into the proper Deferred syntax + if('ajax' in content) { + ajax = content.ajax; + once = ajax && ajax.once !== FALSE; + delete content.ajax; + + content.text = function(event, api) { + var loading = text || $(this).attr(api.options.content.attr) || 'Loading...', + + deferred = $.ajax( + $.extend({}, ajax, { context: api }) + ) + .then(ajax.success, NULL, ajax.error) + .then(function(content) { + if(content && once) { api.set('content.text', content); } + return content; + }, + function(xhr, status, error) { + if(api.destroyed || xhr.status === 0) { return; } + api.set('content.text', status + ': ' + error); + }); + + return !once ? (api.set('content.text', loading), deferred) : loading; + }; + } + + if('title' in content) { + if($.isPlainObject(content.title)) { + content.button = content.title.button; + content.title = content.title.text; + } + + if(invalidContent(content.title || FALSE)) { + content.title = FALSE; + } + } + } + + if('position' in opts && invalidOpt(opts.position)) { + opts.position = { my: opts.position, at: opts.position }; + } + + if('show' in opts && invalidOpt(opts.show)) { + opts.show = opts.show.jquery ? { target: opts.show } : + opts.show === TRUE ? { ready: TRUE } : { event: opts.show }; + } + + if('hide' in opts && invalidOpt(opts.hide)) { + opts.hide = opts.hide.jquery ? { target: opts.hide } : { event: opts.hide }; + } + + if('style' in opts && invalidOpt(opts.style)) { + opts.style = { classes: opts.style }; + } + + // Sanitize plugin options + $.each(PLUGINS, function() { + this.sanitize && this.sanitize(opts); + }); + + return opts; +} + +// Setup builtin .set() option checks +CHECKS = PROTOTYPE.checks = { + builtin: { + // Core checks + '^id$': function(obj, o, v, prev) { + var id = v === TRUE ? QTIP.nextid : v, + new_id = NAMESPACE + '-' + id; + + if(id !== FALSE && id.length > 0 && !$('#'+new_id).length) { + this._id = new_id; + + if(this.rendered) { + this.tooltip[0].id = this._id; + this.elements.content[0].id = this._id + '-content'; + this.elements.title[0].id = this._id + '-title'; + } + } + else { obj[o] = prev; } + }, + '^prerender': function(obj, o, v) { + v && !this.rendered && this.render(this.options.show.ready); + }, + + // Content checks + '^content.text$': function(obj, o, v) { + this._updateContent(v); + }, + '^content.attr$': function(obj, o, v, prev) { + if(this.options.content.text === this.target.attr(prev)) { + this._updateContent( this.target.attr(v) ); + } + }, + '^content.title$': function(obj, o, v) { + // Remove title if content is null + if(!v) { return this._removeTitle(); } + + // If title isn't already created, create it now and update + v && !this.elements.title && this._createTitle(); + this._updateTitle(v); + }, + '^content.button$': function(obj, o, v) { + this._updateButton(v); + }, + '^content.title.(text|button)$': function(obj, o, v) { + this.set('content.'+o, v); // Backwards title.text/button compat + }, + + // Position checks + '^position.(my|at)$': function(obj, o, v){ + 'string' === typeof v && (this.position[o] = obj[o] = new CORNER(v, o === 'at')); + }, + '^position.container$': function(obj, o, v){ + this.rendered && this.tooltip.appendTo(v); + }, + + // Show checks + '^show.ready$': function(obj, o, v) { + v && (!this.rendered && this.render(TRUE) || this.toggle(TRUE)); + }, + + // Style checks + '^style.classes$': function(obj, o, v, p) { + this.rendered && this.tooltip.removeClass(p).addClass(v); + }, + '^style.(width|height)': function(obj, o, v) { + this.rendered && this.tooltip.css(o, v); + }, + '^style.widget|content.title': function() { + this.rendered && this._setWidget(); + }, + '^style.def': function(obj, o, v) { + this.rendered && this.tooltip.toggleClass(CLASS_DEFAULT, !!v); + }, + + // Events check + '^events.(render|show|move|hide|focus|blur)$': function(obj, o, v) { + this.rendered && this.tooltip[($.isFunction(v) ? '' : 'un') + 'bind']('tooltip'+o, v); + }, + + // Properties which require event reassignment + '^(show|hide|position).(event|target|fixed|inactive|leave|distance|viewport|adjust)': function() { + if(!this.rendered) { return; } + + // Set tracking flag + var posOptions = this.options.position; + this.tooltip.attr('tracking', posOptions.target === 'mouse' && posOptions.adjust.mouse); + + // Reassign events + this._unassignEvents(); + this._assignEvents(); + } + } +}; + +// Dot notation converter +function convertNotation(options, notation) { + var i = 0, obj, option = options, + + // Split notation into array + levels = notation.split('.'); + + // Loop through + while( option = option[ levels[i++] ] ) { + if(i < levels.length) { obj = option; } + } + + return [obj || options, levels.pop()]; +} + +PROTOTYPE.get = function(notation) { + if(this.destroyed) { return this; } + + var o = convertNotation(this.options, notation.toLowerCase()), + result = o[0][ o[1] ]; + + return result.precedance ? result.string() : result; +}; + +function setCallback(notation, args) { + var category, rule, match; + + for(category in this.checks) { + for(rule in this.checks[category]) { + if(match = (new RegExp(rule, 'i')).exec(notation)) { + args.push(match); + + if(category === 'builtin' || this.plugins[category]) { + this.checks[category][rule].apply( + this.plugins[category] || this, args + ); + } + } + } + } +} + +var rmove = /^position\.(my|at|adjust|target|container|viewport)|style|content|show\.ready/i, + rrender = /^prerender|show\.ready/i; + +PROTOTYPE.set = function(option, value) { + if(this.destroyed) { return this; } + + var rendered = this.rendered, + reposition = FALSE, + options = this.options, + checks = this.checks, + name; + + // Convert singular option/value pair into object form + if('string' === typeof option) { + name = option; option = {}; option[name] = value; + } + else { option = $.extend({}, option); } + + // Set all of the defined options to their new values + $.each(option, function(notation, value) { + if(rendered && rrender.test(notation)) { + delete option[notation]; return; + } + + // Set new obj value + var obj = convertNotation(options, notation.toLowerCase()), previous; + previous = obj[0][ obj[1] ]; + obj[0][ obj[1] ] = value && value.nodeType ? $(value) : value; + + // Also check if we need to reposition + reposition = rmove.test(notation) || reposition; + + // Set the new params for the callback + option[notation] = [obj[0], obj[1], value, previous]; + }); + + // Re-sanitize options + sanitizeOptions(options); + + /* + * Execute any valid callbacks for the set options + * Also set positioning flag so we don't get loads of redundant repositioning calls. + */ + this.positioning = TRUE; + $.each(option, $.proxy(setCallback, this)); + this.positioning = FALSE; + + // Update position if needed + if(this.rendered && this.tooltip[0].offsetWidth > 0 && reposition) { + this.reposition( options.position.target === 'mouse' ? NULL : this.cache.event ); + } + + return this; +}; +;PROTOTYPE._update = function(content, element, reposition) { + var self = this, + cache = this.cache; + + // Make sure tooltip is rendered and content is defined. If not return + if(!this.rendered || !content) { return FALSE; } + + // Use function to parse content + if($.isFunction(content)) { + content = content.call(this.elements.target, cache.event, this) || ''; + } + + // Handle deferred content + if($.isFunction(content.then)) { + cache.waiting = TRUE; + return content.then(function(c) { + cache.waiting = FALSE; + return self._update(c, element); + }, NULL, function(e) { + return self._update(e, element); + }); + } + + // If content is null... return false + if(content === FALSE || (!content && content !== '')) { return FALSE; } + + // Append new content if its a DOM array and show it if hidden + if(content.jquery && content.length > 0) { + element.empty().append( + content.css({ display: 'block', visibility: 'visible' }) + ); + } + + // Content is a regular string, insert the new content + else { element.html(content); } + + // Wait for content to be loaded, and reposition + return this._waitForContent(element).then(function(images) { + if(self.rendered && self.tooltip[0].offsetWidth > 0) { + self.reposition(cache.event, !images.length); + } + }); +}; + +PROTOTYPE._waitForContent = function(element) { + var cache = this.cache; + + // Set flag + cache.waiting = TRUE; + + // If imagesLoaded is included, ensure images have loaded and return promise + return ( $.fn.imagesLoaded ? element.imagesLoaded() : $.Deferred().resolve([]) ) + .done(function() { cache.waiting = FALSE; }) + .promise(); +}; + +PROTOTYPE._updateContent = function(content, reposition) { + this._update(content, this.elements.content, reposition); +}; + +PROTOTYPE._updateTitle = function(content, reposition) { + if(this._update(content, this.elements.title, reposition) === FALSE) { + this._removeTitle(FALSE); + } +}; + +PROTOTYPE._createTitle = function() +{ + var elements = this.elements, + id = this._id+'-title'; + + // Destroy previous title element, if present + if(elements.titlebar) { this._removeTitle(); } + + // Create title bar and title elements + elements.titlebar = $('
', { + 'class': NAMESPACE + '-titlebar ' + (this.options.style.widget ? createWidgetClass('header') : '') + }) + .append( + elements.title = $('
', { + 'id': id, + 'class': NAMESPACE + '-title', + 'aria-atomic': TRUE + }) + ) + .insertBefore(elements.content) + + // Button-specific events + .delegate('.qtip-close', 'mousedown keydown mouseup keyup mouseout', function(event) { + $(this).toggleClass('ui-state-active ui-state-focus', event.type.substr(-4) === 'down'); + }) + .delegate('.qtip-close', 'mouseover mouseout', function(event){ + $(this).toggleClass('ui-state-hover', event.type === 'mouseover'); + }); + + // Create button if enabled + if(this.options.content.button) { this._createButton(); } +}; + +PROTOTYPE._removeTitle = function(reposition) +{ + var elements = this.elements; + + if(elements.title) { + elements.titlebar.remove(); + elements.titlebar = elements.title = elements.button = NULL; + + // Reposition if enabled + if(reposition !== FALSE) { this.reposition(); } + } +}; +;PROTOTYPE._createPosClass = function(my) { + return NAMESPACE + '-pos-' + (my || this.options.position.my).abbrev(); +}; + +PROTOTYPE.reposition = function(event, effect) { + if(!this.rendered || this.positioning || this.destroyed) { return this; } + + // Set positioning flag + this.positioning = TRUE; + + var cache = this.cache, + tooltip = this.tooltip, + posOptions = this.options.position, + target = posOptions.target, + my = posOptions.my, + at = posOptions.at, + viewport = posOptions.viewport, + container = posOptions.container, + adjust = posOptions.adjust, + method = adjust.method.split(' '), + tooltipWidth = tooltip.outerWidth(FALSE), + tooltipHeight = tooltip.outerHeight(FALSE), + targetWidth = 0, + targetHeight = 0, + type = tooltip.css('position'), + position = { left: 0, top: 0 }, + visible = tooltip[0].offsetWidth > 0, + isScroll = event && event.type === 'scroll', + win = $(window), + doc = container[0].ownerDocument, + mouse = this.mouse, + pluginCalculations, offset, adjusted, newClass; + + // Check if absolute position was passed + if($.isArray(target) && target.length === 2) { + // Force left top and set position + at = { x: LEFT, y: TOP }; + position = { left: target[0], top: target[1] }; + } + + // Check if mouse was the target + else if(target === 'mouse') { + // Force left top to allow flipping + at = { x: LEFT, y: TOP }; + + // Use the mouse origin that caused the show event, if distance hiding is enabled + if((!adjust.mouse || this.options.hide.distance) && cache.origin && cache.origin.pageX) { + event = cache.origin; + } + + // Use cached event for resize/scroll events + else if(!event || (event && (event.type === 'resize' || event.type === 'scroll'))) { + event = cache.event; + } + + // Otherwise, use the cached mouse coordinates if available + else if(mouse && mouse.pageX) { + event = mouse; + } + + // Calculate body and container offset and take them into account below + if(type !== 'static') { position = container.offset(); } + if(doc.body.offsetWidth !== (window.innerWidth || doc.documentElement.clientWidth)) { + offset = $(document.body).offset(); + } + + // Use event coordinates for position + position = { + left: event.pageX - position.left + (offset && offset.left || 0), + top: event.pageY - position.top + (offset && offset.top || 0) + }; + + // Scroll events are a pain, some browsers + if(adjust.mouse && isScroll && mouse) { + position.left -= (mouse.scrollX || 0) - win.scrollLeft(); + position.top -= (mouse.scrollY || 0) - win.scrollTop(); + } + } + + // Target wasn't mouse or absolute... + else { + // Check if event targetting is being used + if(target === 'event') { + if(event && event.target && event.type !== 'scroll' && event.type !== 'resize') { + cache.target = $(event.target); + } + else if(!event.target) { + cache.target = this.elements.target; + } + } + else if(target !== 'event'){ + cache.target = $(target.jquery ? target : this.elements.target); + } + target = cache.target; + + // Parse the target into a jQuery object and make sure there's an element present + target = $(target).eq(0); + if(target.length === 0) { return this; } + + // Check if window or document is the target + else if(target[0] === document || target[0] === window) { + targetWidth = BROWSER.iOS ? window.innerWidth : target.width(); + targetHeight = BROWSER.iOS ? window.innerHeight : target.height(); + + if(target[0] === window) { + position = { + top: (viewport || target).scrollTop(), + left: (viewport || target).scrollLeft() + }; + } + } + + // Check if the target is an element + else if(PLUGINS.imagemap && target.is('area')) { + pluginCalculations = PLUGINS.imagemap(this, target, at, PLUGINS.viewport ? method : FALSE); + } + + // Check if the target is an SVG element + else if(PLUGINS.svg && target && target[0].ownerSVGElement) { + pluginCalculations = PLUGINS.svg(this, target, at, PLUGINS.viewport ? method : FALSE); + } + + // Otherwise use regular jQuery methods + else { + targetWidth = target.outerWidth(FALSE); + targetHeight = target.outerHeight(FALSE); + position = target.offset(); + } + + // Parse returned plugin values into proper variables + if(pluginCalculations) { + targetWidth = pluginCalculations.width; + targetHeight = pluginCalculations.height; + offset = pluginCalculations.offset; + position = pluginCalculations.position; + } + + // Adjust position to take into account offset parents + position = this.reposition.offset(target, position, container); + + // Adjust for position.fixed tooltips (and also iOS scroll bug in v3.2-4.0 & v4.3-4.3.2) + if((BROWSER.iOS > 3.1 && BROWSER.iOS < 4.1) || + (BROWSER.iOS >= 4.3 && BROWSER.iOS < 4.33) || + (!BROWSER.iOS && type === 'fixed') + ){ + position.left -= win.scrollLeft(); + position.top -= win.scrollTop(); + } + + // Adjust position relative to target + if(!pluginCalculations || (pluginCalculations && pluginCalculations.adjustable !== FALSE)) { + position.left += at.x === RIGHT ? targetWidth : at.x === CENTER ? targetWidth / 2 : 0; + position.top += at.y === BOTTOM ? targetHeight : at.y === CENTER ? targetHeight / 2 : 0; + } + } + + // Adjust position relative to tooltip + position.left += adjust.x + (my.x === RIGHT ? -tooltipWidth : my.x === CENTER ? -tooltipWidth / 2 : 0); + position.top += adjust.y + (my.y === BOTTOM ? -tooltipHeight : my.y === CENTER ? -tooltipHeight / 2 : 0); + + // Use viewport adjustment plugin if enabled + if(PLUGINS.viewport) { + adjusted = position.adjusted = PLUGINS.viewport( + this, position, posOptions, targetWidth, targetHeight, tooltipWidth, tooltipHeight + ); + + // Apply offsets supplied by positioning plugin (if used) + if(offset && adjusted.left) { position.left += offset.left; } + if(offset && adjusted.top) { position.top += offset.top; } + + // Apply any new 'my' position + if(adjusted.my) { this.position.my = adjusted.my; } + } + + // Viewport adjustment is disabled, set values to zero + else { position.adjusted = { left: 0, top: 0 }; } + + // Set tooltip position class if it's changed + if(cache.posClass !== (newClass = this._createPosClass(this.position.my))) { + tooltip.removeClass(cache.posClass).addClass( (cache.posClass = newClass) ); + } + + // tooltipmove event + if(!this._trigger('move', [position, viewport.elem || viewport], event)) { return this; } + delete position.adjusted; + + // If effect is disabled, target it mouse, no animation is defined or positioning gives NaN out, set CSS directly + if(effect === FALSE || !visible || isNaN(position.left) || isNaN(position.top) || target === 'mouse' || !$.isFunction(posOptions.effect)) { + tooltip.css(position); + } + + // Use custom function if provided + else if($.isFunction(posOptions.effect)) { + posOptions.effect.call(tooltip, this, $.extend({}, position)); + tooltip.queue(function(next) { + // Reset attributes to avoid cross-browser rendering bugs + $(this).css({ opacity: '', height: '' }); + if(BROWSER.ie) { this.style.removeAttribute('filter'); } + + next(); + }); + } + + // Set positioning flag + this.positioning = FALSE; + + return this; +}; + +// Custom (more correct for qTip!) offset calculator +PROTOTYPE.reposition.offset = function(elem, pos, container) { + if(!container[0]) { return pos; } + + var ownerDocument = $(elem[0].ownerDocument), + quirks = !!BROWSER.ie && document.compatMode !== 'CSS1Compat', + parent = container[0], + scrolled, position, parentOffset, overflow; + + function scroll(e, i) { + pos.left += i * e.scrollLeft(); + pos.top += i * e.scrollTop(); + } + + // Compensate for non-static containers offset + do { + if((position = $.css(parent, 'position')) !== 'static') { + if(position === 'fixed') { + parentOffset = parent.getBoundingClientRect(); + scroll(ownerDocument, -1); + } + else { + parentOffset = $(parent).position(); + parentOffset.left += (parseFloat($.css(parent, 'borderLeftWidth')) || 0); + parentOffset.top += (parseFloat($.css(parent, 'borderTopWidth')) || 0); + } + + pos.left -= parentOffset.left + (parseFloat($.css(parent, 'marginLeft')) || 0); + pos.top -= parentOffset.top + (parseFloat($.css(parent, 'marginTop')) || 0); + + // If this is the first parent element with an overflow of "scroll" or "auto", store it + if(!scrolled && (overflow = $.css(parent, 'overflow')) !== 'hidden' && overflow !== 'visible') { scrolled = $(parent); } + } + } + while((parent = parent.offsetParent)); + + // Compensate for containers scroll if it also has an offsetParent (or in IE quirks mode) + if(scrolled && (scrolled[0] !== ownerDocument[0] || quirks)) { + scroll(scrolled, 1); + } + + return pos; +}; + +// Corner class +var C = (CORNER = PROTOTYPE.reposition.Corner = function(corner, forceY) { + corner = ('' + corner).replace(/([A-Z])/, ' $1').replace(/middle/gi, CENTER).toLowerCase(); + this.x = (corner.match(/left|right/i) || corner.match(/center/) || ['inherit'])[0].toLowerCase(); + this.y = (corner.match(/top|bottom|center/i) || ['inherit'])[0].toLowerCase(); + this.forceY = !!forceY; + + var f = corner.charAt(0); + this.precedance = (f === 't' || f === 'b' ? Y : X); +}).prototype; + +C.invert = function(z, center) { + this[z] = this[z] === LEFT ? RIGHT : this[z] === RIGHT ? LEFT : center || this[z]; +}; + +C.string = function(join) { + var x = this.x, y = this.y; + + var result = x !== y ? + (x === 'center' || y !== 'center' && (this.precedance === Y || this.forceY) ? + [y,x] : [x,y] + ) : + [x]; + + return join !== false ? result.join(' ') : result; +}; + +C.abbrev = function() { + var result = this.string(false); + return result[0].charAt(0) + (result[1] && result[1].charAt(0) || ''); +}; + +C.clone = function() { + return new CORNER( this.string(), this.forceY ); +}; + +; +PROTOTYPE.toggle = function(state, event) { + var cache = this.cache, + options = this.options, + tooltip = this.tooltip; + + // Try to prevent flickering when tooltip overlaps show element + if(event) { + if((/over|enter/).test(event.type) && cache.event && (/out|leave/).test(cache.event.type) && + options.show.target.add(event.target).length === options.show.target.length && + tooltip.has(event.relatedTarget).length) { + return this; + } + + // Cache event + cache.event = $.event.fix(event); + } + + // If we're currently waiting and we've just hidden... stop it + this.waiting && !state && (this.hiddenDuringWait = TRUE); + + // Render the tooltip if showing and it isn't already + if(!this.rendered) { return state ? this.render(1) : this; } + else if(this.destroyed || this.disabled) { return this; } + + var type = state ? 'show' : 'hide', + opts = this.options[type], + otherOpts = this.options[ !state ? 'show' : 'hide' ], + posOptions = this.options.position, + contentOptions = this.options.content, + width = this.tooltip.css('width'), + visible = this.tooltip.is(':visible'), + animate = state || opts.target.length === 1, + sameTarget = !event || opts.target.length < 2 || cache.target[0] === event.target, + identicalState, allow, showEvent, delay, after; + + // Detect state if valid one isn't provided + if((typeof state).search('boolean|number')) { state = !visible; } + + // Check if the tooltip is in an identical state to the new would-be state + identicalState = !tooltip.is(':animated') && visible === state && sameTarget; + + // Fire tooltip(show/hide) event and check if destroyed + allow = !identicalState ? !!this._trigger(type, [90]) : NULL; + + // Check to make sure the tooltip wasn't destroyed in the callback + if(this.destroyed) { return this; } + + // If the user didn't stop the method prematurely and we're showing the tooltip, focus it + if(allow !== FALSE && state) { this.focus(event); } + + // If the state hasn't changed or the user stopped it, return early + if(!allow || identicalState) { return this; } + + // Set ARIA hidden attribute + $.attr(tooltip[0], 'aria-hidden', !!!state); + + // Execute state specific properties + if(state) { + // Store show origin coordinates + this.mouse && (cache.origin = $.event.fix(this.mouse)); + + // Update tooltip content & title if it's a dynamic function + if($.isFunction(contentOptions.text)) { this._updateContent(contentOptions.text, FALSE); } + if($.isFunction(contentOptions.title)) { this._updateTitle(contentOptions.title, FALSE); } + + // Cache mousemove events for positioning purposes (if not already tracking) + if(!trackingBound && posOptions.target === 'mouse' && posOptions.adjust.mouse) { + $(document).bind('mousemove.'+NAMESPACE, this._storeMouse); + trackingBound = TRUE; + } + + // Update the tooltip position (set width first to prevent viewport/max-width issues) + if(!width) { tooltip.css('width', tooltip.outerWidth(FALSE)); } + this.reposition(event, arguments[2]); + if(!width) { tooltip.css('width', ''); } + + // Hide other tooltips if tooltip is solo + if(!!opts.solo) { + (typeof opts.solo === 'string' ? $(opts.solo) : $(SELECTOR, opts.solo)) + .not(tooltip).not(opts.target).qtip('hide', $.Event('tooltipsolo')); + } + } + else { + // Clear show timer if we're hiding + clearTimeout(this.timers.show); + + // Remove cached origin on hide + delete cache.origin; + + // Remove mouse tracking event if not needed (all tracking qTips are hidden) + if(trackingBound && !$(SELECTOR+'[tracking="true"]:visible', opts.solo).not(tooltip).length) { + $(document).unbind('mousemove.'+NAMESPACE); + trackingBound = FALSE; + } + + // Blur the tooltip + this.blur(event); + } + + // Define post-animation, state specific properties + after = $.proxy(function() { + if(state) { + // Prevent antialias from disappearing in IE by removing filter + if(BROWSER.ie) { tooltip[0].style.removeAttribute('filter'); } + + // Remove overflow setting to prevent tip bugs + tooltip.css('overflow', ''); + + // Autofocus elements if enabled + if('string' === typeof opts.autofocus) { + $(this.options.show.autofocus, tooltip).focus(); + } + + // If set, hide tooltip when inactive for delay period + this.options.show.target.trigger('qtip-'+this.id+'-inactive'); + } + else { + // Reset CSS states + tooltip.css({ + display: '', + visibility: '', + opacity: '', + left: '', + top: '' + }); + } + + // tooltipvisible/tooltiphidden events + this._trigger(state ? 'visible' : 'hidden'); + }, this); + + // If no effect type is supplied, use a simple toggle + if(opts.effect === FALSE || animate === FALSE) { + tooltip[ type ](); + after(); + } + + // Use custom function if provided + else if($.isFunction(opts.effect)) { + tooltip.stop(1, 1); + opts.effect.call(tooltip, this); + tooltip.queue('fx', function(n) { + after(); n(); + }); + } + + // Use basic fade function by default + else { tooltip.fadeTo(90, state ? 1 : 0, after); } + + // If inactive hide method is set, active it + if(state) { opts.target.trigger('qtip-'+this.id+'-inactive'); } + + return this; +}; + +PROTOTYPE.show = function(event) { return this.toggle(TRUE, event); }; + +PROTOTYPE.hide = function(event) { return this.toggle(FALSE, event); }; +;PROTOTYPE.focus = function(event) { + if(!this.rendered || this.destroyed) { return this; } + + var qtips = $(SELECTOR), + tooltip = this.tooltip, + curIndex = parseInt(tooltip[0].style.zIndex, 10), + newIndex = QTIP.zindex + qtips.length, + focusedElem; + + // Only update the z-index if it has changed and tooltip is not already focused + if(!tooltip.hasClass(CLASS_FOCUS)) { + // tooltipfocus event + if(this._trigger('focus', [newIndex], event)) { + // Only update z-index's if they've changed + if(curIndex !== newIndex) { + // Reduce our z-index's and keep them properly ordered + qtips.each(function() { + if(this.style.zIndex > curIndex) { + this.style.zIndex = this.style.zIndex - 1; + } + }); + + // Fire blur event for focused tooltip + qtips.filter('.' + CLASS_FOCUS).qtip('blur', event); + } + + // Set the new z-index + tooltip.addClass(CLASS_FOCUS)[0].style.zIndex = newIndex; + } + } + + return this; +}; + +PROTOTYPE.blur = function(event) { + if(!this.rendered || this.destroyed) { return this; } + + // Set focused status to FALSE + this.tooltip.removeClass(CLASS_FOCUS); + + // tooltipblur event + this._trigger('blur', [ this.tooltip.css('zIndex') ], event); + + return this; +}; +;PROTOTYPE.disable = function(state) { + if(this.destroyed) { return this; } + + // If 'toggle' is passed, toggle the current state + if(state === 'toggle') { + state = !(this.rendered ? this.tooltip.hasClass(CLASS_DISABLED) : this.disabled); + } + + // Disable if no state passed + else if('boolean' !== typeof state) { + state = TRUE; + } + + if(this.rendered) { + this.tooltip.toggleClass(CLASS_DISABLED, state) + .attr('aria-disabled', state); + } + + this.disabled = !!state; + + return this; +}; + +PROTOTYPE.enable = function() { return this.disable(FALSE); }; +;PROTOTYPE._createButton = function() +{ + var self = this, + elements = this.elements, + tooltip = elements.tooltip, + button = this.options.content.button, + isString = typeof button === 'string', + close = isString ? button : 'Close tooltip'; + + if(elements.button) { elements.button.remove(); } + + // Use custom button if one was supplied by user, else use default + if(button.jquery) { + elements.button = button; + } + else { + elements.button = $('', { + 'class': 'qtip-close ' + (this.options.style.widget ? '' : NAMESPACE+'-icon'), + 'title': close, + 'aria-label': close + }) + .prepend( + $('', { + 'class': 'ui-icon ui-icon-close', + 'html': '×' + }) + ); + } + + // Create button and setup attributes + elements.button.appendTo(elements.titlebar || tooltip) + .attr('role', 'button') + .click(function(event) { + if(!tooltip.hasClass(CLASS_DISABLED)) { self.hide(event); } + return FALSE; + }); +}; + +PROTOTYPE._updateButton = function(button) +{ + // Make sure tooltip is rendered and if not, return + if(!this.rendered) { return FALSE; } + + var elem = this.elements.button; + if(button) { this._createButton(); } + else { elem.remove(); } +}; +;// Widget class creator +function createWidgetClass(cls) { + return WIDGET.concat('').join(cls ? '-'+cls+' ' : ' '); +} + +// Widget class setter method +PROTOTYPE._setWidget = function() +{ + var on = this.options.style.widget, + elements = this.elements, + tooltip = elements.tooltip, + disabled = tooltip.hasClass(CLASS_DISABLED); + + tooltip.removeClass(CLASS_DISABLED); + CLASS_DISABLED = on ? 'ui-state-disabled' : 'qtip-disabled'; + tooltip.toggleClass(CLASS_DISABLED, disabled); + + tooltip.toggleClass('ui-helper-reset '+createWidgetClass(), on).toggleClass(CLASS_DEFAULT, this.options.style.def && !on); + + if(elements.content) { + elements.content.toggleClass( createWidgetClass('content'), on); + } + if(elements.titlebar) { + elements.titlebar.toggleClass( createWidgetClass('header'), on); + } + if(elements.button) { + elements.button.toggleClass(NAMESPACE+'-icon', !on); + } +}; +;function delay(callback, duration) { + // If tooltip has displayed, start hide timer + if(duration > 0) { + return setTimeout( + $.proxy(callback, this), duration + ); + } + else{ callback.call(this); } +} + +function showMethod(event) { + if(this.tooltip.hasClass(CLASS_DISABLED)) { return; } + + // Clear hide timers + clearTimeout(this.timers.show); + clearTimeout(this.timers.hide); + + // Start show timer + this.timers.show = delay.call(this, + function() { this.toggle(TRUE, event); }, + this.options.show.delay + ); +} + +function hideMethod(event) { + if(this.tooltip.hasClass(CLASS_DISABLED) || this.destroyed) { return; } + + // Check if new target was actually the tooltip element + var relatedTarget = $(event.relatedTarget), + ontoTooltip = relatedTarget.closest(SELECTOR)[0] === this.tooltip[0], + ontoTarget = relatedTarget[0] === this.options.show.target[0]; + + // Clear timers and stop animation queue + clearTimeout(this.timers.show); + clearTimeout(this.timers.hide); + + // Prevent hiding if tooltip is fixed and event target is the tooltip. + // Or if mouse positioning is enabled and cursor momentarily overlaps + if(this !== relatedTarget[0] && + (this.options.position.target === 'mouse' && ontoTooltip) || + (this.options.hide.fixed && ( + (/mouse(out|leave|move)/).test(event.type) && (ontoTooltip || ontoTarget)) + )) + { + try { + event.preventDefault(); + event.stopImmediatePropagation(); + } catch(e) {} + + return; + } + + // If tooltip has displayed, start hide timer + this.timers.hide = delay.call(this, + function() { this.toggle(FALSE, event); }, + this.options.hide.delay, + this + ); +} + +function inactiveMethod(event) { + if(this.tooltip.hasClass(CLASS_DISABLED) || !this.options.hide.inactive) { return; } + + // Clear timer + clearTimeout(this.timers.inactive); + + this.timers.inactive = delay.call(this, + function(){ this.hide(event); }, + this.options.hide.inactive + ); +} + +function repositionMethod(event) { + if(this.rendered && this.tooltip[0].offsetWidth > 0) { this.reposition(event); } +} + +// Store mouse coordinates +PROTOTYPE._storeMouse = function(event) { + (this.mouse = $.event.fix(event)).type = 'mousemove'; + return this; +}; + +// Bind events +PROTOTYPE._bind = function(targets, events, method, suffix, context) { + if(!targets || !method || !events.length) { return; } + var ns = '.' + this._id + (suffix ? '-'+suffix : ''); + $(targets).bind( + (events.split ? events : events.join(ns + ' ')) + ns, + $.proxy(method, context || this) + ); + return this; +}; +PROTOTYPE._unbind = function(targets, suffix) { + targets && $(targets).unbind('.' + this._id + (suffix ? '-'+suffix : '')); + return this; +}; + +// Global delegation helper +function delegate(selector, events, method) { + $(document.body).delegate(selector, + (events.split ? events : events.join('.'+NAMESPACE + ' ')) + '.'+NAMESPACE, + function() { + var api = QTIP.api[ $.attr(this, ATTR_ID) ]; + api && !api.disabled && method.apply(api, arguments); + } + ); +} +// Event trigger +PROTOTYPE._trigger = function(type, args, event) { + var callback = $.Event('tooltip'+type); + callback.originalEvent = (event && $.extend({}, event)) || this.cache.event || NULL; + + this.triggering = type; + this.tooltip.trigger(callback, [this].concat(args || [])); + this.triggering = FALSE; + + return !callback.isDefaultPrevented(); +}; + +PROTOTYPE._bindEvents = function(showEvents, hideEvents, showTargets, hideTargets, showMethod, hideMethod) { + // Get tasrgets that lye within both + var similarTargets = showTargets.filter( hideTargets ).add( hideTargets.filter(showTargets) ), + toggleEvents = []; + + // If hide and show targets are the same... + if(similarTargets.length) { + + // Filter identical show/hide events + $.each(hideEvents, function(i, type) { + var showIndex = $.inArray(type, showEvents); + + // Both events are identical, remove from both hide and show events + // and append to toggleEvents + showIndex > -1 && toggleEvents.push( showEvents.splice( showIndex, 1 )[0] ); + }); + + // Toggle events are special case of identical show/hide events, which happen in sequence + if(toggleEvents.length) { + // Bind toggle events to the similar targets + this._bind(similarTargets, toggleEvents, function(event) { + var state = this.rendered ? this.tooltip[0].offsetWidth > 0 : false; + (state ? hideMethod : showMethod).call(this, event); + }); + + // Remove the similar targets from the regular show/hide bindings + showTargets = showTargets.not(similarTargets); + hideTargets = hideTargets.not(similarTargets); + } + } + + // Apply show/hide/toggle events + this._bind(showTargets, showEvents, showMethod); + this._bind(hideTargets, hideEvents, hideMethod); +}; + +PROTOTYPE._assignInitialEvents = function(event) { + var options = this.options, + showTarget = options.show.target, + hideTarget = options.hide.target, + showEvents = options.show.event ? $.trim('' + options.show.event).split(' ') : [], + hideEvents = options.hide.event ? $.trim('' + options.hide.event).split(' ') : []; + + // Catch remove/removeqtip events on target element to destroy redundant tooltips + this._bind(this.elements.target, ['remove', 'removeqtip'], function(event) { + this.destroy(true); + }, 'destroy'); + + /* + * Make sure hoverIntent functions properly by using mouseleave as a hide event if + * mouseenter/mouseout is used for show.event, even if it isn't in the users options. + */ + if(/mouse(over|enter)/i.test(options.show.event) && !/mouse(out|leave)/i.test(options.hide.event)) { + hideEvents.push('mouseleave'); + } + + /* + * Also make sure initial mouse targetting works correctly by caching mousemove coords + * on show targets before the tooltip has rendered. Also set onTarget when triggered to + * keep mouse tracking working. + */ + this._bind(showTarget, 'mousemove', function(event) { + this._storeMouse(event); + this.cache.onTarget = TRUE; + }); + + // Define hoverIntent function + function hoverIntent(event) { + // Only continue if tooltip isn't disabled + if(this.disabled || this.destroyed) { return FALSE; } + + // Cache the event data + this.cache.event = event && $.event.fix(event); + this.cache.target = event && $(event.target); + + // Start the event sequence + clearTimeout(this.timers.show); + this.timers.show = delay.call(this, + function() { this.render(typeof event === 'object' || options.show.ready); }, + options.prerender ? 0 : options.show.delay + ); + } + + // Filter and bind events + this._bindEvents(showEvents, hideEvents, showTarget, hideTarget, hoverIntent, function() { + if(!this.timers) { return FALSE; } + clearTimeout(this.timers.show); + }); + + // Prerendering is enabled, create tooltip now + if(options.show.ready || options.prerender) { hoverIntent.call(this, event); } +}; + +// Event assignment method +PROTOTYPE._assignEvents = function() { + var self = this, + options = this.options, + posOptions = options.position, + + tooltip = this.tooltip, + showTarget = options.show.target, + hideTarget = options.hide.target, + containerTarget = posOptions.container, + viewportTarget = posOptions.viewport, + documentTarget = $(document), + bodyTarget = $(document.body), + windowTarget = $(window), + + showEvents = options.show.event ? $.trim('' + options.show.event).split(' ') : [], + hideEvents = options.hide.event ? $.trim('' + options.hide.event).split(' ') : []; + + + // Assign passed event callbacks + $.each(options.events, function(name, callback) { + self._bind(tooltip, name === 'toggle' ? ['tooltipshow','tooltiphide'] : ['tooltip'+name], callback, null, tooltip); + }); + + // Hide tooltips when leaving current window/frame (but not select/option elements) + if(/mouse(out|leave)/i.test(options.hide.event) && options.hide.leave === 'window') { + this._bind(documentTarget, ['mouseout', 'blur'], function(event) { + if(!/select|option/.test(event.target.nodeName) && !event.relatedTarget) { + this.hide(event); + } + }); + } + + // Enable hide.fixed by adding appropriate class + if(options.hide.fixed) { + hideTarget = hideTarget.add( tooltip.addClass(CLASS_FIXED) ); + } + + /* + * Make sure hoverIntent functions properly by using mouseleave to clear show timer if + * mouseenter/mouseout is used for show.event, even if it isn't in the users options. + */ + else if(/mouse(over|enter)/i.test(options.show.event)) { + this._bind(hideTarget, 'mouseleave', function() { + clearTimeout(this.timers.show); + }); + } + + // Hide tooltip on document mousedown if unfocus events are enabled + if(('' + options.hide.event).indexOf('unfocus') > -1) { + this._bind(containerTarget.closest('html'), ['mousedown', 'touchstart'], function(event) { + var elem = $(event.target), + enabled = this.rendered && !this.tooltip.hasClass(CLASS_DISABLED) && this.tooltip[0].offsetWidth > 0, + isAncestor = elem.parents(SELECTOR).filter(this.tooltip[0]).length > 0; + + if(elem[0] !== this.target[0] && elem[0] !== this.tooltip[0] && !isAncestor && + !this.target.has(elem[0]).length && enabled + ) { + this.hide(event); + } + }); + } + + // Check if the tooltip hides when inactive + if('number' === typeof options.hide.inactive) { + // Bind inactive method to show target(s) as a custom event + this._bind(showTarget, 'qtip-'+this.id+'-inactive', inactiveMethod, 'inactive'); + + // Define events which reset the 'inactive' event handler + this._bind(hideTarget.add(tooltip), QTIP.inactiveEvents, inactiveMethod); + } + + // Filter and bind events + this._bindEvents(showEvents, hideEvents, showTarget, hideTarget, showMethod, hideMethod); + + // Mouse movement bindings + this._bind(showTarget.add(tooltip), 'mousemove', function(event) { + // Check if the tooltip hides when mouse is moved a certain distance + if('number' === typeof options.hide.distance) { + var origin = this.cache.origin || {}, + limit = this.options.hide.distance, + abs = Math.abs; + + // Check if the movement has gone beyond the limit, and hide it if so + if(abs(event.pageX - origin.pageX) >= limit || abs(event.pageY - origin.pageY) >= limit) { + this.hide(event); + } + } + + // Cache mousemove coords on show targets + this._storeMouse(event); + }); + + // Mouse positioning events + if(posOptions.target === 'mouse') { + // If mouse adjustment is on... + if(posOptions.adjust.mouse) { + // Apply a mouseleave event so we don't get problems with overlapping + if(options.hide.event) { + // Track if we're on the target or not + this._bind(showTarget, ['mouseenter', 'mouseleave'], function(event) { + if(!this.cache) {return FALSE; } + this.cache.onTarget = event.type === 'mouseenter'; + }); + } + + // Update tooltip position on mousemove + this._bind(documentTarget, 'mousemove', function(event) { + // Update the tooltip position only if the tooltip is visible and adjustment is enabled + if(this.rendered && this.cache.onTarget && !this.tooltip.hasClass(CLASS_DISABLED) && this.tooltip[0].offsetWidth > 0) { + this.reposition(event); + } + }); + } + } + + // Adjust positions of the tooltip on window resize if enabled + if(posOptions.adjust.resize || viewportTarget.length) { + this._bind( $.event.special.resize ? viewportTarget : windowTarget, 'resize', repositionMethod ); + } + + // Adjust tooltip position on scroll of the window or viewport element if present + if(posOptions.adjust.scroll) { + this._bind( windowTarget.add(posOptions.container), 'scroll', repositionMethod ); + } +}; + +// Un-assignment method +PROTOTYPE._unassignEvents = function() { + var options = this.options, + showTargets = options.show.target, + hideTargets = options.hide.target, + targets = $.grep([ + this.elements.target[0], + this.rendered && this.tooltip[0], + options.position.container[0], + options.position.viewport[0], + options.position.container.closest('html')[0], // unfocus + window, + document + ], function(i) { + return typeof i === 'object'; + }); + + // Add show and hide targets if they're valid + if(showTargets && showTargets.toArray) { + targets = targets.concat(showTargets.toArray()); + } + if(hideTargets && hideTargets.toArray) { + targets = targets.concat(hideTargets.toArray()); + } + + // Unbind the events + this._unbind(targets) + ._unbind(targets, 'destroy') + ._unbind(targets, 'inactive'); +}; + +// Apply common event handlers using delegate (avoids excessive .bind calls!) +$(function() { + delegate(SELECTOR, ['mouseenter', 'mouseleave'], function(event) { + var state = event.type === 'mouseenter', + tooltip = $(event.currentTarget), + target = $(event.relatedTarget || event.target), + options = this.options; + + // On mouseenter... + if(state) { + // Focus the tooltip on mouseenter (z-index stacking) + this.focus(event); + + // Clear hide timer on tooltip hover to prevent it from closing + tooltip.hasClass(CLASS_FIXED) && !tooltip.hasClass(CLASS_DISABLED) && clearTimeout(this.timers.hide); + } + + // On mouseleave... + else { + // When mouse tracking is enabled, hide when we leave the tooltip and not onto the show target (if a hide event is set) + if(options.position.target === 'mouse' && options.position.adjust.mouse && + options.hide.event && options.show.target && !target.closest(options.show.target[0]).length) { + this.hide(event); + } + } + + // Add hover class + tooltip.toggleClass(CLASS_HOVER, state); + }); + + // Define events which reset the 'inactive' event handler + delegate('['+ATTR_ID+']', INACTIVE_EVENTS, inactiveMethod); +}); +;// Initialization method +function init(elem, id, opts) { + var obj, posOptions, attr, config, title, + + // Setup element references + docBody = $(document.body), + + // Use document body instead of document element if needed + newTarget = elem[0] === document ? docBody : elem, + + // Grab metadata from element if plugin is present + metadata = (elem.metadata) ? elem.metadata(opts.metadata) : NULL, + + // If metadata type if HTML5, grab 'name' from the object instead, or use the regular data object otherwise + metadata5 = opts.metadata.type === 'html5' && metadata ? metadata[opts.metadata.name] : NULL, + + // Grab data from metadata.name (or data-qtipopts as fallback) using .data() method, + html5 = elem.data(opts.metadata.name || 'qtipopts'); + + // If we don't get an object returned attempt to parse it manualyl without parseJSON + try { html5 = typeof html5 === 'string' ? $.parseJSON(html5) : html5; } catch(e) {} + + // Merge in and sanitize metadata + config = $.extend(TRUE, {}, QTIP.defaults, opts, + typeof html5 === 'object' ? sanitizeOptions(html5) : NULL, + sanitizeOptions(metadata5 || metadata)); + + // Re-grab our positioning options now we've merged our metadata and set id to passed value + posOptions = config.position; + config.id = id; + + // Setup missing content if none is detected + if('boolean' === typeof config.content.text) { + attr = elem.attr(config.content.attr); + + // Grab from supplied attribute if available + if(config.content.attr !== FALSE && attr) { config.content.text = attr; } + + // No valid content was found, abort render + else { return FALSE; } + } + + // Setup target options + if(!posOptions.container.length) { posOptions.container = docBody; } + if(posOptions.target === FALSE) { posOptions.target = newTarget; } + if(config.show.target === FALSE) { config.show.target = newTarget; } + if(config.show.solo === TRUE) { config.show.solo = posOptions.container.closest('body'); } + if(config.hide.target === FALSE) { config.hide.target = newTarget; } + if(config.position.viewport === TRUE) { config.position.viewport = posOptions.container; } + + // Ensure we only use a single container + posOptions.container = posOptions.container.eq(0); + + // Convert position corner values into x and y strings + posOptions.at = new CORNER(posOptions.at, TRUE); + posOptions.my = new CORNER(posOptions.my); + + // Destroy previous tooltip if overwrite is enabled, or skip element if not + if(elem.data(NAMESPACE)) { + if(config.overwrite) { + elem.qtip('destroy', true); + } + else if(config.overwrite === FALSE) { + return FALSE; + } + } + + // Add has-qtip attribute + elem.attr(ATTR_HAS, id); + + // Remove title attribute and store it if present + if(config.suppress && (title = elem.attr('title'))) { + // Final attr call fixes event delegatiom and IE default tooltip showing problem + elem.removeAttr('title').attr(oldtitle, title).attr('title', ''); + } + + // Initialize the tooltip and add API reference + obj = new QTip(elem, config, id, !!attr); + elem.data(NAMESPACE, obj); + + return obj; +} + +// jQuery $.fn extension method +QTIP = $.fn.qtip = function(options, notation, newValue) +{ + var command = ('' + options).toLowerCase(), // Parse command + returned = NULL, + args = $.makeArray(arguments).slice(1), + event = args[args.length - 1], + opts = this[0] ? $.data(this[0], NAMESPACE) : NULL; + + // Check for API request + if((!arguments.length && opts) || command === 'api') { + return opts; + } + + // Execute API command if present + else if('string' === typeof options) { + this.each(function() { + var api = $.data(this, NAMESPACE); + if(!api) { return TRUE; } + + // Cache the event if possible + if(event && event.timeStamp) { api.cache.event = event; } + + // Check for specific API commands + if(notation && (command === 'option' || command === 'options')) { + if(newValue !== undefined || $.isPlainObject(notation)) { + api.set(notation, newValue); + } + else { + returned = api.get(notation); + return FALSE; + } + } + + // Execute API command + else if(api[command]) { + api[command].apply(api, args); + } + }); + + return returned !== NULL ? returned : this; + } + + // No API commands. validate provided options and setup qTips + else if('object' === typeof options || !arguments.length) { + // Sanitize options first + opts = sanitizeOptions($.extend(TRUE, {}, options)); + + return this.each(function(i) { + var api, id; + + // Find next available ID, or use custom ID if provided + id = $.isArray(opts.id) ? opts.id[i] : opts.id; + id = !id || id === FALSE || id.length < 1 || QTIP.api[id] ? QTIP.nextid++ : id; + + // Initialize the qTip and re-grab newly sanitized options + api = init($(this), id, opts); + if(api === FALSE) { return TRUE; } + else { QTIP.api[id] = api; } + + // Initialize plugins + $.each(PLUGINS, function() { + if(this.initialize === 'initialize') { this(api); } + }); + + // Assign initial pre-render events + api._assignInitialEvents(event); + }); + } +}; + +// Expose class +$.qtip = QTip; + +// Populated in render method +QTIP.api = {}; +;$.each({ + /* Allow other plugins to successfully retrieve the title of an element with a qTip applied */ + attr: function(attr, val) { + if(this.length) { + var self = this[0], + title = 'title', + api = $.data(self, 'qtip'); + + if(attr === title && api && 'object' === typeof api && api.options.suppress) { + if(arguments.length < 2) { + return $.attr(self, oldtitle); + } + + // If qTip is rendered and title was originally used as content, update it + if(api && api.options.content.attr === title && api.cache.attr) { + api.set('content.text', val); + } + + // Use the regular attr method to set, then cache the result + return this.attr(oldtitle, val); + } + } + + return $.fn['attr'+replaceSuffix].apply(this, arguments); + }, + + /* Allow clone to correctly retrieve cached title attributes */ + clone: function(keepData) { + var titles = $([]), title = 'title', + + // Clone our element using the real clone method + elems = $.fn['clone'+replaceSuffix].apply(this, arguments); + + // Grab all elements with an oldtitle set, and change it to regular title attribute, if keepData is false + if(!keepData) { + elems.filter('['+oldtitle+']').attr('title', function() { + return $.attr(this, oldtitle); + }) + .removeAttr(oldtitle); + } + + return elems; + } +}, function(name, func) { + if(!func || $.fn[name+replaceSuffix]) { return TRUE; } + + var old = $.fn[name+replaceSuffix] = $.fn[name]; + $.fn[name] = function() { + return func.apply(this, arguments) || old.apply(this, arguments); + }; +}); + +/* Fire off 'removeqtip' handler in $.cleanData if jQuery UI not present (it already does similar). + * This snippet is taken directly from jQuery UI source code found here: + * http://code.jquery.com/ui/jquery-ui-git.js + */ +if(!$.ui) { + $['cleanData'+replaceSuffix] = $.cleanData; + $.cleanData = function( elems ) { + for(var i = 0, elem; (elem = $( elems[i] )).length; i++) { + if(elem.attr(ATTR_HAS)) { + try { elem.triggerHandler('removeqtip'); } + catch( e ) {} + } + } + $['cleanData'+replaceSuffix].apply(this, arguments); + }; +} +;// qTip version +QTIP.version = '2.2.1'; + +// Base ID for all qTips +QTIP.nextid = 0; + +// Inactive events array +QTIP.inactiveEvents = INACTIVE_EVENTS; + +// Base z-index for all qTips +QTIP.zindex = 15000; + +// Define configuration defaults +QTIP.defaults = { + prerender: FALSE, + id: FALSE, + overwrite: TRUE, + suppress: TRUE, + content: { + text: TRUE, + attr: 'title', + title: FALSE, + button: FALSE + }, + position: { + my: 'top left', + at: 'bottom right', + target: FALSE, + container: FALSE, + viewport: FALSE, + adjust: { + x: 0, y: 0, + mouse: TRUE, + scroll: TRUE, + resize: TRUE, + method: 'flipinvert flipinvert' + }, + effect: function(api, pos, viewport) { + $(this).animate(pos, { + duration: 200, + queue: FALSE + }); + } + }, + show: { + target: FALSE, + event: 'mouseenter', + effect: TRUE, + delay: 90, + solo: FALSE, + ready: FALSE, + autofocus: FALSE + }, + hide: { + target: FALSE, + event: 'mouseleave', + effect: TRUE, + delay: 0, + fixed: FALSE, + inactive: FALSE, + leave: 'window', + distance: FALSE + }, + style: { + classes: '', + widget: FALSE, + width: FALSE, + height: FALSE, + def: TRUE + }, + events: { + render: NULL, + move: NULL, + show: NULL, + hide: NULL, + toggle: NULL, + visible: NULL, + hidden: NULL, + focus: NULL, + blur: NULL + } +}; +;var TIP, + +// .bind()/.on() namespace +TIPNS = '.qtip-tip', + +// Common CSS strings +MARGIN = 'margin', +BORDER = 'border', +COLOR = 'color', +BG_COLOR = 'background-color', +TRANSPARENT = 'transparent', +IMPORTANT = ' !important', + +// Check if the browser supports elements +HASCANVAS = !!document.createElement('canvas').getContext, + +// Invalid colour values used in parseColours() +INVALID = /rgba?\(0, 0, 0(, 0)?\)|transparent|#123456/i; + +// Camel-case method, taken from jQuery source +// http://code.jquery.com/jquery-1.8.0.js +function camel(s) { return s.charAt(0).toUpperCase() + s.slice(1); } + +/* + * Modified from Modernizr's testPropsAll() + * http://modernizr.com/downloads/modernizr-latest.js + */ +var cssProps = {}, cssPrefixes = ["Webkit", "O", "Moz", "ms"]; +function vendorCss(elem, prop) { + var ucProp = prop.charAt(0).toUpperCase() + prop.slice(1), + props = (prop + ' ' + cssPrefixes.join(ucProp + ' ') + ucProp).split(' '), + cur, val, i = 0; + + // If the property has already been mapped... + if(cssProps[prop]) { return elem.css(cssProps[prop]); } + + while((cur = props[i++])) { + if((val = elem.css(cur)) !== undefined) { + return cssProps[prop] = cur, val; + } + } +} + +// Parse a given elements CSS property into an int +function intCss(elem, prop) { + return Math.ceil(parseFloat(vendorCss(elem, prop))); +} + + +// VML creation (for IE only) +if(!HASCANVAS) { + var createVML = function(tag, props, style) { + return ''; + }; +} + +// Canvas only definitions +else { + var PIXEL_RATIO = window.devicePixelRatio || 1, + BACKING_STORE_RATIO = (function() { + var context = document.createElement('canvas').getContext('2d'); + return context.backingStorePixelRatio || context.webkitBackingStorePixelRatio || context.mozBackingStorePixelRatio || + context.msBackingStorePixelRatio || context.oBackingStorePixelRatio || 1; + }()), + SCALE = PIXEL_RATIO / BACKING_STORE_RATIO; +} + + +function Tip(qtip, options) { + this._ns = 'tip'; + this.options = options; + this.offset = options.offset; + this.size = [ options.width, options.height ]; + + // Initialize + this.init( (this.qtip = qtip) ); +} + +$.extend(Tip.prototype, { + init: function(qtip) { + var context, tip; + + // Create tip element and prepend to the tooltip + tip = this.element = qtip.elements.tip = $('
', { 'class': NAMESPACE+'-tip' }).prependTo(qtip.tooltip); + + // Create tip drawing element(s) + if(HASCANVAS) { + // save() as soon as we create the canvas element so FF2 doesn't bork on our first restore()! + context = $('').appendTo(this.element)[0].getContext('2d'); + + // Setup constant parameters + context.lineJoin = 'miter'; + context.miterLimit = 100000; + context.save(); + } + else { + context = createVML('shape', 'coordorigin="0,0"', 'position:absolute;'); + this.element.html(context + context); + + // Prevent mousing down on the tip since it causes problems with .live() handling in IE due to VML + qtip._bind( $('*', tip).add(tip), ['click', 'mousedown'], function(event) { event.stopPropagation(); }, this._ns); + } + + // Bind update events + qtip._bind(qtip.tooltip, 'tooltipmove', this.reposition, this._ns, this); + + // Create it + this.create(); + }, + + _swapDimensions: function() { + this.size[0] = this.options.height; + this.size[1] = this.options.width; + }, + _resetDimensions: function() { + this.size[0] = this.options.width; + this.size[1] = this.options.height; + }, + + _useTitle: function(corner) { + var titlebar = this.qtip.elements.titlebar; + return titlebar && ( + corner.y === TOP || (corner.y === CENTER && this.element.position().top + (this.size[1] / 2) + this.options.offset < titlebar.outerHeight(TRUE)) + ); + }, + + _parseCorner: function(corner) { + var my = this.qtip.options.position.my; + + // Detect corner and mimic properties + if(corner === FALSE || my === FALSE) { + corner = FALSE; + } + else if(corner === TRUE) { + corner = new CORNER( my.string() ); + } + else if(!corner.string) { + corner = new CORNER(corner); + corner.fixed = TRUE; + } + + return corner; + }, + + _parseWidth: function(corner, side, use) { + var elements = this.qtip.elements, + prop = BORDER + camel(side) + 'Width'; + + return (use ? intCss(use, prop) : ( + intCss(elements.content, prop) || + intCss(this._useTitle(corner) && elements.titlebar || elements.content, prop) || + intCss(elements.tooltip, prop) + )) || 0; + }, + + _parseRadius: function(corner) { + var elements = this.qtip.elements, + prop = BORDER + camel(corner.y) + camel(corner.x) + 'Radius'; + + return BROWSER.ie < 9 ? 0 : + intCss(this._useTitle(corner) && elements.titlebar || elements.content, prop) || + intCss(elements.tooltip, prop) || 0; + }, + + _invalidColour: function(elem, prop, compare) { + var val = elem.css(prop); + return !val || (compare && val === elem.css(compare)) || INVALID.test(val) ? FALSE : val; + }, + + _parseColours: function(corner) { + var elements = this.qtip.elements, + tip = this.element.css('cssText', ''), + borderSide = BORDER + camel(corner[ corner.precedance ]) + camel(COLOR), + colorElem = this._useTitle(corner) && elements.titlebar || elements.content, + css = this._invalidColour, color = []; + + // Attempt to detect the background colour from various elements, left-to-right precedance + color[0] = css(tip, BG_COLOR) || css(colorElem, BG_COLOR) || css(elements.content, BG_COLOR) || + css(elements.tooltip, BG_COLOR) || tip.css(BG_COLOR); + + // Attempt to detect the correct border side colour from various elements, left-to-right precedance + color[1] = css(tip, borderSide, COLOR) || css(colorElem, borderSide, COLOR) || + css(elements.content, borderSide, COLOR) || css(elements.tooltip, borderSide, COLOR) || elements.tooltip.css(borderSide); + + // Reset background and border colours + $('*', tip).add(tip).css('cssText', BG_COLOR+':'+TRANSPARENT+IMPORTANT+';'+BORDER+':0'+IMPORTANT+';'); + + return color; + }, + + _calculateSize: function(corner) { + var y = corner.precedance === Y, + width = this.options['width'], + height = this.options['height'], + isCenter = corner.abbrev() === 'c', + base = (y ? width: height) * (isCenter ? 0.5 : 1), + pow = Math.pow, + round = Math.round, + bigHyp, ratio, result, + + smallHyp = Math.sqrt( pow(base, 2) + pow(height, 2) ), + hyp = [ (this.border / base) * smallHyp, (this.border / height) * smallHyp ]; + + hyp[2] = Math.sqrt( pow(hyp[0], 2) - pow(this.border, 2) ); + hyp[3] = Math.sqrt( pow(hyp[1], 2) - pow(this.border, 2) ); + + bigHyp = smallHyp + hyp[2] + hyp[3] + (isCenter ? 0 : hyp[0]); + ratio = bigHyp / smallHyp; + + result = [ round(ratio * width), round(ratio * height) ]; + return y ? result : result.reverse(); + }, + + // Tip coordinates calculator + _calculateTip: function(corner, size, scale) { + scale = scale || 1; + size = size || this.size; + + var width = size[0] * scale, + height = size[1] * scale, + width2 = Math.ceil(width / 2), height2 = Math.ceil(height / 2), + + // Define tip coordinates in terms of height and width values + tips = { + br: [0,0, width,height, width,0], + bl: [0,0, width,0, 0,height], + tr: [0,height, width,0, width,height], + tl: [0,0, 0,height, width,height], + tc: [0,height, width2,0, width,height], + bc: [0,0, width,0, width2,height], + rc: [0,0, width,height2, 0,height], + lc: [width,0, width,height, 0,height2] + }; + + // Set common side shapes + tips.lt = tips.br; tips.rt = tips.bl; + tips.lb = tips.tr; tips.rb = tips.tl; + + return tips[ corner.abbrev() ]; + }, + + // Tip coordinates drawer (canvas) + _drawCoords: function(context, coords) { + context.beginPath(); + context.moveTo(coords[0], coords[1]); + context.lineTo(coords[2], coords[3]); + context.lineTo(coords[4], coords[5]); + context.closePath(); + }, + + create: function() { + // Determine tip corner + var c = this.corner = (HASCANVAS || BROWSER.ie) && this._parseCorner(this.options.corner); + + // If we have a tip corner... + if( (this.enabled = !!this.corner && this.corner.abbrev() !== 'c') ) { + // Cache it + this.qtip.cache.corner = c.clone(); + + // Create it + this.update(); + } + + // Toggle tip element + this.element.toggle(this.enabled); + + return this.corner; + }, + + update: function(corner, position) { + if(!this.enabled) { return this; } + + var elements = this.qtip.elements, + tip = this.element, + inner = tip.children(), + options = this.options, + curSize = this.size, + mimic = options.mimic, + round = Math.round, + color, precedance, context, + coords, bigCoords, translate, newSize, border, BACKING_STORE_RATIO; + + // Re-determine tip if not already set + if(!corner) { corner = this.qtip.cache.corner || this.corner; } + + // Use corner property if we detect an invalid mimic value + if(mimic === FALSE) { mimic = corner; } + + // Otherwise inherit mimic properties from the corner object as necessary + else { + mimic = new CORNER(mimic); + mimic.precedance = corner.precedance; + + if(mimic.x === 'inherit') { mimic.x = corner.x; } + else if(mimic.y === 'inherit') { mimic.y = corner.y; } + else if(mimic.x === mimic.y) { + mimic[ corner.precedance ] = corner[ corner.precedance ]; + } + } + precedance = mimic.precedance; + + // Ensure the tip width.height are relative to the tip position + if(corner.precedance === X) { this._swapDimensions(); } + else { this._resetDimensions(); } + + // Update our colours + color = this.color = this._parseColours(corner); + + // Detect border width, taking into account colours + if(color[1] !== TRANSPARENT) { + // Grab border width + border = this.border = this._parseWidth(corner, corner[corner.precedance]); + + // If border width isn't zero, use border color as fill if it's not invalid (1.0 style tips) + if(options.border && border < 1 && !INVALID.test(color[1])) { color[0] = color[1]; } + + // Set border width (use detected border width if options.border is true) + this.border = border = options.border !== TRUE ? options.border : border; + } + + // Border colour was invalid, set border to zero + else { this.border = border = 0; } + + // Determine tip size + newSize = this.size = this._calculateSize(corner); + tip.css({ + width: newSize[0], + height: newSize[1], + lineHeight: newSize[1]+'px' + }); + + // Calculate tip translation + if(corner.precedance === Y) { + translate = [ + round(mimic.x === LEFT ? border : mimic.x === RIGHT ? newSize[0] - curSize[0] - border : (newSize[0] - curSize[0]) / 2), + round(mimic.y === TOP ? newSize[1] - curSize[1] : 0) + ]; + } + else { + translate = [ + round(mimic.x === LEFT ? newSize[0] - curSize[0] : 0), + round(mimic.y === TOP ? border : mimic.y === BOTTOM ? newSize[1] - curSize[1] - border : (newSize[1] - curSize[1]) / 2) + ]; + } + + // Canvas drawing implementation + if(HASCANVAS) { + // Grab canvas context and clear/save it + context = inner[0].getContext('2d'); + context.restore(); context.save(); + context.clearRect(0,0,6000,6000); + + // Calculate coordinates + coords = this._calculateTip(mimic, curSize, SCALE); + bigCoords = this._calculateTip(mimic, this.size, SCALE); + + // Set the canvas size using calculated size + inner.attr(WIDTH, newSize[0] * SCALE).attr(HEIGHT, newSize[1] * SCALE); + inner.css(WIDTH, newSize[0]).css(HEIGHT, newSize[1]); + + // Draw the outer-stroke tip + this._drawCoords(context, bigCoords); + context.fillStyle = color[1]; + context.fill(); + + // Draw the actual tip + context.translate(translate[0] * SCALE, translate[1] * SCALE); + this._drawCoords(context, coords); + context.fillStyle = color[0]; + context.fill(); + } + + // VML (IE Proprietary implementation) + else { + // Calculate coordinates + coords = this._calculateTip(mimic); + + // Setup coordinates string + coords = 'm' + coords[0] + ',' + coords[1] + ' l' + coords[2] + + ',' + coords[3] + ' ' + coords[4] + ',' + coords[5] + ' xe'; + + // Setup VML-specific offset for pixel-perfection + translate[2] = border && /^(r|b)/i.test(corner.string()) ? + BROWSER.ie === 8 ? 2 : 1 : 0; + + // Set initial CSS + inner.css({ + coordsize: (newSize[0]+border) + ' ' + (newSize[1]+border), + antialias: ''+(mimic.string().indexOf(CENTER) > -1), + left: translate[0] - (translate[2] * Number(precedance === X)), + top: translate[1] - (translate[2] * Number(precedance === Y)), + width: newSize[0] + border, + height: newSize[1] + border + }) + .each(function(i) { + var $this = $(this); + + // Set shape specific attributes + $this[ $this.prop ? 'prop' : 'attr' ]({ + coordsize: (newSize[0]+border) + ' ' + (newSize[1]+border), + path: coords, + fillcolor: color[0], + filled: !!i, + stroked: !i + }) + .toggle(!!(border || i)); + + // Check if border is enabled and add stroke element + !i && $this.html( createVML( + 'stroke', 'weight="'+(border*2)+'px" color="'+color[1]+'" miterlimit="1000" joinstyle="miter"' + ) ); + }); + } + + // Opera bug #357 - Incorrect tip position + // https://github.com/Craga89/qTip2/issues/367 + window.opera && setTimeout(function() { + elements.tip.css({ + display: 'inline-block', + visibility: 'visible' + }); + }, 1); + + // Position if needed + if(position !== FALSE) { this.calculate(corner, newSize); } + }, + + calculate: function(corner, size) { + if(!this.enabled) { return FALSE; } + + var self = this, + elements = this.qtip.elements, + tip = this.element, + userOffset = this.options.offset, + isWidget = elements.tooltip.hasClass('ui-widget'), + position = { }, + precedance, corners; + + // Inherit corner if not provided + corner = corner || this.corner; + precedance = corner.precedance; + + // Determine which tip dimension to use for adjustment + size = size || this._calculateSize(corner); + + // Setup corners and offset array + corners = [ corner.x, corner.y ]; + if(precedance === X) { corners.reverse(); } + + // Calculate tip position + $.each(corners, function(i, side) { + var b, bc, br; + + if(side === CENTER) { + b = precedance === Y ? LEFT : TOP; + position[ b ] = '50%'; + position[MARGIN+'-' + b] = -Math.round(size[ precedance === Y ? 0 : 1 ] / 2) + userOffset; + } + else { + b = self._parseWidth(corner, side, elements.tooltip); + bc = self._parseWidth(corner, side, elements.content); + br = self._parseRadius(corner); + + position[ side ] = Math.max(-self.border, i ? bc : (userOffset + (br > b ? br : -b))); + } + }); + + // Adjust for tip size + position[ corner[precedance] ] -= size[ precedance === X ? 0 : 1 ]; + + // Set and return new position + tip.css({ margin: '', top: '', bottom: '', left: '', right: '' }).css(position); + return position; + }, + + reposition: function(event, api, pos, viewport) { + if(!this.enabled) { return; } + + var cache = api.cache, + newCorner = this.corner.clone(), + adjust = pos.adjusted, + method = api.options.position.adjust.method.split(' '), + horizontal = method[0], + vertical = method[1] || method[0], + shift = { left: FALSE, top: FALSE, x: 0, y: 0 }, + offset, css = {}, props; + + function shiftflip(direction, precedance, popposite, side, opposite) { + // Horizontal - Shift or flip method + if(direction === SHIFT && newCorner.precedance === precedance && adjust[side] && newCorner[popposite] !== CENTER) { + newCorner.precedance = newCorner.precedance === X ? Y : X; + } + else if(direction !== SHIFT && adjust[side]){ + newCorner[precedance] = newCorner[precedance] === CENTER ? + (adjust[side] > 0 ? side : opposite) : (newCorner[precedance] === side ? opposite : side); + } + } + + function shiftonly(xy, side, opposite) { + if(newCorner[xy] === CENTER) { + css[MARGIN+'-'+side] = shift[xy] = offset[MARGIN+'-'+side] - adjust[side]; + } + else { + props = offset[opposite] !== undefined ? + [ adjust[side], -offset[side] ] : [ -adjust[side], offset[side] ]; + + if( (shift[xy] = Math.max(props[0], props[1])) > props[0] ) { + pos[side] -= adjust[side]; + shift[side] = FALSE; + } + + css[ offset[opposite] !== undefined ? opposite : side ] = shift[xy]; + } + } + + // If our tip position isn't fixed e.g. doesn't adjust with viewport... + if(this.corner.fixed !== TRUE) { + // Perform shift/flip adjustments + shiftflip(horizontal, X, Y, LEFT, RIGHT); + shiftflip(vertical, Y, X, TOP, BOTTOM); + + // Update and redraw the tip if needed (check cached details of last drawn tip) + if(newCorner.string() !== cache.corner.string() || cache.cornerTop !== adjust.top || cache.cornerLeft !== adjust.left) { + this.update(newCorner, FALSE); + } + } + + // Setup tip offset properties + offset = this.calculate(newCorner); + + // Readjust offset object to make it left/top + if(offset.right !== undefined) { offset.left = -offset.right; } + if(offset.bottom !== undefined) { offset.top = -offset.bottom; } + offset.user = this.offset; + + // Perform shift adjustments + if(shift.left = (horizontal === SHIFT && !!adjust.left)) { shiftonly(X, LEFT, RIGHT); } + if(shift.top = (vertical === SHIFT && !!adjust.top)) { shiftonly(Y, TOP, BOTTOM); } + + /* + * If the tip is adjusted in both dimensions, or in a + * direction that would cause it to be anywhere but the + * outer border, hide it! + */ + this.element.css(css).toggle( + !((shift.x && shift.y) || (newCorner.x === CENTER && shift.y) || (newCorner.y === CENTER && shift.x)) + ); + + // Adjust position to accomodate tip dimensions + pos.left -= offset.left.charAt ? offset.user : + horizontal !== SHIFT || shift.top || !shift.left && !shift.top ? offset.left + this.border : 0; + pos.top -= offset.top.charAt ? offset.user : + vertical !== SHIFT || shift.left || !shift.left && !shift.top ? offset.top + this.border : 0; + + // Cache details + cache.cornerLeft = adjust.left; cache.cornerTop = adjust.top; + cache.corner = newCorner.clone(); + }, + + destroy: function() { + // Unbind events + this.qtip._unbind(this.qtip.tooltip, this._ns); + + // Remove the tip element(s) + if(this.qtip.elements.tip) { + this.qtip.elements.tip.find('*') + .remove().end().remove(); + } + } +}); + +TIP = PLUGINS.tip = function(api) { + return new Tip(api, api.options.style.tip); +}; + +// Initialize tip on render +TIP.initialize = 'render'; + +// Setup plugin sanitization options +TIP.sanitize = function(options) { + if(options.style && 'tip' in options.style) { + var opts = options.style.tip; + if(typeof opts !== 'object') { opts = options.style.tip = { corner: opts }; } + if(!(/string|boolean/i).test(typeof opts.corner)) { opts.corner = TRUE; } + } +}; + +// Add new option checks for the plugin +CHECKS.tip = { + '^position.my|style.tip.(corner|mimic|border)$': function() { + // Make sure a tip can be drawn + this.create(); + + // Reposition the tooltip + this.qtip.reposition(); + }, + '^style.tip.(height|width)$': function(obj) { + // Re-set dimensions and redraw the tip + this.size = [ obj.width, obj.height ]; + this.update(); + + // Reposition the tooltip + this.qtip.reposition(); + }, + '^content.title|style.(classes|widget)$': function() { + this.update(); + } +}; + +// Extend original qTip defaults +$.extend(TRUE, QTIP.defaults, { + style: { + tip: { + corner: TRUE, + mimic: FALSE, + width: 6, + height: 6, + border: TRUE, + offset: 0 + } + } +}); +;var MODAL, OVERLAY, + MODALCLASS = 'qtip-modal', + MODALSELECTOR = '.'+MODALCLASS; + +OVERLAY = function() +{ + var self = this, + focusableElems = {}, + current, onLast, + prevState, elem; + + // Modified code from jQuery UI 1.10.0 source + // http://code.jquery.com/ui/1.10.0/jquery-ui.js + function focusable(element) { + // Use the defined focusable checker when possible + if($.expr[':'].focusable) { return $.expr[':'].focusable; } + + var isTabIndexNotNaN = !isNaN($.attr(element, 'tabindex')), + nodeName = element.nodeName && element.nodeName.toLowerCase(), + map, mapName, img; + + if('area' === nodeName) { + map = element.parentNode; + mapName = map.name; + if(!element.href || !mapName || map.nodeName.toLowerCase() !== 'map') { + return false; + } + img = $('img[usemap=#' + mapName + ']')[0]; + return !!img && img.is(':visible'); + } + return (/input|select|textarea|button|object/.test( nodeName ) ? + !element.disabled : + 'a' === nodeName ? + element.href || isTabIndexNotNaN : + isTabIndexNotNaN + ); + } + + // Focus inputs using cached focusable elements (see update()) + function focusInputs(blurElems) { + // Blurring body element in IE causes window.open windows to unfocus! + if(focusableElems.length < 1 && blurElems.length) { blurElems.not('body').blur(); } + + // Focus the inputs + else { focusableElems.first().focus(); } + } + + // Steal focus from elements outside tooltip + function stealFocus(event) { + if(!elem.is(':visible')) { return; } + + var target = $(event.target), + tooltip = current.tooltip, + container = target.closest(SELECTOR), + targetOnTop; + + // Determine if input container target is above this + targetOnTop = container.length < 1 ? FALSE : + (parseInt(container[0].style.zIndex, 10) > parseInt(tooltip[0].style.zIndex, 10)); + + // If we're showing a modal, but focus has landed on an input below + // this modal, divert focus to the first visible input in this modal + // or if we can't find one... the tooltip itself + if(!targetOnTop && target.closest(SELECTOR)[0] !== tooltip[0]) { + focusInputs(target); + } + + // Detect when we leave the last focusable element... + onLast = event.target === focusableElems[focusableElems.length - 1]; + } + + $.extend(self, { + init: function() { + // Create document overlay + elem = self.elem = $('
', { + id: 'qtip-overlay', + html: '
', + mousedown: function() { return FALSE; } + }) + .hide(); + + // Make sure we can't focus anything outside the tooltip + $(document.body).bind('focusin'+MODALSELECTOR, stealFocus); + + // Apply keyboard "Escape key" close handler + $(document).bind('keydown'+MODALSELECTOR, function(event) { + if(current && current.options.show.modal.escape && event.keyCode === 27) { + current.hide(event); + } + }); + + // Apply click handler for blur option + elem.bind('click'+MODALSELECTOR, function(event) { + if(current && current.options.show.modal.blur) { + current.hide(event); + } + }); + + return self; + }, + + update: function(api) { + // Update current API reference + current = api; + + // Update focusable elements if enabled + if(api.options.show.modal.stealfocus !== FALSE) { + focusableElems = api.tooltip.find('*').filter(function() { + return focusable(this); + }); + } + else { focusableElems = []; } + }, + + toggle: function(api, state, duration) { + var docBody = $(document.body), + tooltip = api.tooltip, + options = api.options.show.modal, + effect = options.effect, + type = state ? 'show': 'hide', + visible = elem.is(':visible'), + visibleModals = $(MODALSELECTOR).filter(':visible:not(:animated)').not(tooltip), + zindex; + + // Set active tooltip API reference + self.update(api); + + // If the modal can steal the focus... + // Blur the current item and focus anything in the modal we an + if(state && options.stealfocus !== FALSE) { + focusInputs( $(':focus') ); + } + + // Toggle backdrop cursor style on show + elem.toggleClass('blurs', options.blur); + + // Append to body on show + if(state) { + elem.appendTo(document.body); + } + + // Prevent modal from conflicting with show.solo, and don't hide backdrop is other modals are visible + if((elem.is(':animated') && visible === state && prevState !== FALSE) || (!state && visibleModals.length)) { + return self; + } + + // Stop all animations + elem.stop(TRUE, FALSE); + + // Use custom function if provided + if($.isFunction(effect)) { + effect.call(elem, state); + } + + // If no effect type is supplied, use a simple toggle + else if(effect === FALSE) { + elem[ type ](); + } + + // Use basic fade function + else { + elem.fadeTo( parseInt(duration, 10) || 90, state ? 1 : 0, function() { + if(!state) { elem.hide(); } + }); + } + + // Reset position and detach from body on hide + if(!state) { + elem.queue(function(next) { + elem.css({ left: '', top: '' }); + if(!$(MODALSELECTOR).length) { elem.detach(); } + next(); + }); + } + + // Cache the state + prevState = state; + + // If the tooltip is destroyed, set reference to null + if(current.destroyed) { current = NULL; } + + return self; + } + }); + + self.init(); +}; +OVERLAY = new OVERLAY(); + +function Modal(api, options) { + this.options = options; + this._ns = '-modal'; + + this.init( (this.qtip = api) ); +} + +$.extend(Modal.prototype, { + init: function(qtip) { + var tooltip = qtip.tooltip; + + // If modal is disabled... return + if(!this.options.on) { return this; } + + // Set overlay reference + qtip.elements.overlay = OVERLAY.elem; + + // Add unique attribute so we can grab modal tooltips easily via a SELECTOR, and set z-index + tooltip.addClass(MODALCLASS).css('z-index', QTIP.modal_zindex + $(MODALSELECTOR).length); + + // Apply our show/hide/focus modal events + qtip._bind(tooltip, ['tooltipshow', 'tooltiphide'], function(event, api, duration) { + var oEvent = event.originalEvent; + + // Make sure mouseout doesn't trigger a hide when showing the modal and mousing onto backdrop + if(event.target === tooltip[0]) { + if(oEvent && event.type === 'tooltiphide' && /mouse(leave|enter)/.test(oEvent.type) && $(oEvent.relatedTarget).closest(OVERLAY.elem[0]).length) { + try { event.preventDefault(); } catch(e) {} + } + else if(!oEvent || (oEvent && oEvent.type !== 'tooltipsolo')) { + this.toggle(event, event.type === 'tooltipshow', duration); + } + } + }, this._ns, this); + + // Adjust modal z-index on tooltip focus + qtip._bind(tooltip, 'tooltipfocus', function(event, api) { + // If focus was cancelled before it reached us, don't do anything + if(event.isDefaultPrevented() || event.target !== tooltip[0]) { return; } + + var qtips = $(MODALSELECTOR), + + // Keep the modal's lower than other, regular qtips + newIndex = QTIP.modal_zindex + qtips.length, + curIndex = parseInt(tooltip[0].style.zIndex, 10); + + // Set overlay z-index + OVERLAY.elem[0].style.zIndex = newIndex - 1; + + // Reduce modal z-index's and keep them properly ordered + qtips.each(function() { + if(this.style.zIndex > curIndex) { + this.style.zIndex -= 1; + } + }); + + // Fire blur event for focused tooltip + qtips.filter('.' + CLASS_FOCUS).qtip('blur', event.originalEvent); + + // Set the new z-index + tooltip.addClass(CLASS_FOCUS)[0].style.zIndex = newIndex; + + // Set current + OVERLAY.update(api); + + // Prevent default handling + try { event.preventDefault(); } catch(e) {} + }, this._ns, this); + + // Focus any other visible modals when this one hides + qtip._bind(tooltip, 'tooltiphide', function(event) { + if(event.target === tooltip[0]) { + $(MODALSELECTOR).filter(':visible').not(tooltip).last().qtip('focus', event); + } + }, this._ns, this); + }, + + toggle: function(event, state, duration) { + // Make sure default event hasn't been prevented + if(event && event.isDefaultPrevented()) { return this; } + + // Toggle it + OVERLAY.toggle(this.qtip, !!state, duration); + }, + + destroy: function() { + // Remove modal class + this.qtip.tooltip.removeClass(MODALCLASS); + + // Remove bound events + this.qtip._unbind(this.qtip.tooltip, this._ns); + + // Delete element reference + OVERLAY.toggle(this.qtip, FALSE); + delete this.qtip.elements.overlay; + } +}); + + +MODAL = PLUGINS.modal = function(api) { + return new Modal(api, api.options.show.modal); +}; + +// Setup sanitiztion rules +MODAL.sanitize = function(opts) { + if(opts.show) { + if(typeof opts.show.modal !== 'object') { opts.show.modal = { on: !!opts.show.modal }; } + else if(typeof opts.show.modal.on === 'undefined') { opts.show.modal.on = TRUE; } + } +}; + +// Base z-index for all modal tooltips (use qTip core z-index as a base) +QTIP.modal_zindex = QTIP.zindex - 200; + +// Plugin needs to be initialized on render +MODAL.initialize = 'render'; + +// Setup option set checks +CHECKS.modal = { + '^show.modal.(on|blur)$': function() { + // Initialise + this.destroy(); + this.init(); + + // Show the modal if not visible already and tooltip is visible + this.qtip.elems.overlay.toggle( + this.qtip.tooltip[0].offsetWidth > 0 + ); + } +}; + +// Extend original api defaults +$.extend(TRUE, QTIP.defaults, { + show: { + modal: { + on: FALSE, + effect: TRUE, + blur: TRUE, + stealfocus: TRUE, + escape: TRUE + } + } +}); +;PLUGINS.viewport = function(api, position, posOptions, targetWidth, targetHeight, elemWidth, elemHeight) +{ + var target = posOptions.target, + tooltip = api.elements.tooltip, + my = posOptions.my, + at = posOptions.at, + adjust = posOptions.adjust, + method = adjust.method.split(' '), + methodX = method[0], + methodY = method[1] || method[0], + viewport = posOptions.viewport, + container = posOptions.container, + cache = api.cache, + adjusted = { left: 0, top: 0 }, + fixed, newMy, containerOffset, containerStatic, + viewportWidth, viewportHeight, viewportScroll, viewportOffset; + + // If viewport is not a jQuery element, or it's the window/document, or no adjustment method is used... return + if(!viewport.jquery || target[0] === window || target[0] === document.body || adjust.method === 'none') { + return adjusted; + } + + // Cach container details + containerOffset = container.offset() || adjusted; + containerStatic = container.css('position') === 'static'; + + // Cache our viewport details + fixed = tooltip.css('position') === 'fixed'; + viewportWidth = viewport[0] === window ? viewport.width() : viewport.outerWidth(FALSE); + viewportHeight = viewport[0] === window ? viewport.height() : viewport.outerHeight(FALSE); + viewportScroll = { left: fixed ? 0 : viewport.scrollLeft(), top: fixed ? 0 : viewport.scrollTop() }; + viewportOffset = viewport.offset() || adjusted; + + // Generic calculation method + function calculate(side, otherSide, type, adjust, side1, side2, lengthName, targetLength, elemLength) { + var initialPos = position[side1], + mySide = my[side], + atSide = at[side], + isShift = type === SHIFT, + myLength = mySide === side1 ? elemLength : mySide === side2 ? -elemLength : -elemLength / 2, + atLength = atSide === side1 ? targetLength : atSide === side2 ? -targetLength : -targetLength / 2, + sideOffset = viewportScroll[side1] + viewportOffset[side1] - (containerStatic ? 0 : containerOffset[side1]), + overflow1 = sideOffset - initialPos, + overflow2 = initialPos + elemLength - (lengthName === WIDTH ? viewportWidth : viewportHeight) - sideOffset, + offset = myLength - (my.precedance === side || mySide === my[otherSide] ? atLength : 0) - (atSide === CENTER ? targetLength / 2 : 0); + + // shift + if(isShift) { + offset = (mySide === side1 ? 1 : -1) * myLength; + + // Adjust position but keep it within viewport dimensions + position[side1] += overflow1 > 0 ? overflow1 : overflow2 > 0 ? -overflow2 : 0; + position[side1] = Math.max( + -containerOffset[side1] + viewportOffset[side1], + initialPos - offset, + Math.min( + Math.max( + -containerOffset[side1] + viewportOffset[side1] + (lengthName === WIDTH ? viewportWidth : viewportHeight), + initialPos + offset + ), + position[side1], + + // Make sure we don't adjust complete off the element when using 'center' + mySide === 'center' ? initialPos - myLength : 1E9 + ) + ); + + } + + // flip/flipinvert + else { + // Update adjustment amount depending on if using flipinvert or flip + adjust *= (type === FLIPINVERT ? 2 : 0); + + // Check for overflow on the left/top + if(overflow1 > 0 && (mySide !== side1 || overflow2 > 0)) { + position[side1] -= offset + adjust; + newMy.invert(side, side1); + } + + // Check for overflow on the bottom/right + else if(overflow2 > 0 && (mySide !== side2 || overflow1 > 0) ) { + position[side1] -= (mySide === CENTER ? -offset : offset) + adjust; + newMy.invert(side, side2); + } + + // Make sure we haven't made things worse with the adjustment and reset if so + if(position[side1] < viewportScroll && -position[side1] > overflow2) { + position[side1] = initialPos; newMy = my.clone(); + } + } + + return position[side1] - initialPos; + } + + // Set newMy if using flip or flipinvert methods + if(methodX !== 'shift' || methodY !== 'shift') { newMy = my.clone(); } + + // Adjust position based onviewport and adjustment options + adjusted = { + left: methodX !== 'none' ? calculate( X, Y, methodX, adjust.x, LEFT, RIGHT, WIDTH, targetWidth, elemWidth ) : 0, + top: methodY !== 'none' ? calculate( Y, X, methodY, adjust.y, TOP, BOTTOM, HEIGHT, targetHeight, elemHeight ) : 0, + my: newMy + }; + + return adjusted; +}; +;PLUGINS.polys = { + // POLY area coordinate calculator + // Special thanks to Ed Cradock for helping out with this. + // Uses a binary search algorithm to find suitable coordinates. + polygon: function(baseCoords, corner) { + var result = { + width: 0, height: 0, + position: { + top: 1e10, right: 0, + bottom: 0, left: 1e10 + }, + adjustable: FALSE + }, + i = 0, next, + coords = [], + compareX = 1, compareY = 1, + realX = 0, realY = 0, + newWidth, newHeight; + + // First pass, sanitize coords and determine outer edges + i = baseCoords.length; while(i--) { + next = [ parseInt(baseCoords[--i], 10), parseInt(baseCoords[i+1], 10) ]; + + if(next[0] > result.position.right){ result.position.right = next[0]; } + if(next[0] < result.position.left){ result.position.left = next[0]; } + if(next[1] > result.position.bottom){ result.position.bottom = next[1]; } + if(next[1] < result.position.top){ result.position.top = next[1]; } + + coords.push(next); + } + + // Calculate height and width from outer edges + newWidth = result.width = Math.abs(result.position.right - result.position.left); + newHeight = result.height = Math.abs(result.position.bottom - result.position.top); + + // If it's the center corner... + if(corner.abbrev() === 'c') { + result.position = { + left: result.position.left + (result.width / 2), + top: result.position.top + (result.height / 2) + }; + } + else { + // Second pass, use a binary search algorithm to locate most suitable coordinate + while(newWidth > 0 && newHeight > 0 && compareX > 0 && compareY > 0) + { + newWidth = Math.floor(newWidth / 2); + newHeight = Math.floor(newHeight / 2); + + if(corner.x === LEFT){ compareX = newWidth; } + else if(corner.x === RIGHT){ compareX = result.width - newWidth; } + else{ compareX += Math.floor(newWidth / 2); } + + if(corner.y === TOP){ compareY = newHeight; } + else if(corner.y === BOTTOM){ compareY = result.height - newHeight; } + else{ compareY += Math.floor(newHeight / 2); } + + i = coords.length; while(i--) + { + if(coords.length < 2){ break; } + + realX = coords[i][0] - result.position.left; + realY = coords[i][1] - result.position.top; + + if((corner.x === LEFT && realX >= compareX) || + (corner.x === RIGHT && realX <= compareX) || + (corner.x === CENTER && (realX < compareX || realX > (result.width - compareX))) || + (corner.y === TOP && realY >= compareY) || + (corner.y === BOTTOM && realY <= compareY) || + (corner.y === CENTER && (realY < compareY || realY > (result.height - compareY)))) { + coords.splice(i, 1); + } + } + } + result.position = { left: coords[0][0], top: coords[0][1] }; + } + + return result; + }, + + rect: function(ax, ay, bx, by) { + return { + width: Math.abs(bx - ax), + height: Math.abs(by - ay), + position: { + left: Math.min(ax, bx), + top: Math.min(ay, by) + } + }; + }, + + _angles: { + tc: 3 / 2, tr: 7 / 4, tl: 5 / 4, + bc: 1 / 2, br: 1 / 4, bl: 3 / 4, + rc: 2, lc: 1, c: 0 + }, + ellipse: function(cx, cy, rx, ry, corner) { + var c = PLUGINS.polys._angles[ corner.abbrev() ], + rxc = c === 0 ? 0 : rx * Math.cos( c * Math.PI ), + rys = ry * Math.sin( c * Math.PI ); + + return { + width: (rx * 2) - Math.abs(rxc), + height: (ry * 2) - Math.abs(rys), + position: { + left: cx + rxc, + top: cy + rys + }, + adjustable: FALSE + }; + }, + circle: function(cx, cy, r, corner) { + return PLUGINS.polys.ellipse(cx, cy, r, r, corner); + } +}; +;PLUGINS.svg = function(api, svg, corner) +{ + var doc = $(document), + elem = svg[0], + root = $(elem.ownerSVGElement), + ownerDocument = elem.ownerDocument, + strokeWidth2 = (parseInt(svg.css('stroke-width'), 10) || 0) / 2, + frameOffset, mtx, transformed, viewBox, + len, next, i, points, + result, position, dimensions; + + // Ascend the parentNode chain until we find an element with getBBox() + while(!elem.getBBox) { elem = elem.parentNode; } + if(!elem.getBBox || !elem.parentNode) { return FALSE; } + + // Determine which shape calculation to use + switch(elem.nodeName) { + case 'ellipse': + case 'circle': + result = PLUGINS.polys.ellipse( + elem.cx.baseVal.value, + elem.cy.baseVal.value, + (elem.rx || elem.r).baseVal.value + strokeWidth2, + (elem.ry || elem.r).baseVal.value + strokeWidth2, + corner + ); + break; + + case 'line': + case 'polygon': + case 'polyline': + // Determine points object (line has none, so mimic using array) + points = elem.points || [ + { x: elem.x1.baseVal.value, y: elem.y1.baseVal.value }, + { x: elem.x2.baseVal.value, y: elem.y2.baseVal.value } + ]; + + for(result = [], i = -1, len = points.numberOfItems || points.length; ++i < len;) { + next = points.getItem ? points.getItem(i) : points[i]; + result.push.apply(result, [next.x, next.y]); + } + + result = PLUGINS.polys.polygon(result, corner); + break; + + // Unknown shape or rectangle? Use bounding box + default: + result = elem.getBBox(); + result = { + width: result.width, + height: result.height, + position: { + left: result.x, + top: result.y + } + }; + break; + } + + // Shortcut assignments + position = result.position; + root = root[0]; + + // Convert position into a pixel value + if(root.createSVGPoint) { + mtx = elem.getScreenCTM(); + points = root.createSVGPoint(); + + points.x = position.left; + points.y = position.top; + transformed = points.matrixTransform( mtx ); + position.left = transformed.x; + position.top = transformed.y; + } + + // Check the element is not in a child document, and if so, adjust for frame elements offset + if(ownerDocument !== document && api.position.target !== 'mouse') { + frameOffset = $((ownerDocument.defaultView || ownerDocument.parentWindow).frameElement).offset(); + if(frameOffset) { + position.left += frameOffset.left; + position.top += frameOffset.top; + } + } + + // Adjust by scroll offset of owner document + ownerDocument = $(ownerDocument); + position.left += ownerDocument.scrollLeft(); + position.top += ownerDocument.scrollTop(); + + return result; +}; +;PLUGINS.imagemap = function(api, area, corner, adjustMethod) +{ + if(!area.jquery) { area = $(area); } + + var shape = (area.attr('shape') || 'rect').toLowerCase().replace('poly', 'polygon'), + image = $('img[usemap="#'+area.parent('map').attr('name')+'"]'), + coordsString = $.trim(area.attr('coords')), + coordsArray = coordsString.replace(/,$/, '').split(','), + imageOffset, coords, i, next, result, len; + + // If we can't find the image using the map... + if(!image.length) { return FALSE; } + + // Pass coordinates string if polygon + if(shape === 'polygon') { + result = PLUGINS.polys.polygon(coordsArray, corner); + } + + // Otherwise parse the coordinates and pass them as arguments + else if(PLUGINS.polys[shape]) { + for(i = -1, len = coordsArray.length, coords = []; ++i < len;) { + coords.push( parseInt(coordsArray[i], 10) ); + } + + result = PLUGINS.polys[shape].apply( + this, coords.concat(corner) + ); + } + + // If no shapre calculation method was found, return false + else { return FALSE; } + + // Make sure we account for padding and borders on the image + imageOffset = image.offset(); + imageOffset.left += Math.ceil((image.outerWidth(FALSE) - image.width()) / 2); + imageOffset.top += Math.ceil((image.outerHeight(FALSE) - image.height()) / 2); + + // Add image position to offset coordinates + result.position.left += imageOffset.left; + result.position.top += imageOffset.top; + + return result; +}; +;var IE6, + +/* + * BGIFrame adaption (http://plugins.jquery.com/project/bgiframe) + * Special thanks to Brandon Aaron + */ +BGIFRAME = ''; + +function Ie6(api, qtip) { + this._ns = 'ie6'; + this.init( (this.qtip = api) ); +} + +$.extend(Ie6.prototype, { + _scroll : function() { + var overlay = this.qtip.elements.overlay; + overlay && (overlay[0].style.top = $(window).scrollTop() + 'px'); + }, + + init: function(qtip) { + var tooltip = qtip.tooltip, + scroll; + + // Create the BGIFrame element if needed + if($('select, object').length < 1) { + this.bgiframe = qtip.elements.bgiframe = $(BGIFRAME).appendTo(tooltip); + + // Update BGIFrame on tooltip move + qtip._bind(tooltip, 'tooltipmove', this.adjustBGIFrame, this._ns, this); + } + + // redraw() container for width/height calculations + this.redrawContainer = $('
', { id: NAMESPACE+'-rcontainer' }) + .appendTo(document.body); + + // Fixup modal plugin if present too + if( qtip.elements.overlay && qtip.elements.overlay.addClass('qtipmodal-ie6fix') ) { + qtip._bind(window, ['scroll', 'resize'], this._scroll, this._ns, this); + qtip._bind(tooltip, ['tooltipshow'], this._scroll, this._ns, this); + } + + // Set dimensions + this.redraw(); + }, + + adjustBGIFrame: function() { + var tooltip = this.qtip.tooltip, + dimensions = { + height: tooltip.outerHeight(FALSE), + width: tooltip.outerWidth(FALSE) + }, + plugin = this.qtip.plugins.tip, + tip = this.qtip.elements.tip, + tipAdjust, offset; + + // Adjust border offset + offset = parseInt(tooltip.css('borderLeftWidth'), 10) || 0; + offset = { left: -offset, top: -offset }; + + // Adjust for tips plugin + if(plugin && tip) { + tipAdjust = (plugin.corner.precedance === 'x') ? [WIDTH, LEFT] : [HEIGHT, TOP]; + offset[ tipAdjust[1] ] -= tip[ tipAdjust[0] ](); + } + + // Update bgiframe + this.bgiframe.css(offset).css(dimensions); + }, + + // Max/min width simulator function + redraw: function() { + if(this.qtip.rendered < 1 || this.drawing) { return this; } + + var tooltip = this.qtip.tooltip, + style = this.qtip.options.style, + container = this.qtip.options.position.container, + perc, width, max, min; + + // Set drawing flag + this.qtip.drawing = 1; + + // If tooltip has a set height/width, just set it... like a boss! + if(style.height) { tooltip.css(HEIGHT, style.height); } + if(style.width) { tooltip.css(WIDTH, style.width); } + + // Simulate max/min width if not set width present... + else { + // Reset width and add fluid class + tooltip.css(WIDTH, '').appendTo(this.redrawContainer); + + // Grab our tooltip width (add 1 if odd so we don't get wrapping problems.. huzzah!) + width = tooltip.width(); + if(width % 2 < 1) { width += 1; } + + // Grab our max/min properties + max = tooltip.css('maxWidth') || ''; + min = tooltip.css('minWidth') || ''; + + // Parse into proper pixel values + perc = (max + min).indexOf('%') > -1 ? container.width() / 100 : 0; + max = ((max.indexOf('%') > -1 ? perc : 1) * parseInt(max, 10)) || width; + min = ((min.indexOf('%') > -1 ? perc : 1) * parseInt(min, 10)) || 0; + + // Determine new dimension size based on max/min/current values + width = max + min ? Math.min(Math.max(width, min), max) : width; + + // Set the newly calculated width and remvoe fluid class + tooltip.css(WIDTH, Math.round(width)).appendTo(container); + } + + // Set drawing flag + this.drawing = 0; + + return this; + }, + + destroy: function() { + // Remove iframe + this.bgiframe && this.bgiframe.remove(); + + // Remove bound events + this.qtip._unbind([window, this.qtip.tooltip], this._ns); + } +}); + +IE6 = PLUGINS.ie6 = function(api) { + // Proceed only if the browser is IE6 + return BROWSER.ie === 6 ? new Ie6(api) : FALSE; +}; + +IE6.initialize = 'render'; + +CHECKS.ie6 = { + '^content|style$': function() { + this.redraw(); + } +}; +;})); +}( window, document )); \ No newline at end of file diff --git a/config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js b/config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js new file mode 100644 index 00000000000..9c998d87f01 --- /dev/null +++ b/config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js @@ -0,0 +1,104 @@ +/* +tip_centerwindow.js v. 1.21 + +The latest version is available at +http://www.walterzorn.com +or http://www.devira.com +or http://www.walterzorn.de + +Initial author: Walter Zorn +Last modified: 3.6.2008 + +Extension for the tooltip library wz_tooltip.js. +Centers a sticky tooltip in the window's visible clientarea, +optionally even if the window is being scrolled or resized. +*/ + +// Make sure that the core file wz_tooltip.js is included first +if(typeof config == "undefined") + alert("Error:\nThe core tooltip script file 'wz_tooltip.js' must be included first, before the plugin files!"); + +// Here we define new global configuration variable(s) (as members of the +// predefined "config." class). +// From each of these config variables, wz_tooltip.js will automatically derive +// a command which can be passed to Tip() or TagToTip() in order to customize +// tooltips individually. These command names are just the config variable +// name(s) translated to uppercase, +// e.g. from config. CenterWindow a command CENTERWINDOW will automatically be +// created. + +//=================== GLOBAL TOOLTIP CONFIGURATION =========================// +config. CenterWindow = false // true or false - set to true if you want this to be the default behaviour +config. CenterAlways = false // true or false - recenter if window is resized or scrolled +//======= END OF TOOLTIP CONFIG, DO NOT CHANGE ANYTHING BELOW ==============// + + +// Create a new tt_Extension object (make sure that the name of that object, +// here ctrwnd, is unique amongst the extensions available for +// wz_tooltips.js): +var ctrwnd = new tt_Extension(); + +// Implement extension eventhandlers on which our extension should react +ctrwnd.OnLoadConfig = function() +{ + if(tt_aV[CENTERWINDOW]) + { + // Permit CENTERWINDOW only if the tooltip is sticky + if(tt_aV[STICKY]) + { + if(tt_aV[CENTERALWAYS]) + { + // IE doesn't support style.position "fixed" + if(tt_ie) + tt_AddEvtFnc(window, "scroll", Ctrwnd_DoCenter); + else + tt_aElt[0].style.position = "fixed"; + tt_AddEvtFnc(window, "resize", Ctrwnd_DoCenter); + } + return true; + } + tt_aV[CENTERWINDOW] = false; + } + return false; +}; +// We react on the first OnMouseMove event to center the tip on that occasion +ctrwnd.OnMoveBefore = Ctrwnd_DoCenter; +ctrwnd.OnKill = function() +{ + if(tt_aV[CENTERWINDOW] && tt_aV[CENTERALWAYS]) + { + tt_RemEvtFnc(window, "resize", Ctrwnd_DoCenter); + if(tt_ie) + tt_RemEvtFnc(window, "scroll", Ctrwnd_DoCenter); + else + tt_aElt[0].style.position = "absolute"; + } + return false; +}; +// Helper function +function Ctrwnd_DoCenter() +{ + if(tt_aV[CENTERWINDOW]) + { + var x, y, dx, dy; + + // Here we use some functions and variables (tt_w, tt_h) which the + // extension API of wz_tooltip.js provides for us + if(tt_ie || !tt_aV[CENTERALWAYS]) + { + dx = tt_GetScrollX(); + dy = tt_GetScrollY(); + } + else + { + dx = 0; + dy = 0; + } + // Position the tip, offset from the center by OFFSETX and OFFSETY + x = (tt_GetClientW() - tt_w) / 2 + dx + tt_aV[OFFSETX]; + y = (tt_GetClientH() - tt_h) / 2 + dy + tt_aV[OFFSETY]; + tt_SetTipPos(x, y); + return true; + } + return false; +} diff --git a/config/plugins/visualizations/graphviz/static/js/tip_followscroll.js b/config/plugins/visualizations/graphviz/static/js/tip_followscroll.js new file mode 100644 index 00000000000..060d48b56f4 --- /dev/null +++ b/config/plugins/visualizations/graphviz/static/js/tip_followscroll.js @@ -0,0 +1,88 @@ +/* +tip_followscroll.js v. 1.11 + +The latest version is available at +http://www.walterzorn.com +or http://www.devira.com +or http://www.walterzorn.de + +Initial author: Walter Zorn +Last modified: 3.6.2008 + +Extension for the tooltip library wz_tooltip.js. +Lets a "sticky" tooltip keep its position inside the clientarea if the window +is scrolled. +*/ + +// Make sure that the core file wz_tooltip.js is included first +if(typeof config == "undefined") + alert("Error:\nThe core tooltip script file 'wz_tooltip.js' must be included first, before the plugin files!"); + +// Here we define new global configuration variable(s) (as members of the +// predefined "config." class). +// From each of these config variables, wz_tooltip.js will automatically derive +// a command which can be passed to Tip() or TagToTip() in order to customize +// tooltips individually. These command names are just the config variable +// name(s) translated to uppercase, +// e.g. from config. FollowScroll a command FOLLOWSCROLL will automatically be +// created. + +//=================== GLOBAL TOOLTIP CONFIGURATION ======================// +config. FollowScroll = false // true or false - set to true if you want this to be the default behaviour +//======= END OF TOOLTIP CONFIG, DO NOT CHANGE ANYTHING BELOW ==============// + + +// Create a new tt_Extension object (make sure that the name of that object, +// here fscrl, is unique amongst the extensions available for +// wz_tooltips.js): +var fscrl = new tt_Extension(); + +// Implement extension eventhandlers on which our extension should react +fscrl.OnShow = function() +{ + if(tt_aV[FOLLOWSCROLL]) + { + // Permit FOLLOWSCROLL only if the tooltip is sticky + if(tt_aV[STICKY]) + { + var x = tt_x - tt_GetScrollX(), y = tt_y - tt_GetScrollY(); + + if(tt_ie) + { + fscrl.MoveOnScrl.offX = x; + fscrl.MoveOnScrl.offY = y; + fscrl.AddRemEvtFncs(tt_AddEvtFnc); + } + else + { + tt_SetTipPos(x, y); + tt_aElt[0].style.position = "fixed"; + } + return true; + } + tt_aV[FOLLOWSCROLL] = false; + } + return false; +}; +fscrl.OnHide = function() +{ + if(tt_aV[FOLLOWSCROLL]) + { + if(tt_ie) + fscrl.AddRemEvtFncs(tt_RemEvtFnc); + else + tt_aElt[0].style.position = "absolute"; + } +}; +// Helper functions (encapsulate in the class to avoid conflicts with other +// extensions) +fscrl.MoveOnScrl = function() +{ + tt_SetTipPos(fscrl.MoveOnScrl.offX + tt_GetScrollX(), fscrl.MoveOnScrl.offY + tt_GetScrollY()); +}; +fscrl.AddRemEvtFncs = function(PAddRem) +{ + PAddRem(window, "resize", fscrl.MoveOnScrl); + PAddRem(window, "scroll", fscrl.MoveOnScrl); +}; + diff --git a/config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js b/config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js new file mode 100644 index 00000000000..fdd20f192ac --- /dev/null +++ b/config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js @@ -0,0 +1,631 @@ +$(function() { // on dom ready + + + ///// show/hide Labels + $('#nodeLabelCheck').change(function() { + if ($(this).is(":checked")) { + + showNodeLabel = 'data(id)'; //.replace(/[^0-9\.]+/g, "")'; // change to label or name if needed + } else { + showNodeLabel = ""; + } + + cy.style() + .selector('node') + .css({ + 'content': showNodeLabel + }) + .update(); + }); + + $('#linkLabelCheck').change(function() { + if ($(this).is(":checked")) { + showEdgeLabel = "data(id)"; // change to label or name if needed + } else { + showEdgeLabel = ""; + } + + cy.style() + .selector('edge') + .css({ + 'content': showEdgeLabel + }) + .update(); + }); + + + //////// change the shape of the graph + $('#selectShape').change(function() { + + $("select option:selected").each(function() { + shape = $(this).val(); + }); + cy.makeLayout({ + 'name': shape + }) + .run(); + + $('#selectShape').blur(); + }); + + //////// highlighting outgoing nodes + + $('#showOutNode').change(function() { + if ($('#showOutNode').is(":checked")) { + showOut = true; + cy.nodes().on("tapend", highlightOut); + + } else { + showOut = false; + cy.nodes().off("tapend", highlightOut); + + resetHighlightOut(showIn, showOut); + } + }); + + + //////// highlighting incoming nodes + + $('#showInNode').change(function() { + + if ($('#showInNode').is(":checked")) { + showIn = true; + cy.nodes().on("tapend", highlightIn); + + + } else { + showIn = false; + cy.nodes().off("tapend", highlightIn); + resetHighlightIn(showIn, showOut); + + cy.nodes().removeClass('connectedNodeIn'); + } + + }); + + //// show number of contained nodes for a collapsed node + $('#collapseCount').change(function() { + checkBoxes(); + }); + + ////expand(Load) nodes + $('#expandNode').click(function() { + var selectedNode = cy.nodes(':selected'); + + if (selectedNode.hasClass('superNode')) { + unColNode(); + } else { + expandNodes(selectedNode); + $('.btn.expNode').prop('disabled', true); + } + + }); + + //// disable/unable buttons + $(document).on('click', function() { + + var selectedNode = cy.nodes(':selected'); + + if (selectedNode.outgoers().length == 0) { + + $('.btn.colNode').prop('disabled', true); + + + } else if (selectedNode.hasClass('superNode')) { + + $('.btn.colNode').prop('disabled', true); + + } else { + + $('.btn.colNode').prop('disabled', false); + + } + + if (selectedNode.hasClass('toBeExpaned') || selectedNode.hasClass('superNode')) { + + $('.btn.expNode').prop('disabled', false); + + } else { + + $('.btn.expNode').prop('disabled', true); + + } + + if (cy.nodes(":selected").length > 0) { + + $('.btn.delNode').prop('disabled', false); + } else { + + $('.btn.delNode').prop('disabled', true); + } + + + }); + + + ///// keyboard commands + + $(document).keypress(function(e) { + + var selectedNode = cy.nodes(':selected'); + + if (e.which == 101 && selectedNode.size() != 0) { // 101 for 'e' = expand + + if (selectedNode.hasClass('toBeExpaned')) { + + expandNodes(selectedNode); + + } else if (selectedNode.hasClass('superNode')) { + + unColNode(); + } + + + } + if (e.which == 99 && selectedNode.size() != 0 && !selectedNode.hasClass('superNode') && selectedNode.outgoers().length != 0) { // 99 for 'c' = collapse + + colNode(); + + } + + if (e.which == 100 && selectedNode.size() != 0) { // 100 for 'd' = delete + deleteSelectedNodes(); + } + + + }); + + /////////////// tool Panel movement + + $(document).on('click', '.slider-arrow.show', function() { + $(".slider-arrow, .panel").animate({ + left: "+=243" + }, 700, function() { + // Animation complete. + }); + $(this).html('«').removeClass('show').addClass('hide'); + + document.getElementById('cy').style.left = "243px"; + //document.getElementById('cy').style.width="80%"; + + cy.resize(); + + + }); + + $(document).on('click', '.slider-arrow.hide', function() { + $(".slider-arrow, .panel").animate({ + left: "-=243" + }, 700, function() { + // Animation complete. + }); + $(this).html('»').removeClass('hide').addClass('show'); + document.getElementById('cy').style.left = "0px"; + // document.getElementById('cy').style.width="100%"; + cy.resize(); + }); + + //////////////////panel for Node info + + $(document).on('click', '.slider-arrow-forNode.show', function() { + $(".slider-arrow-forNode, .nodePanel").animate({ + right: "+=248" + }, 700, function() { + // Animation complete. + }); + $(this).html('»').removeClass('show').addClass('hide'); + + document.getElementById('cy').style.right = "248px"; + //document.getElementById('cy').style.width="80%"; + + cy.resize(); + + + }); + + $(document).on('click', '.slider-arrow-forNode.hide', function() { + $(".slider-arrow-forNode, .nodePanel").animate({ + right: "-=248" + }, 700, function() { + // Animation complete. + }); + $(this).html('«').removeClass('hide').addClass('show'); + document.getElementById('cy').style.right = "0px"; + // document.getElementById('cy').style.width="100%"; + cy.resize(); + }); + + + + +}) // on dom ready END + +///////// finding outgoing Nodes +function highlightOut() { + + var selectedNode = this; + + var connectedNodes = selectedNode.outgoers(); + + if (selectedNode.hasClass('selectedNodeOut')) { + + connectedNodes.removeClass('connectedNodeOut'); + selectedNode.removeClass('selectedNodeOut'); + + cy.style() + .selector('.connectedNodeOut') + .css({ + 'opacity': 0.8 + }) + .update(); + } else { + + cy.nodes().not(this).removeClass('connectedNodeOut'); + cy.nodes().not(this).removeClass('selectedNodeOut'); + cy.edges().not(this).removeClass('connectedNodeOut'); + + connectedNodes.addClass('connectedNodeOut'); + selectedNode.addClass('selectedNodeOut'); + cy.style() + .selector('.connectedNodeOut') + .css({ + 'background-color': '#FE2E64', + 'line-color': '#FE2E64', + 'target-arrow-color': '#FE2E64', + 'source-arrow-color': '#FE2E64', + 'opacity': 0.8 + }) + .update(); + + cy.style() + .selector('.selectedNodeOut') + .css({ + 'background-color': '#FE2E64', + 'line-color': '#FE2E64', + 'target-arrow-color': '#FE2E64', + 'source-arrow-color': '#FE2E64', + 'opacity': 0.8 + }) + .update(); + } +} + +/////// reset highlighting of outgoing nodes +function resetHighlightOut(showIn, showOut) { + + cy.style() + .selector('.connectedNodeOut') + .css({ + 'opacity': 0.8, + 'background-color': '#888888', + 'line-color': '#ddd', + 'target-arrow-color': '#ddd' + }) + .update(); + + + if (!showIn && !showOut) { + cy.style() + .selector('.selectedNodeOut') + .css({ + 'opacity': 0.8, + 'background-color': '#888888', // + 'border-width': 0 + }) + .update(); + + } + cy.nodes().removeClass('selectedNodeOut'); + cy.nodes().removeClass('connectedNodeOut'); + cy.edges().removeClass('connectedNodeOut'); +} + +//////////// find inComing nodes + +function highlightIn() { + + var selectedNode = this; + var connectedNodes = selectedNode.incomers(); + + if (selectedNode.hasClass('selectedNodeIn')) { + + cy.style() + .selector('.connectedNodeIn') + .css({ + 'opacity': 0.8 + }) + .update(); + connectedNodes.removeClass('connectedNodeIn'); + selectedNode.removeClass('selectedNodeIn'); + + } else { + + cy.nodes().not(this).removeClass('connectedNodeIn'); + cy.nodes().not(this).removeClass('selectedNodeIn'); + cy.edges().not(this).removeClass('connectedNodeIn'); + + connectedNodes.addClass('connectedNodeIn'); + selectedNode.addClass('selectedNodeIn'); + cy.style() + .selector('.connectedNodeIn') + .css({ + 'background-color': '#FE2E64', + 'line-color': '#FE2E64', + 'target-arrow-color': '#FE2E64', + 'source-arrow-color': '#FE2E64', + 'opacity': 0.8 + }) + .update(); + cy.style() + .selector('.selectedNodeIn') + .css({ + 'background-color': '#FE2E64', + 'line-color': '#FE2E64', + 'target-arrow-color': '#FE2E64', + 'source-arrow-color': '#FE2E64', + 'opacity': 0.8 + }) + .update(); + } +} + + +/////// reset highlighting of incoming nodes +function resetHighlightIn(showIn, showOut) { + + cy.style() + .selector('.connectedNodeIn') + .css({ + 'opacity': 0.8, + 'background-color': '#888888', + 'line-color': '#ddd', + 'target-arrow-color': '#ddd' + }) + .update(); + + if (!showIn && !showOut) { + cy.style() + .selector('.selectedNodeIn') + .css({ + 'opacity': 0.8, + 'background-color': '#888888', // + 'border-width': 0 + }) + .update(); + } + + cy.nodes().removeClass('selectedNodeIn'); + cy.nodes().removeClass('connectedNodeIn'); + cy.edges().removeClass('connectedNodeIn'); + +} + + +////// export PNG +function exportFunction() { + + var pngPic = cy.png(); + downloadURI(pngPic, "graph"); //// tested on Chrome and Firefox +} + +function downloadURI(uri, fname) { + + var link = document.createElement("a"); + link.download = fname; + + link.href = uri; + document.body.appendChild(link); + link.click(); + // Cleanup the DOM + document.body.removeChild(link); + delete link; +} + +///// restore Graph structure +function restorGraphStructure() { + + resetCollapse(); + + var shape = ""; + $("select option:selected").each(function() { + shape = $(this).val(); + }); + cy.makeLayout({ + 'name': shape + }) + .run(); + +} + +// show node info on the right panel +function showNodeInfo(node) { + + var str = ""; + var nodeContent = node.data(); + + var fieldName = []; + var i = 0; + var values = []; + var j = 0; + + for (var key in nodeContent) { + + if (key == 'group' || key == 'data') { + continue; + } + + fieldName[i] = key; + i++; + values[j] = nodeContent[key]; + j++; + + } + + + var childNodes = node.outgoers().nodes(); + var childNum = childNodes.length; + + var parentNodes = node.incomers().nodes(); + var parentNum = parentNodes.length; + var degree = node.degree(); + + var table = createTable(fieldName, values, degree, parentNum, childNum); + + $('#nodeInfoDiv').html("

Node Description

" + table); + for (var i = 0; i < fieldName.length; i++) { + + if (isValidUrl(values[i])) { + + var e = document.createElement("div"); + e.id = "linkDiv"; + $('#nodeInfoDiv').append(e); + + var url = values[i]; + + document.getElementById("linkDiv").innerHTML += "
" + fieldName[i] + "
"; + $('') + : '') + ); +} +function tt_MkMainDivDom() +{ + var el = document.createElement("div"); + if(el) + el.id = "WzTtDiV"; + return el; +} +function tt_GetMainDivRefs() +{ + tt_aElt[0] = tt_GetElt("WzTtDiV"); + if(tt_ie56 && tt_aElt[0]) + { + tt_aElt[tt_aElt.length - 1] = tt_GetElt("WzTtIfRm"); + if(!tt_aElt[tt_aElt.length - 1]) + tt_aElt[0] = null; + } + if(tt_aElt[0]) + { + var css = tt_aElt[0].style; + + css.visibility = "hidden"; + css.position = "absolute"; + css.overflow = "hidden"; + return true; + } + return false; +} +function tt_ResetMainDiv() +{ + tt_SetTipPos(0, 0); + tt_aElt[0].innerHTML = ""; + tt_aElt[0].style.width = "0px"; + tt_h = 0; +} +function tt_IsW3cBox() +{ + var css = tt_aElt[0].style; + + css.padding = "10px"; + css.width = "40px"; + tt_bBoxOld = (tt_GetDivW(tt_aElt[0]) == 40); + css.padding = "0px"; + tt_ResetMainDiv(); +} +function tt_OpaSupport() +{ + var css = tt_body.style; + + tt_flagOpa = (typeof(css.KhtmlOpacity) != tt_u) ? 2 + : (typeof(css.KHTMLOpacity) != tt_u) ? 3 + : (typeof(css.MozOpacity) != tt_u) ? 4 + : (typeof(css.opacity) != tt_u) ? 5 + : (typeof(css.filter) != tt_u) ? 1 + : 0; +} +// Ported from http://dean.edwards.name/weblog/2006/06/again/ +// (Dean Edwards et al.) +function tt_SetOnloadFnc() +{ + tt_AddEvtFnc(document, "DOMContentLoaded", tt_HideSrcTags); + tt_AddEvtFnc(window, "load", tt_HideSrcTags); + if(tt_body.attachEvent) + tt_body.attachEvent("onreadystatechange", + function() { + if(tt_body.readyState == "complete") + tt_HideSrcTags(); + } ); + if(/WebKit|KHTML/i.test(navigator.userAgent)) + { + var t = setInterval(function() { + if(/loaded|complete/.test(document.readyState)) + { + clearInterval(t); + tt_HideSrcTags(); + } + }, 10); + } +} +function tt_HideSrcTags() +{ + if(!window.tt_HideSrcTags || window.tt_HideSrcTags.done) + return; + window.tt_HideSrcTags.done = true; + if(!tt_HideSrcTagsRecurs(tt_body)) + tt_Err("There are HTML elements to be converted to tooltips.\nIf you" + + " want these HTML elements to be automatically hidden, you" + + " must edit wz_tooltip.js, and set TagsToTip in the global" + + " tooltip configuration to true.", true); +} +function tt_HideSrcTagsRecurs(dad) +{ + var ovr, asT2t; + // Walk the DOM tree for tags that have an onmouseover or onclick attribute + // containing a TagToTip('...') call. + // (.childNodes first since .children is bugous in Safari) + var a = dad.childNodes || dad.children || null; + + for(var i = a ? a.length : 0; i;) + {--i; + if(!tt_HideSrcTagsRecurs(a[i])) + return false; + ovr = a[i].getAttribute ? (a[i].getAttribute("onmouseover") || a[i].getAttribute("onclick")) + : (typeof a[i].onmouseover == "function") ? (a[i].onmouseover || a[i].onclick) + : null; + if(ovr) + { + asT2t = ovr.toString().match(/TagToTip\s*\(\s*'[^'.]+'\s*[\),]/); + if(asT2t && asT2t.length) + { + if(!tt_HideSrcTag(asT2t[0])) + return false; + } + } + } + return true; +} +function tt_HideSrcTag(sT2t) +{ + var id, el; + + // The ID passed to the found TagToTip() call identifies an HTML element + // to be converted to a tooltip, so hide that element + id = sT2t.replace(/.+'([^'.]+)'.+/, "$1"); + el = tt_GetElt(id); + if(el) + { + if(tt_Debug && !TagsToTip) + return false; + else + el.style.display = "none"; + } + else + tt_Err("Invalid ID\n'" + id + "'\npassed to TagToTip()." + + " There exists no HTML element with that ID.", true); + return true; +} +function tt_Tip(arg, t2t) +{ + if(!tt_db || (tt_iState & 0x8)) + return; + if(tt_iState) + tt_Hide(); + if(!tt_Enabled) + return; + tt_t2t = t2t; + if(!tt_ReadCmds(arg)) + return; + tt_iState = 0x1 | 0x4; + tt_AdaptConfig1(); + tt_MkTipContent(arg); + tt_MkTipSubDivs(); + tt_FormatTip(); + tt_bJmpVert = false; + tt_bJmpHorz = false; + tt_maxPosX = tt_GetClientW() + tt_GetScrollX() - tt_w - 1; + tt_maxPosY = tt_GetClientH() + tt_GetScrollY() - tt_h - 1; + tt_AdaptConfig2(); + // Ensure the tip be shown and positioned before the first onmousemove + tt_OverInit(); + tt_ShowInit(); + tt_Move(); +} +function tt_ReadCmds(a) +{ + var i; + + // First load the global config values, to initialize also values + // for which no command is passed + i = 0; + for(var j in config) + tt_aV[i++] = config[j]; + // Then replace each cached config value for which a command is + // passed (ensure the # of command args plus value args be even) + if(a.length & 1) + { + for(i = a.length - 1; i > 0; i -= 2) + tt_aV[a[i - 1]] = a[i]; + return true; + } + tt_Err("Incorrect call of Tip() or TagToTip().\n" + + "Each command must be followed by a value.", true); + return false; +} +function tt_AdaptConfig1() +{ + tt_ExtCallFncs(0, "LoadConfig"); + // Inherit unspecified title formattings from body + if(!tt_aV[TITLEBGCOLOR].length) + tt_aV[TITLEBGCOLOR] = tt_aV[BORDERCOLOR]; + if(!tt_aV[TITLEFONTCOLOR].length) + tt_aV[TITLEFONTCOLOR] = tt_aV[BGCOLOR]; + if(!tt_aV[TITLEFONTFACE].length) + tt_aV[TITLEFONTFACE] = tt_aV[FONTFACE]; + if(!tt_aV[TITLEFONTSIZE].length) + tt_aV[TITLEFONTSIZE] = tt_aV[FONTSIZE]; + if(tt_aV[CLOSEBTN]) + { + // Use title colours for non-specified closebutton colours + if(!tt_aV[CLOSEBTNCOLORS]) + tt_aV[CLOSEBTNCOLORS] = new Array("", "", "", ""); + for(var i = 4; i;) + {--i; + if(!tt_aV[CLOSEBTNCOLORS][i].length) + tt_aV[CLOSEBTNCOLORS][i] = (i & 1) ? tt_aV[TITLEFONTCOLOR] : tt_aV[TITLEBGCOLOR]; + } + // Enforce titlebar be shown + if(!tt_aV[TITLE].length) + tt_aV[TITLE] = " "; + } + // Circumvents broken display of images and fade-in flicker in Geckos < 1.8 + if(tt_aV[OPACITY] == 100 && typeof tt_aElt[0].style.MozOpacity != tt_u && !Array.every) + tt_aV[OPACITY] = 99; + // Smartly shorten the delay for fade-in tooltips + if(tt_aV[FADEIN] && tt_flagOpa && tt_aV[DELAY] > 100) + tt_aV[DELAY] = Math.max(tt_aV[DELAY] - tt_aV[FADEIN], 100); +} +function tt_AdaptConfig2() +{ + if(tt_aV[CENTERMOUSE]) + { + tt_aV[OFFSETX] -= ((tt_w - (tt_aV[SHADOW] ? tt_aV[SHADOWWIDTH] : 0)) >> 1); + tt_aV[JUMPHORZ] = false; + } +} +// Expose content globally so extensions can modify it +function tt_MkTipContent(a) +{ + if(tt_t2t) + { + if(tt_aV[COPYCONTENT]) + tt_sContent = tt_t2t.innerHTML; + else + tt_sContent = ""; + } + else + tt_sContent = a[0]; + tt_ExtCallFncs(0, "CreateContentString"); +} +function tt_MkTipSubDivs() +{ + var sCss = 'position:relative;margin:0px;padding:0px;border-width:0px;left:0px;top:0px;line-height:normal;width:auto;', + sTbTrTd = ' cellspacing="0" cellpadding="0" border="0" style="' + sCss + '">' + + '' + + tt_aV[TITLE] + + '' + + (tt_aV[CLOSEBTN] ? + ('') + : '') + + '
' + + '' + + tt_aV[CLOSEBTNTEXT] + + '
') + : '') + + '
' + + '' + + tt_sContent + + '
' + + (tt_aV[SHADOW] + ? ('
' + + '
') + : '') + ); + tt_GetSubDivRefs(); + // Convert DOM node to tip + if(tt_t2t && !tt_aV[COPYCONTENT]) + tt_El2Tip(); + tt_ExtCallFncs(0, "SubDivsCreated"); +} +function tt_GetSubDivRefs() +{ + var aId = new Array("WzTiTl", "WzTiTlTb", "WzTiTlI", "WzClOsE", "WzBoDy", "WzBoDyI", "WzTtShDwB", "WzTtShDwR"); + + for(var i = aId.length; i; --i) + tt_aElt[i] = tt_GetElt(aId[i - 1]); +} +function tt_FormatTip() +{ + var css, w, h, pad = tt_aV[PADDING], padT, wBrd = tt_aV[BORDERWIDTH], + iOffY, iOffSh, iAdd = (pad + wBrd) << 1; + + //--------- Title DIV ---------- + if(tt_aV[TITLE].length) + { + padT = tt_aV[TITLEPADDING]; + css = tt_aElt[1].style; + css.background = tt_aV[TITLEBGCOLOR]; + css.paddingTop = css.paddingBottom = padT + "px"; + css.paddingLeft = css.paddingRight = (padT + 2) + "px"; + css = tt_aElt[3].style; + css.color = tt_aV[TITLEFONTCOLOR]; + if(tt_aV[WIDTH] == -1) + css.whiteSpace = "nowrap"; + css.fontFamily = tt_aV[TITLEFONTFACE]; + css.fontSize = tt_aV[TITLEFONTSIZE]; + css.fontWeight = "bold"; + css.textAlign = tt_aV[TITLEALIGN]; + // Close button DIV + if(tt_aElt[4]) + { + css = tt_aElt[4].style; + css.background = tt_aV[CLOSEBTNCOLORS][0]; + css.color = tt_aV[CLOSEBTNCOLORS][1]; + css.fontFamily = tt_aV[TITLEFONTFACE]; + css.fontSize = tt_aV[TITLEFONTSIZE]; + css.fontWeight = "bold"; + } + if(tt_aV[WIDTH] > 0) + tt_w = tt_aV[WIDTH]; + else + { + tt_w = tt_GetDivW(tt_aElt[3]) + tt_GetDivW(tt_aElt[4]); + // Some spacing between title DIV and closebutton + if(tt_aElt[4]) + tt_w += pad; + // Restrict auto width to max width + if(tt_aV[WIDTH] < -1 && tt_w > -tt_aV[WIDTH]) + tt_w = -tt_aV[WIDTH]; + } + // Ensure the top border of the body DIV be covered by the title DIV + iOffY = -wBrd; + } + else + { + tt_w = 0; + iOffY = 0; + } + + //-------- Body DIV ------------ + css = tt_aElt[5].style; + css.top = iOffY + "px"; + if(wBrd) + { + css.borderColor = tt_aV[BORDERCOLOR]; + css.borderStyle = tt_aV[BORDERSTYLE]; + css.borderWidth = wBrd + "px"; + } + if(tt_aV[BGCOLOR].length) + css.background = tt_aV[BGCOLOR]; + if(tt_aV[BGIMG].length) + css.backgroundImage = "url(" + tt_aV[BGIMG] + ")"; + css.padding = pad + "px"; + css.textAlign = tt_aV[TEXTALIGN]; + if(tt_aV[HEIGHT]) + { + css.overflow = "auto"; + if(tt_aV[HEIGHT] > 0) + css.height = (tt_aV[HEIGHT] + iAdd) + "px"; + else + tt_h = iAdd - tt_aV[HEIGHT]; + } + // TD inside body DIV + css = tt_aElt[6].style; + css.color = tt_aV[FONTCOLOR]; + css.fontFamily = tt_aV[FONTFACE]; + css.fontSize = tt_aV[FONTSIZE]; + css.fontWeight = tt_aV[FONTWEIGHT]; + css.textAlign = tt_aV[TEXTALIGN]; + if(tt_aV[WIDTH] > 0) + w = tt_aV[WIDTH]; + // Width like title (if existent) + else if(tt_aV[WIDTH] == -1 && tt_w) + w = tt_w; + else + { + // Measure width of the body's inner TD, as some browsers would expand + // the container and outer body DIV to 100% + w = tt_GetDivW(tt_aElt[6]); + // Restrict auto width to max width + if(tt_aV[WIDTH] < -1 && w > -tt_aV[WIDTH]) + w = -tt_aV[WIDTH]; + } + if(w > tt_w) + tt_w = w; + tt_w += iAdd; + + //--------- Shadow DIVs ------------ + if(tt_aV[SHADOW]) + { + tt_w += tt_aV[SHADOWWIDTH]; + iOffSh = Math.floor((tt_aV[SHADOWWIDTH] * 4) / 3); + // Bottom shadow + css = tt_aElt[7].style; + css.top = iOffY + "px"; + css.left = iOffSh + "px"; + css.width = (tt_w - iOffSh - tt_aV[SHADOWWIDTH]) + "px"; + css.height = tt_aV[SHADOWWIDTH] + "px"; + css.background = tt_aV[SHADOWCOLOR]; + // Right shadow + css = tt_aElt[8].style; + css.top = iOffSh + "px"; + css.left = (tt_w - tt_aV[SHADOWWIDTH]) + "px"; + css.width = tt_aV[SHADOWWIDTH] + "px"; + css.background = tt_aV[SHADOWCOLOR]; + } + else + iOffSh = 0; + + //-------- Container DIV ------- + tt_SetTipOpa(tt_aV[FADEIN] ? 0 : tt_aV[OPACITY]); + tt_FixSize(iOffY, iOffSh); +} +// Fixate the size so it can't dynamically change while the tooltip is moving. +function tt_FixSize(iOffY, iOffSh) +{ + var wIn, wOut, h, add, pad = tt_aV[PADDING], wBrd = tt_aV[BORDERWIDTH], i; + + tt_aElt[0].style.width = tt_w + "px"; + tt_aElt[0].style.pixelWidth = tt_w; + wOut = tt_w - ((tt_aV[SHADOW]) ? tt_aV[SHADOWWIDTH] : 0); + // Body + wIn = wOut; + if(!tt_bBoxOld) + wIn -= (pad + wBrd) << 1; + tt_aElt[5].style.width = wIn + "px"; + // Title + if(tt_aElt[1]) + { + wIn = wOut - ((tt_aV[TITLEPADDING] + 2) << 1); + if(!tt_bBoxOld) + wOut = wIn; + tt_aElt[1].style.width = wOut + "px"; + tt_aElt[2].style.width = wIn + "px"; + } + // Max height specified + if(tt_h) + { + h = tt_GetDivH(tt_aElt[5]); + if(h > tt_h) + { + if(!tt_bBoxOld) + tt_h -= (pad + wBrd) << 1; + tt_aElt[5].style.height = tt_h + "px"; + } + } + tt_h = tt_GetDivH(tt_aElt[0]) + iOffY; + // Right shadow + if(tt_aElt[8]) + tt_aElt[8].style.height = (tt_h - iOffSh) + "px"; + i = tt_aElt.length - 1; + if(tt_aElt[i]) + { + tt_aElt[i].style.width = tt_w + "px"; + tt_aElt[i].style.height = tt_h + "px"; + } +} +function tt_DeAlt(el) +{ + var aKid; + + if(el) + { + if(el.alt) + el.alt = ""; + if(el.title) + el.title = ""; + aKid = el.childNodes || el.children || null; + if(aKid) + { + for(var i = aKid.length; i;) + tt_DeAlt(aKid[--i]); + } + } +} +// This hack removes the native tooltips over links in Opera +function tt_OpDeHref(el) +{ + if(!tt_op) + return; + if(tt_elDeHref) + tt_OpReHref(); + while(el) + { + if(el.hasAttribute && el.hasAttribute("href")) + { + el.t_href = el.getAttribute("href"); + el.t_stats = window.status; + el.removeAttribute("href"); + el.style.cursor = "hand"; + tt_AddEvtFnc(el, "mousedown", tt_OpReHref); + window.status = el.t_href; + tt_elDeHref = el; + break; + } + el = tt_GetDad(el); + } +} +function tt_OpReHref() +{ + if(tt_elDeHref) + { + tt_elDeHref.setAttribute("href", tt_elDeHref.t_href); + tt_RemEvtFnc(tt_elDeHref, "mousedown", tt_OpReHref); + window.status = tt_elDeHref.t_stats; + tt_elDeHref = null; + } +} +function tt_El2Tip() +{ + var css = tt_t2t.style; + + // Store previous positioning + tt_t2t.t_cp = css.position; + tt_t2t.t_cl = css.left; + tt_t2t.t_ct = css.top; + tt_t2t.t_cd = css.display; + // Store the tag's parent element so we can restore that DOM branch + // when the tooltip is being hidden + tt_t2tDad = tt_GetDad(tt_t2t); + tt_MovDomNode(tt_t2t, tt_t2tDad, tt_aElt[6]); + css.display = "block"; + css.position = "static"; + css.left = css.top = css.marginLeft = css.marginTop = "0px"; +} +function tt_UnEl2Tip() +{ + // Restore positioning and display + var css = tt_t2t.style; + + css.display = tt_t2t.t_cd; + tt_MovDomNode(tt_t2t, tt_GetDad(tt_t2t), tt_t2tDad); + css.position = tt_t2t.t_cp; + css.left = tt_t2t.t_cl; + css.top = tt_t2t.t_ct; + tt_t2tDad = null; +} +function tt_OverInit() +{ + if(window.event) + tt_over = window.event.target || window.event.srcElement; + else + tt_over = tt_ovr_; + tt_DeAlt(tt_over); + tt_OpDeHref(tt_over); +} +function tt_ShowInit() +{ + tt_tShow.Timer("tt_Show()", tt_aV[DELAY], true); + if(tt_aV[CLICKCLOSE] || tt_aV[CLICKSTICKY]) + tt_AddEvtFnc(document, "mouseup", tt_OnLClick); +} +function tt_Show() +{ + var css = tt_aElt[0].style; + + // Override the z-index of the topmost wz_dragdrop.js D&D item + css.zIndex = Math.max((window.dd && dd.z) ? (dd.z + 2) : 0, 1010); + if(tt_aV[STICKY] || !tt_aV[FOLLOWMOUSE]) + tt_iState &= ~0x4; + if(tt_aV[EXCLUSIVE]) + tt_iState |= 0x8; + if(tt_aV[DURATION] > 0) + tt_tDurt.Timer("tt_HideInit()", tt_aV[DURATION], true); + tt_ExtCallFncs(0, "Show") + css.visibility = "visible"; + tt_iState |= 0x2; + if(tt_aV[FADEIN]) + tt_Fade(0, 0, tt_aV[OPACITY], Math.round(tt_aV[FADEIN] / tt_aV[FADEINTERVAL])); + tt_ShowIfrm(); +} +function tt_ShowIfrm() +{ + if(tt_ie56) + { + var ifrm = tt_aElt[tt_aElt.length - 1]; + if(ifrm) + { + var css = ifrm.style; + css.zIndex = tt_aElt[0].style.zIndex - 1; + css.display = "block"; + } + } +} +function tt_Move(e) +{ + if(e) + tt_ovr_ = e.target || e.srcElement; + e = e || window.event; + if(e) + { + tt_musX = tt_GetEvtX(e); + tt_musY = tt_GetEvtY(e); + } + if(tt_iState & 0x4) + { + // Prevent jam of mousemove events + if(!tt_op && !tt_ie) + { + if(tt_bWait) + return; + tt_bWait = true; + tt_tWaitMov.Timer("tt_bWait = false;", 1, true); + } + if(tt_aV[FIX]) + { + tt_iState &= ~0x4; + tt_PosFix(); + } + else if(!tt_ExtCallFncs(e, "MoveBefore")) + tt_SetTipPos(tt_Pos(0), tt_Pos(1)); + tt_ExtCallFncs([tt_musX, tt_musY], "MoveAfter") + } +} +function tt_Pos(iDim) +{ + var iX, bJmpMod, cmdAlt, cmdOff, cx, iMax, iScrl, iMus, bJmp; + + // Map values according to dimension to calculate + if(iDim) + { + bJmpMod = tt_aV[JUMPVERT]; + cmdAlt = ABOVE; + cmdOff = OFFSETY; + cx = tt_h; + iMax = tt_maxPosY; + iScrl = tt_GetScrollY(); + iMus = tt_musY; + bJmp = tt_bJmpVert; + } + else + { + bJmpMod = tt_aV[JUMPHORZ]; + cmdAlt = LEFT; + cmdOff = OFFSETX; + cx = tt_w; + iMax = tt_maxPosX; + iScrl = tt_GetScrollX(); + iMus = tt_musX; + bJmp = tt_bJmpHorz; + } + if(bJmpMod) + { + if(tt_aV[cmdAlt] && (!bJmp || tt_CalcPosAlt(iDim) >= iScrl + 16)) + iX = tt_PosAlt(iDim); + else if(!tt_aV[cmdAlt] && bJmp && tt_CalcPosDef(iDim) > iMax - 16) + iX = tt_PosAlt(iDim); + else + iX = tt_PosDef(iDim); + } + else + { + iX = iMus; + if(tt_aV[cmdAlt]) + iX -= cx + tt_aV[cmdOff] - (tt_aV[SHADOW] ? tt_aV[SHADOWWIDTH] : 0); + else + iX += tt_aV[cmdOff]; + } + // Prevent tip from extending past clientarea boundary + if(iX > iMax) + iX = bJmpMod ? tt_PosAlt(iDim) : iMax; + // In case of insufficient space on both sides, ensure the left/upper part + // of the tip be visible + if(iX < iScrl) + iX = bJmpMod ? tt_PosDef(iDim) : iScrl; + return iX; +} +function tt_PosDef(iDim) +{ + if(iDim) + tt_bJmpVert = tt_aV[ABOVE]; + else + tt_bJmpHorz = tt_aV[LEFT]; + return tt_CalcPosDef(iDim); +} +function tt_PosAlt(iDim) +{ + if(iDim) + tt_bJmpVert = !tt_aV[ABOVE]; + else + tt_bJmpHorz = !tt_aV[LEFT]; + return tt_CalcPosAlt(iDim); +} +function tt_CalcPosDef(iDim) +{ + return iDim ? (tt_musY + tt_aV[OFFSETY]) : (tt_musX + tt_aV[OFFSETX]); +} +function tt_CalcPosAlt(iDim) +{ + var cmdOff = iDim ? OFFSETY : OFFSETX; + var dx = tt_aV[cmdOff] - (tt_aV[SHADOW] ? tt_aV[SHADOWWIDTH] : 0); + if(tt_aV[cmdOff] > 0 && dx <= 0) + dx = 1; + return((iDim ? (tt_musY - tt_h) : (tt_musX - tt_w)) - dx); +} +function tt_PosFix() +{ + var iX, iY; + + if(typeof(tt_aV[FIX][0]) == "number") + { + iX = tt_aV[FIX][0]; + iY = tt_aV[FIX][1]; + } + else + { + if(typeof(tt_aV[FIX][0]) == "string") + el = tt_GetElt(tt_aV[FIX][0]); + // First slot in array is direct reference to HTML element + else + el = tt_aV[FIX][0]; + iX = tt_aV[FIX][1]; + iY = tt_aV[FIX][2]; + // By default, vert pos is related to bottom edge of HTML element + if(!tt_aV[ABOVE] && el) + iY += tt_GetDivH(el); + for(; el; el = el.offsetParent) + { + iX += el.offsetLeft || 0; + iY += el.offsetTop || 0; + } + } + // For a fixed tip positioned above the mouse, use the bottom edge as anchor + // (recommended by Christophe Rebeschini, 31.1.2008) + if(tt_aV[ABOVE]) + iY -= tt_h; + tt_SetTipPos(iX, iY); +} +function tt_Fade(a, now, z, n) +{ + if(n) + { + now += Math.round((z - now) / n); + if((z > a) ? (now >= z) : (now <= z)) + now = z; + else + tt_tFade.Timer( + "tt_Fade(" + + a + "," + now + "," + z + "," + (n - 1) + + ")", + tt_aV[FADEINTERVAL], + true + ); + } + now ? tt_SetTipOpa(now) : tt_Hide(); +} +function tt_SetTipOpa(opa) +{ + // To circumvent the opacity nesting flaws of IE, we set the opacity + // for each sub-DIV separately, rather than for the container DIV. + tt_SetOpa(tt_aElt[5], opa); + if(tt_aElt[1]) + tt_SetOpa(tt_aElt[1], opa); + if(tt_aV[SHADOW]) + { + opa = Math.round(opa * 0.8); + tt_SetOpa(tt_aElt[7], opa); + tt_SetOpa(tt_aElt[8], opa); + } +} +function tt_OnCloseBtnOver(iOver) +{ + var css = tt_aElt[4].style; + + iOver <<= 1; + css.background = tt_aV[CLOSEBTNCOLORS][iOver]; + css.color = tt_aV[CLOSEBTNCOLORS][iOver + 1]; +} +function tt_OnLClick(e) +{ + // Ignore right-clicks + e = e || window.event; + if(!((e.button && e.button & 2) || (e.which && e.which == 3))) + { + if(tt_aV[CLICKSTICKY] && (tt_iState & 0x4)) + { + tt_aV[STICKY] = true; + tt_iState &= ~0x4; + } + else if(tt_aV[CLICKCLOSE]) + tt_HideInit(); + } +} +function tt_Int(x) +{ + var y; + + return(isNaN(y = parseInt(x)) ? 0 : y); +} +Number.prototype.Timer = function(s, iT, bUrge) +{ + if(!this.value || bUrge) + this.value = window.setTimeout(s, iT); +} +Number.prototype.EndTimer = function() +{ + if(this.value) + { + window.clearTimeout(this.value); + this.value = 0; + } +} +function tt_GetWndCliSiz(s) +{ + var db, y = window["inner" + s], sC = "client" + s, sN = "number"; + if(typeof y == sN) + { + var y2; + return( + // Gecko or Opera with scrollbar + // ... quirks mode + ((db = document.body) && typeof(y2 = db[sC]) == sN && y2 && y2 <= y) ? y2 + // ... strict mode + : ((db = document.documentElement) && typeof(y2 = db[sC]) == sN && y2 && y2 <= y) ? y2 + // No scrollbar, or clientarea size == 0, or other browser (KHTML etc.) + : y + ); + } + // IE + return( + // document.documentElement.client+s functional, returns > 0 + ((db = document.documentElement) && (y = db[sC])) ? y + // ... not functional, in which case document.body.client+s + // is the clientarea size, fortunately + : document.body[sC] + ); +} +function tt_SetOpa(el, opa) +{ + var css = el.style; + + tt_opa = opa; + if(tt_flagOpa == 1) + { + if(opa < 100) + { + // Hacks for bugs of IE: + // 1.) Once a CSS filter has been applied, fonts are no longer + // anti-aliased, so we store the previous 'non-filter' to be + // able to restore it + if(typeof(el.filtNo) == tt_u) + el.filtNo = css.filter; + // 2.) A DIV cannot be made visible in a single step if an + // opacity < 100 has been applied while the DIV was hidden + var bVis = css.visibility != "hidden"; + // 3.) In IE6, applying an opacity < 100 has no effect if the + // element has no layout (position, size, zoom, ...) + css.zoom = "100%"; + if(!bVis) + css.visibility = "visible"; + css.filter = "alpha(opacity=" + opa + ")"; + if(!bVis) + css.visibility = "hidden"; + } + else if(typeof(el.filtNo) != tt_u) + // Restore 'non-filter' + css.filter = el.filtNo; + } + else + { + opa /= 100.0; + switch(tt_flagOpa) + { + case 2: + css.KhtmlOpacity = opa; break; + case 3: + css.KHTMLOpacity = opa; break; + case 4: + css.MozOpacity = opa; break; + case 5: + css.opacity = opa; break; + } + } +} +function tt_Err(sErr, bIfDebug) +{ + if(tt_Debug || !bIfDebug) + alert("Tooltip Script Error Message:\n\n" + sErr); +} + +//============ EXTENSION (PLUGIN) MANAGER ===============// +function tt_ExtCmdEnum() +{ + var s; + + // Add new command(s) to the commands enum + for(var i in config) + { + s = "window." + i.toString().toUpperCase(); + if(eval("typeof(" + s + ") == tt_u")) + { + eval(s + " = " + tt_aV.length); + tt_aV[tt_aV.length] = null; + } + } +} +function tt_ExtCallFncs(arg, sFnc) +{ + var b = false; + for(var i = tt_aExt.length; i;) + {--i; + var fnc = tt_aExt[i]["On" + sFnc]; + // Call the method the extension has defined for this event + if(fnc && fnc(arg)) + b = true; + } + return b; +} + +tt_Init(); diff --git a/config/plugins/visualizations/graphviz/templates/graphviz.mako b/config/plugins/visualizations/graphviz/templates/graphviz.mako new file mode 100644 index 00000000000..4abf7300cae --- /dev/null +++ b/config/plugins/visualizations/graphviz/templates/graphviz.mako @@ -0,0 +1,171 @@ + + + + + + + + ${hda.name} | ${visualization_name} +<% + root = h.url_for( '/' ) +%> + + ${h.stylesheet_link( root + 'plugins/visualizations/graphviz/static/css/style.css' )} + + ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/jquery.qtip.js' )} + ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/cytoscape.min.js' )} + ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/collapse.js' )} + ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/toolPanelFunctions.js' )} + ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/graphVis.js' )} + + + +## ---------------------------------------------------------------------------- + + ${h.javascript_link( root + 'plugins/visualizations/graphviz/static/js/wz_tooltip.js' )} + + +
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+
+ « + + + From 1fa7c103865d12d76e7450ed4eb4404498d04d71 Mon Sep 17 00:00:00 2001 From: Dave B Date: Wed, 5 Aug 2015 16:53:34 -0400 Subject: [PATCH 003/178] Populate env.sh files with X_ROOT_DIR. Where X is tool_dependency.name.upper() --- .../galaxy_install/tool_dependencies/recipe/step_handler.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py index 9f77e2cf9b2..a73172240e2 100755 --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -915,6 +915,10 @@ class SetEnvironment( RecipeStep ): # Currently the only action supported in this category is "environment_variable". cmds = install_environment.environment_commands( 'set_environment' ) env_var_dicts = action_dict.get( 'environment_variable', [] ) + root_dir_dict = dict( action='set_to', + name='%s_ROOT_DIR' % tool_dependency.name.upper(), + value=install_environment.install_dir ) + env_var_dicts.append( root_dir_dict ) for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. env_var_dict = self.handle_environment_variables( install_environment=install_environment, From 5810a853b0370d09a3f3eb9fc80e8e90bfe8c791 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Tue, 18 Aug 2015 13:58:30 -0400 Subject: [PATCH 004/178] Move manual_builds.txt to manual_builds.txt.sample to allow for customization --- .gitignore | 1 + scripts/common_startup.sh | 1 + .../shared/ucsc/{manual_builds.txt => manual_builds.txt.sample} | 0 3 files changed, 2 insertions(+) rename tool-data/shared/ucsc/{manual_builds.txt => manual_builds.txt.sample} (100%) diff --git a/.gitignore b/.gitignore index e43721a088c..1bb752fda18 100644 --- a/.gitignore +++ b/.gitignore @@ -76,6 +76,7 @@ tool-data/shared/igv/igv_build_sites.txt tool-data/shared/rviewer/rviewer_build_sites.txt tool-data/shared/ncbi/builds.txt tool-data/shared/ucsc/builds.txt +tool-data/shared/ucsc/manual_builds.txt tool-data/shared/ensembl/builds.txt tool-data/shared/ucsc/publicbuilds.txt tool-data/shared/ucsc/ucsc_build_sites.txt diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh index 34c7e261500..a0ed759db95 100755 --- a/scripts/common_startup.sh +++ b/scripts/common_startup.sh @@ -16,6 +16,7 @@ SAMPLES=" config/shed_data_manager_conf.xml.sample lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/manual_builds.txt.sample tool-data/shared/ucsc/ucsc_build_sites.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample diff --git a/tool-data/shared/ucsc/manual_builds.txt b/tool-data/shared/ucsc/manual_builds.txt.sample similarity index 100% rename from tool-data/shared/ucsc/manual_builds.txt rename to tool-data/shared/ucsc/manual_builds.txt.sample From 785f81989627db26b3799b0e6d5123213fcec9e4 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 26 Aug 2015 17:11:28 -0500 Subject: [PATCH 005/178] Add developer documentation to docs --- doc/source/dev/faq.rst | 12 ++++++++++++ doc/source/dev/index.rst | 13 +++++++++++++ doc/source/index.rst | 2 ++ 3 files changed, 27 insertions(+) create mode 100644 doc/source/dev/faq.rst create mode 100644 doc/source/dev/index.rst diff --git a/doc/source/dev/faq.rst b/doc/source/dev/faq.rst new file mode 100644 index 00000000000..d8883d7e82c --- /dev/null +++ b/doc/source/dev/faq.rst @@ -0,0 +1,12 @@ +How Do I... +=========== + +This section contains a number of smaller topics with links and examples meant +to provide relatively concrete answers for specific tool development scenarios. + +... interact with the Galaxy codebase interactively? +---------------------------------------------------- + +This can be done with either IPython/Jupyter or a plain python console, depending on your preferences:: + + python -i scripts/db_shell.py diff --git a/doc/source/dev/index.rst b/doc/source/dev/index.rst new file mode 100644 index 00000000000..39e83526283 --- /dev/null +++ b/doc/source/dev/index.rst @@ -0,0 +1,13 @@ +Developer Documentation +======================= + +There are two primary areas of documentation developers will be interested in: + +- `Codebase Documentation`_ for developers of Galaxy +- `API Documentation`_ for developers of third party tools interacting with Galaxy + +Additionally there is an `FAQ`_ document for new Galaxy developers answering common "How Do I..." questions. + +.. _Codebase Documentation: ../lib/modules.html +.. _API Documentation: ../api_doc.html +.. _FAQ: faq.html diff --git a/doc/source/index.rst b/doc/source/index.rst index a2d2fbf1bf2..04b95d047e4 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -36,6 +36,8 @@ Contents Releases + Developer Documentation + Indices and tables ================== From 86c3175fcda4ff85505ecfcd78cf2b302909a7a7 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 26 Aug 2015 17:36:14 -0500 Subject: [PATCH 006/178] Extract quickstart, reorg GX/TS Doc index --- doc/source/_api_quickstart.rst | 186 +++++++++++++++++++++++++++++++ doc/source/api/quickstart.rst | 185 +++++++++++++++++++++++++++++++ doc/source/api_doc.rst | 193 +-------------------------------- doc/source/ts_api_doc.rst | 10 +- 4 files changed, 381 insertions(+), 193 deletions(-) create mode 100644 doc/source/_api_quickstart.rst create mode 100644 doc/source/api/quickstart.rst diff --git a/doc/source/_api_quickstart.rst b/doc/source/_api_quickstart.rst new file mode 100644 index 00000000000..309850b5089 --- /dev/null +++ b/doc/source/_api_quickstart.rst @@ -0,0 +1,186 @@ +Quickstart +========== + +Log in as your user, navigate to the API Keys page in the User menu, and +generate a new API key. Make a note of the API key, and then pull up a +terminal. Now we'll use the display.py script in your galaxy/scripts/api +directory for a short example:: + + % ./display.py my_key http://localhost:4096/api/histories + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc + name: Unnamed history + id: 8c49be448cfe29bc + #2: /api/histories/33b43b4e7093c91f + name: output test + id: 33b43b4e7093c91f + +The result is a Collection of the histories of the user specified by the API +key (you). To look at the details of a particular history, say #1 above, do +the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc + Member Information + ------------------ + state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} + state: ok + contents_url: /api/histories/8c49be448cfe29bc/contents + id: 8c49be448cfe29bc + name: Unnamed history + +This gives detailed information about the specific member in question, in this +case the History. To view history contents, do the following:: + + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + name: Pasted Entry + type: file + id: 6f91353f3eb0fa4a + +What we have here is another Collection of items containing all of the datasets +in this particular history. Finally, to view details of a particular dataset +in this collection, execute the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + Member Information + ------------------ + misc_blurb: 1 line + name: Pasted Entry + data_type: txt + deleted: False + file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat + state: ok + download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt + visible: True + genome_build: ? + model_class: HistoryDatasetAssociation + file_size: 17 + metadata_data_lines: 1 + id: 6f91353f3eb0fa4a + misc_info: uploaded txt file + metadata_dbkey: ? + +And now you've successfully used the API to request and select a history, +browse the contents of that history, and then look at detailed information +about a particular dataset. + +For a more comprehensive Data Library example, set the following option in your +galaxy.ini as well, and restart galaxy again:: + + admin_users = you@example.org + library_import_dir = /path/to/some/directory + +In the directory you specified for 'library_import_dir', create some +subdirectories, and put (or symlink) files to import into Galaxy into those +subdirectories. + +In Galaxy, create an account that matches the address you put in 'admin_users', +then browse to that user's preferences and generate a new API Key. Copy the +key to your clipboard and then use these scripts:: + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + + 0 elements in collection + + % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' + Response + -------- + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 + Member Information + ------------------ + synopsis: None + contents_url: /api/libraries/f3f73e481f432006/contents + description: API Test Library + name: api_test + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + + % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' + Response + -------- + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: api_test_folder1 + id: 28202595c0d2591fa4f9089d2303fd89 + + % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 + Response + -------- + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: 2.bed + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: 3.bed + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: /api_test_folder1 + type: folder + id: 28202595c0d2591fa4f9089d2303fd89 + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: /api_test_folder1/2.bed + type: file + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: /api_test_folder1/3.bed + type: file + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + Member Information + ------------------ + misc_blurb: 68 regions + metadata_endCol: 3 + data_type: bed + metadata_columns: 6 + metadata_nameCol: 4 + uploaded_by: nate@... + metadata_strandCol: 6 + name: 2.bed + genome_build: hg19 + metadata_comment_lines: None + metadata_startCol: 2 + metadata_chromCol: 1 + file_size: 4272 + metadata_data_lines: 68 + message: + metadata_dbkey: hg19 + misc_info: uploaded bed file + date_uploaded: 2010-06-22T17:01:51.266119 + metadata_column_types: str, int, int, str, int, str + +Other parameters are valid when uploading, they are the same parameters as are +used in the web form, like 'link_data_only' and etc. + +The request and response format should be considered alpha and are subject to change. + + diff --git a/doc/source/api/quickstart.rst b/doc/source/api/quickstart.rst new file mode 100644 index 00000000000..8e9043de638 --- /dev/null +++ b/doc/source/api/quickstart.rst @@ -0,0 +1,185 @@ +Quickstart +========== + +Log in as your user, navigate to the API Keys page in the User menu, and +generate a new API key. Make a note of the API key, and then pull up a +terminal. Now we'll use the display.py script in your galaxy/scripts/api +directory for a short example:: + + % ./display.py my_key http://localhost:4096/api/histories + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc + name: Unnamed history + id: 8c49be448cfe29bc + #2: /api/histories/33b43b4e7093c91f + name: output test + id: 33b43b4e7093c91f + +The result is a Collection of the histories of the user specified by the API +key (you). To look at the details of a particular history, say #1 above, do +the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc + Member Information + ------------------ + state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} + state: ok + contents_url: /api/histories/8c49be448cfe29bc/contents + id: 8c49be448cfe29bc + name: Unnamed history + +This gives detailed information about the specific member in question, in this +case the History. To view history contents, do the following:: + + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + name: Pasted Entry + type: file + id: 6f91353f3eb0fa4a + +What we have here is another Collection of items containing all of the datasets +in this particular history. Finally, to view details of a particular dataset +in this collection, execute the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + Member Information + ------------------ + misc_blurb: 1 line + name: Pasted Entry + data_type: txt + deleted: False + file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat + state: ok + download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt + visible: True + genome_build: ? + model_class: HistoryDatasetAssociation + file_size: 17 + metadata_data_lines: 1 + id: 6f91353f3eb0fa4a + misc_info: uploaded txt file + metadata_dbkey: ? + +And now you've successfully used the API to request and select a history, +browse the contents of that history, and then look at detailed information +about a particular dataset. + +For a more comprehensive Data Library example, set the following option in your +galaxy.ini as well, and restart galaxy again:: + + admin_users = you@example.org + library_import_dir = /path/to/some/directory + +In the directory you specified for 'library_import_dir', create some +subdirectories, and put (or symlink) files to import into Galaxy into those +subdirectories. + +In Galaxy, create an account that matches the address you put in 'admin_users', +then browse to that user's preferences and generate a new API Key. Copy the +key to your clipboard and then use these scripts:: + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + + 0 elements in collection + + % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' + Response + -------- + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 + Member Information + ------------------ + synopsis: None + contents_url: /api/libraries/f3f73e481f432006/contents + description: API Test Library + name: api_test + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + + % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' + Response + -------- + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: api_test_folder1 + id: 28202595c0d2591fa4f9089d2303fd89 + + % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 + Response + -------- + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: 2.bed + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: 3.bed + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: /api_test_folder1 + type: folder + id: 28202595c0d2591fa4f9089d2303fd89 + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: /api_test_folder1/2.bed + type: file + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: /api_test_folder1/3.bed + type: file + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + Member Information + ------------------ + misc_blurb: 68 regions + metadata_endCol: 3 + data_type: bed + metadata_columns: 6 + metadata_nameCol: 4 + uploaded_by: nate@... + metadata_strandCol: 6 + name: 2.bed + genome_build: hg19 + metadata_comment_lines: None + metadata_startCol: 2 + metadata_chromCol: 1 + file_size: 4272 + metadata_data_lines: 68 + message: + metadata_dbkey: hg19 + misc_info: uploaded bed file + date_uploaded: 2010-06-22T17:01:51.266119 + metadata_column_types: str, int, int, str, int, str + +Other parameters are valid when uploading, they are the same parameters as are +used in the web form, like 'link_data_only' and etc. + +The request and response format should be considered alpha and are subject to change. + diff --git a/doc/source/api_doc.rst b/doc/source/api_doc.rst index 1a657105284..b8acafaac48 100644 --- a/doc/source/api_doc.rst +++ b/doc/source/api_doc.rst @@ -1,8 +1,6 @@ Galaxy API Documentation -************************ +======================== -Background -========== In addition to being accessible through a web interface, Galaxy can also be accessed programmatically, through shell scripts and other programs. The web interface is appropriate for things like exploratory analysis, visualization, @@ -20,191 +18,12 @@ The Galaxy API addresses these and other situations by exposing Galaxy internals through an additional interface, known as an Application Programming Interface, or API. -Quickstart -========== -Log in as your user, navigate to the API Keys page in the User menu, and -generate a new API key. Make a note of the API key, and then pull up a -terminal. Now we'll use the display.py script in your galaxy/scripts/api -directory for a short example:: +.. toctree:: + :maxdepth: 3 - % ./display.py my_key http://localhost:4096/api/histories - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc - name: Unnamed history - id: 8c49be448cfe29bc - #2: /api/histories/33b43b4e7093c91f - name: output test - id: 33b43b4e7093c91f + Galaxy API Quickstart -The result is a Collection of the histories of the user specified by the API -key (you). To look at the details of a particular history, say #1 above, do -the following:: + Galaxy API Guidelines - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc - Member Information - ------------------ - state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} - state: ok - contents_url: /api/histories/8c49be448cfe29bc/contents - id: 8c49be448cfe29bc - name: Unnamed history - -This gives detailed information about the specific member in question, in this -case the History. To view history contents, do the following:: - - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - name: Pasted Entry - type: file - id: 6f91353f3eb0fa4a - -What we have here is another Collection of items containing all of the datasets -in this particular history. Finally, to view details of a particular dataset -in this collection, execute the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - Member Information - ------------------ - misc_blurb: 1 line - name: Pasted Entry - data_type: txt - deleted: False - file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat - state: ok - download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt - visible: True - genome_build: ? - model_class: HistoryDatasetAssociation - file_size: 17 - metadata_data_lines: 1 - id: 6f91353f3eb0fa4a - misc_info: uploaded txt file - metadata_dbkey: ? - -And now you've successfully used the API to request and select a history, -browse the contents of that history, and then look at detailed information -about a particular dataset. - -For a more comprehensive Data Library example, set the following option in your -galaxy.ini as well, and restart galaxy again:: - - admin_users = you@example.org - library_import_dir = /path/to/some/directory - -In the directory you specified for 'library_import_dir', create some -subdirectories, and put (or symlink) files to import into Galaxy into those -subdirectories. - -In Galaxy, create an account that matches the address you put in 'admin_users', -then browse to that user's preferences and generate a new API Key. Copy the -key to your clipboard and then use these scripts:: - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - - 0 elements in collection - - % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' - Response - -------- - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 - Member Information - ------------------ - synopsis: None - contents_url: /api/libraries/f3f73e481f432006/contents - description: API Test Library - name: api_test - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - - % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' - Response - -------- - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: api_test_folder1 - id: 28202595c0d2591fa4f9089d2303fd89 - - % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 - Response - -------- - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: 2.bed - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: 3.bed - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: /api_test_folder1 - type: folder - id: 28202595c0d2591fa4f9089d2303fd89 - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: /api_test_folder1/2.bed - type: file - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: /api_test_folder1/3.bed - type: file - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - Member Information - ------------------ - misc_blurb: 68 regions - metadata_endCol: 3 - data_type: bed - metadata_columns: 6 - metadata_nameCol: 4 - uploaded_by: nate@... - metadata_strandCol: 6 - name: 2.bed - genome_build: hg19 - metadata_comment_lines: None - metadata_startCol: 2 - metadata_chromCol: 1 - file_size: 4272 - metadata_data_lines: 68 - message: - metadata_dbkey: hg19 - misc_info: uploaded bed file - date_uploaded: 2010-06-22T17:01:51.266119 - metadata_column_types: str, int, int, str, int, str - -Other parameters are valid when uploading, they are the same parameters as are -used in the web form, like 'link_data_only' and etc. - -The request and response format should be considered alpha and are subject to change. - -.. include:: api/guidelines.rst - -.. include:: lib/galaxy.webapps.galaxy.api.rst + Galaxy API Documentation diff --git a/doc/source/ts_api_doc.rst b/doc/source/ts_api_doc.rst index f69a9483a26..99b6c8c1be6 100644 --- a/doc/source/ts_api_doc.rst +++ b/doc/source/ts_api_doc.rst @@ -1,8 +1,6 @@ Tool Shed API Documentation -*************************** +=========================== -Introduction -============ The Galaxy Tool Shed can be accessed programmatically using API described here via shell scripts and other programs. To interact with the API you first need to log in as your user, navigate @@ -13,7 +11,7 @@ key you have to attach to every request as a parameter. Example: GET https://toolshed.g2.bx.psu.edu/api/repositories?q=fastq?key=SOME_KEY_HERE +.. toctree:: + :maxdepth: 3 -.. include:: api/guidelines.rst - -.. include:: lib/galaxy.webapps.tool_shed.api.rst + Toolshed API Documentation From 0bfa99725463f1807816e5c0bdeacf46eb186c55 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 26 Aug 2015 17:41:02 -0500 Subject: [PATCH 007/178] Remove unused file --- doc/source/_api_quickstart.rst | 186 --------------------------------- 1 file changed, 186 deletions(-) delete mode 100644 doc/source/_api_quickstart.rst diff --git a/doc/source/_api_quickstart.rst b/doc/source/_api_quickstart.rst deleted file mode 100644 index 309850b5089..00000000000 --- a/doc/source/_api_quickstart.rst +++ /dev/null @@ -1,186 +0,0 @@ -Quickstart -========== - -Log in as your user, navigate to the API Keys page in the User menu, and -generate a new API key. Make a note of the API key, and then pull up a -terminal. Now we'll use the display.py script in your galaxy/scripts/api -directory for a short example:: - - % ./display.py my_key http://localhost:4096/api/histories - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc - name: Unnamed history - id: 8c49be448cfe29bc - #2: /api/histories/33b43b4e7093c91f - name: output test - id: 33b43b4e7093c91f - -The result is a Collection of the histories of the user specified by the API -key (you). To look at the details of a particular history, say #1 above, do -the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc - Member Information - ------------------ - state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} - state: ok - contents_url: /api/histories/8c49be448cfe29bc/contents - id: 8c49be448cfe29bc - name: Unnamed history - -This gives detailed information about the specific member in question, in this -case the History. To view history contents, do the following:: - - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - name: Pasted Entry - type: file - id: 6f91353f3eb0fa4a - -What we have here is another Collection of items containing all of the datasets -in this particular history. Finally, to view details of a particular dataset -in this collection, execute the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - Member Information - ------------------ - misc_blurb: 1 line - name: Pasted Entry - data_type: txt - deleted: False - file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat - state: ok - download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt - visible: True - genome_build: ? - model_class: HistoryDatasetAssociation - file_size: 17 - metadata_data_lines: 1 - id: 6f91353f3eb0fa4a - misc_info: uploaded txt file - metadata_dbkey: ? - -And now you've successfully used the API to request and select a history, -browse the contents of that history, and then look at detailed information -about a particular dataset. - -For a more comprehensive Data Library example, set the following option in your -galaxy.ini as well, and restart galaxy again:: - - admin_users = you@example.org - library_import_dir = /path/to/some/directory - -In the directory you specified for 'library_import_dir', create some -subdirectories, and put (or symlink) files to import into Galaxy into those -subdirectories. - -In Galaxy, create an account that matches the address you put in 'admin_users', -then browse to that user's preferences and generate a new API Key. Copy the -key to your clipboard and then use these scripts:: - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - - 0 elements in collection - - % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' - Response - -------- - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 - Member Information - ------------------ - synopsis: None - contents_url: /api/libraries/f3f73e481f432006/contents - description: API Test Library - name: api_test - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - - % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' - Response - -------- - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: api_test_folder1 - id: 28202595c0d2591fa4f9089d2303fd89 - - % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 - Response - -------- - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: 2.bed - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: 3.bed - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: /api_test_folder1 - type: folder - id: 28202595c0d2591fa4f9089d2303fd89 - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: /api_test_folder1/2.bed - type: file - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: /api_test_folder1/3.bed - type: file - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - Member Information - ------------------ - misc_blurb: 68 regions - metadata_endCol: 3 - data_type: bed - metadata_columns: 6 - metadata_nameCol: 4 - uploaded_by: nate@... - metadata_strandCol: 6 - name: 2.bed - genome_build: hg19 - metadata_comment_lines: None - metadata_startCol: 2 - metadata_chromCol: 1 - file_size: 4272 - metadata_data_lines: 68 - message: - metadata_dbkey: hg19 - misc_info: uploaded bed file - date_uploaded: 2010-06-22T17:01:51.266119 - metadata_column_types: str, int, int, str, int, str - -Other parameters are valid when uploading, they are the same parameters as are -used in the web form, like 'link_data_only' and etc. - -The request and response format should be considered alpha and are subject to change. - - From b1841e22d924b53a3a75306bf773b0b0ad4f02a6 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Tue, 1 Sep 2015 10:55:41 -0400 Subject: [PATCH 008/178] Client build: do not drop console when compressing, when not compressing do not mangle variable names --- client/grunt-tasks/scripts.js | 61 ++++++++++--------- .../galaxy.interactive_environments.js.map | 2 +- static/maps/libs/jquery/jqtouch.js.map | 2 +- static/maps/libs/raven.js.map | 2 +- static/maps/libs/toastr.js.map | 2 +- .../collection/list-collection-creator.js.map | 2 +- static/maps/mvc/data.js.map | 2 +- static/maps/mvc/dataset/dataset-choice.js.map | 2 +- static/maps/mvc/form/form-parameters.js.map | 2 +- static/maps/mvc/form/form-repeat.js.map | 2 +- .../maps/mvc/form/form-select-content.js.map | 2 +- static/maps/mvc/form/form-view.js.map | 2 +- static/maps/mvc/history/options-menu.js.map | 2 +- static/maps/mvc/job/job-model.js.map | 2 +- .../library/library-foldertoolbar-view.js.map | 2 +- static/maps/mvc/list/list-panel.js.map | 2 +- static/maps/mvc/tools/tools-form-base.js.map | 2 +- .../maps/mvc/tools/tools-form-workflow.js.map | 2 +- static/maps/mvc/tools/tools-jobs.js.map | 2 +- static/maps/mvc/ui/ui-frames.js.map | 2 +- static/maps/mvc/ui/ui-select.js.map | 2 +- static/maps/utils/deferred.js.map | 2 +- static/maps/utils/graph.js.map | 2 +- static/maps/utils/metrics-logger.js.map | 2 +- static/maps/utils/uploadbox.js.map | 2 +- static/maps/utils/utils.js.map | 2 +- static/maps/viz/trackster.js.map | 2 +- static/maps/viz/trackster/filters.js.map | 2 +- static/maps/viz/visualization.js.map | 2 +- .../galaxy.interactive_environments.js | 2 +- static/scripts/libs/jquery/jqtouch.js | 2 +- static/scripts/libs/raven.js | 2 +- static/scripts/libs/toastr.js | 2 +- .../mvc/collection/list-collection-creator.js | 2 +- static/scripts/mvc/data.js | 2 +- static/scripts/mvc/dataset/dataset-choice.js | 2 +- static/scripts/mvc/form/form-parameters.js | 2 +- static/scripts/mvc/form/form-repeat.js | 2 +- .../scripts/mvc/form/form-select-content.js | 2 +- static/scripts/mvc/form/form-view.js | 2 +- static/scripts/mvc/history/options-menu.js | 2 +- static/scripts/mvc/job/job-model.js | 2 +- .../mvc/library/library-foldertoolbar-view.js | 4 +- static/scripts/mvc/list/list-panel.js | 2 +- static/scripts/mvc/tools/tools-form-base.js | 2 +- .../scripts/mvc/tools/tools-form-workflow.js | 2 +- static/scripts/mvc/tools/tools-jobs.js | 2 +- static/scripts/mvc/ui/ui-frames.js | 2 +- static/scripts/mvc/ui/ui-select.js | 2 +- static/scripts/utils/deferred.js | 2 +- static/scripts/utils/graph.js | 2 +- static/scripts/utils/metrics-logger.js | 2 +- static/scripts/utils/uploadbox.js | 2 +- static/scripts/utils/utils.js | 2 +- static/scripts/viz/trackster.js | 2 +- static/scripts/viz/trackster/filters.js | 2 +- static/scripts/viz/visualization.js | 2 +- 57 files changed, 90 insertions(+), 85 deletions(-) diff --git a/client/grunt-tasks/scripts.js b/client/grunt-tasks/scripts.js index 4cd1902b9a5..a6dd9b0b2c3 100644 --- a/client/grunt-tasks/scripts.js +++ b/client/grunt-tasks/scripts.js @@ -7,35 +7,17 @@ module.exports = function( grunt ){ "use strict"; var app = grunt.config.get( 'app' ), - paths = grunt.config.get( 'paths' ); - - grunt.config( 'uglify', { - target : { - files: [{ - expand : true, - cwd : paths.srcSymlink, - src : '**/*.js', - dest : paths.dist - }], - } - }); - - if (grunt.option('develop')){ - grunt.config( 'uglify.options', { + paths = grunt.config.get( 'paths' ), + // uglify settings used when scripts are decompressed/not-minified + decompressedSettings = { + mangle : false, beautify : true, compress : { drop_debugger : false } - }); - } else { - grunt.config( 'uglify.target.options', { - sourceMap : true, - sourceMapName : function( path ){ - // rewrite name to have all source maps in 'static/maps' - return path.replace( paths.dist, paths.maps ) + '.map'; - } - }); - grunt.config( 'uglify.options', { + }, + // uglify settings used when scripts are compressed/minified + compressedSettings = { mangle : { screw_ie8 : true }, @@ -55,16 +37,39 @@ module.exports = function( grunt ){ if_return : true, join_vars : true, cascade : true, - drop_console : true + } + }; + + grunt.config( 'uglify', { + target : { + files: [{ + expand : true, + cwd : paths.srcSymlink, + src : '**/*.js', + dest : paths.dist + }], + } + }); + + + if (grunt.option( 'develop' )){ + grunt.config( 'uglify.options', decompressedSettings ); + + } else { + grunt.config( 'uglify.target.options', { + sourceMap : true, + sourceMapName : function( path ){ + // rewrite name to have all source maps in 'static/maps' + return path.replace( paths.dist, paths.maps ) + '.map'; } }); + grunt.config( 'uglify.options', compressedSettings ); } - // -------------------------------------------------------------------------- decompress for easier debugging grunt.registerTask( 'decompress', function(){ grunt.log.writeln( "decompressing... (don't forget to call 'grunt' again before committing)" ); - grunt.config( 'uglify.options', { beautify: true }); + grunt.config( 'uglify.options', decompressedSettings ); grunt.config( 'uglify.target.options', {}); grunt.task.run( 'uglify' ); }); diff --git a/static/maps/galaxy.interactive_environments.js.map b/static/maps/galaxy.interactive_environments.js.map index ea0fd8db98b..ee5a8e61608 100644 --- a/static/maps/galaxy.interactive_environments.js.map +++ b/static/maps/galaxy.interactive_environments.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/maps/mvc/list/list-panel.js.map b/static/maps/mvc/list/list-panel.js.map index 7c68ea934dd..10e7d811c56 100644 --- a/static/maps/mvc/list/list-panel.js.map +++ b/static/maps/mvc/list/list-panel.js.map @@ -1 +1 @@ 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    "].join(""))},toString:function(){return"ListCollectionCreator"}}),j=function(a,b,c){var e,g=jQuery.Deferred(),h=Galaxy.modal||new d.View;return b=_.defaults(b||{},{elements:a,oncancel:function(){h.hide(),g.reject("cancelled")},oncreate:function(a,b){h.hide(),g.resolve(b)}}),e=new c(b),h.show({title:b.title||f("Create a collection"),body:e.$el,width:"80%",height:"min-content",closing_events:!0}),e.render(),window._collectionCreator=e,g},k=function(a,b){return b=b||{},b.title=f("Create a collection from a list of datasets"),j(a,b,i)};return{DatasetCollectionElementView:h,ListCollectionCreator:i,collectionCreatorModal:j,listCollectionCreatorModal:k,createListCollection:g}}); //# sourceMappingURL=../../../maps/mvc/collection/list-collection-creator.js.map \ No newline at end of file diff --git a/static/scripts/mvc/data.js b/static/scripts/mvc/data.js index 886481931b9..958ec47ee8b 100644 --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -1,2 +1,2 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames","mvc/ui/icon-button"],function(a,b,c){var d=Backbone.Model.extend({}),e=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.get("metadata")||this._set_metadata(),this.on("change",this._set_metadata,this)},_set_metadata:function(){var a=new d;_.each(_.keys(this.attributes),function(b){if(0===b.indexOf("metadata_")){var c=b.split("metadata_")[1];a.set(c,this.attributes[b]),delete this.attributes[b]}},this),this.set("metadata",a,{silent:!0})},get_metadata:function(a){return this.attributes.metadata.get(a)},urlRoot:galaxy_config.root+"api/datasets"}),f=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:!1}),initialize:function(){e.prototype.initialize.call(this),this.attributes.chunk_index=this.attributes.first_data_chunk?1:0,this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id,this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof)return null;var a=this,b=$.Deferred();return $.getJSON(this.attributes.chunk_url,{chunk:a.attributes.chunk_index++}).success(function(c){var d;""!==c.ck_data?d=c:(a.attributes.at_eof=!0,d=null),b.resolve(d)}),b}}),g=Backbone.Collection.extend({model:e}),h=Backbone.View.extend({initialize:function(a){this.row_count=0,this.loading_chunk=!1,new k({model:a.model,$el:this.$el})},expand_to_container:function(){this.$el.height()").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var a=$("").attr({id:"content_table",cellpadding:0});this.$el.append(a);var b=this.model.get_metadata("column_names"),c=$("").appendTo(a),d=$("").appendTo(c);if(b)d.append("");else for(var e=1;e<=this.model.get_metadata("columns");e++)d.append("");var f=this,g=this.model.get("first_data_chunk");g?this._renderChunk(g):$.when(f.model.get_next_chunk()).then(function(a){f._renderChunk(a)}),this.scroll_elt.scroll(function(){f.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(a,b,c){var d=$("
    "+b.join("")+""+e+"").text(a),e=this.model.get_metadata("column_types");return void 0!==c?d.attr("colspan",c).addClass("stringalign"):e&&b"),d=this.model.get_metadata("columns");return this.row_count%2!==0&&c.addClass("dark_row"),b.length===d?_.each(b,function(a,b){c.append(this._renderCell(a,b))},this):b.length>d?(_.each(b.slice(0,d-1),function(a,b){c.append(this._renderCell(a,b))},this),c.append(this._renderCell(b.slice(d-1).join(" "),d-1))):d>5&&b.length===d-1?(_.each(b,function(a,b){c.append(this._renderCell(a,b))},this),c.append($(""))):c.append(this._renderCell(a,0,d)),this.row_count++,c},_renderChunk:function(a){var b=this.$el.find("table");_.each(a.ck_data.split("\n"),function(a){""!==a&&b.append(this._renderRow(a))},this)}}),i=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),scroll_elt=_.find(this.$el.parents(),function(a){return"auto"===$(a).css("overflow")}),scroll_elt||(scroll_elt=window),this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),j=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:a.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),k=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(a){function b(a,b){for(var c=0;c").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var a=$("").attr({id:"content_table",cellpadding:0});this.$el.append(a);var b=this.model.get_metadata("column_names"),c=$("").appendTo(a),d=$("").appendTo(c);if(b)d.append("");else for(var e=1;e<=this.model.get_metadata("columns");e++)d.append("");var f=this,g=this.model.get("first_data_chunk");g?this._renderChunk(g):$.when(f.model.get_next_chunk()).then(function(a){f._renderChunk(a)}),this.scroll_elt.scroll(function(){f.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(a,b,c){var d=$("'}})}); +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(a,b,c,d,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(a,c){this.app=a;var f=this;this.model=new b.Model(c),this.setElement(this._template(c));var g=this.$el;this.settings=new d.View({title:"Upload configuration",container:g.find("#settings"),placement:"bottom"});var h=this.app.select_genome.value();this.select_genome=new e.View({css:"genome",onchange:function(a){f.model.set("genome",a),f.app.updateGenome(a,!0)},data:f.app.list_genomes,container:g.find("#genome"),value:h}),this.model.set("genome",h);var i=this.app.select_extension.value();this.select_extension=new e.View({css:"extension",onchange:function(a){f.model.set("extension",a),f.app.updateExtension(a,!0)},data:f.app.list_extensions,container:g.find("#extension"),value:i}),this.model.set("extension",i),g.find("#symbol").on("click",function(){f._removeRow()}),g.find("#extension-info").on("click",function(a){f.app.showExtensionInfo({$el:$(a.target),title:f.select_extension.text(),extension:f.select_extension.value()})}).on("mousedown",function(a){a.preventDefault()}),g.find("#settings").on("click",function(){f._showSettings()}).on("mousedown",function(a){a.preventDefault()}),g.find("#text-content").on("change input",function(a){f.model.set("url_paste",$(a.target).val()),f.model.set("file_size",$(a.target).val().length)}),g.find("#space_to_tabs").on("change",function(a){f.model.set("space_to_tabs",$(a.target).prop("checked"))}),this.model.on("change:percentage",function(){f._refreshPercentage()}),this.model.on("change:status",function(){f._refreshStatus()}),this.model.on("change:info",function(){f._refreshInfo()}),this.model.on("change:genome",function(){f._refreshGenome()}),this.model.on("change:extension",function(){f._refreshExtension()}),this.model.on("change:file_size",function(){f._refreshFileSize()}),this.model.on("remove",function(){f.remove()}),this.app.collection.on("reset",function(){f.remove()})},render:function(){var b=this.model.get("file_name"),c=this.model.get("file_size"),d=this.model.get("file_mode"),e=this.$el;if(e.find("#title").html(b),e.find("#size").html(a.bytesToString(c)),e.find("#mode").removeClass().addClass("mode"),"new"==d){var f=e.find("#text"),g=this.options.padding,h=e.width()-2*g,i=e.height()-g;f.css("width",h+"px"),f.css("top",i+"px"),e.height(i+f.height()+2*g),f.show(),e.find("#mode").addClass("fa fa-pencil")}"local"==d&&e.find("#mode").addClass("fa fa-laptop"),"ftp"==d&&e.find("#mode").addClass("fa fa-code-fork")},remove:function(){this.select_genome.remove(),this.select_extension.remove(),Backbone.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var a=this.model.get("info");a?this.$el.find("#info").html("Failed: "+a).show():this.$el.find("#info").hide()},_refreshPercentage:function(){var a=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:a+"%"}),this.$el.find("#percentage").html(100!=a?a+"%":"Adding to history...")},_refreshStatus:function(){var a=this.$el,b=this.model.get("status"),c=this.status_classes[b],d=this.$el.find("#symbol");d.removeClass(),d.addClass(c),"init"==b?(this.select_genome.enable(),this.select_extension.enable(),a.find("#text-content").attr("disabled",!1),a.find("#space_to_tabs").attr("disabled",!1)):(this.select_genome.disable(),this.select_extension.disable(),a.find("#text-content").attr("disabled",!0),a.find("#space_to_tabs").attr("disabled",!0)),"success"==b&&(a.addClass("success"),a.find("#percentage").html("100%")),"error"==b&&(a.addClass("danger"),a.find(".progress").remove())},_refreshFileSize:function(){var b=this.model.get("file_size");this.$el.find("#size").html(a.bytesToString(b))},_removeRow:function(){var a=this.model.get("status");("init"==a||"success"==a||"error"==a)&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new c(this).$el),this.settings.show())},_template:function(a){return''}})}); //# sourceMappingURL=../../../maps/mvc/upload/upload-row.js.map \ No newline at end of file From 53f7ac02d23939c8b17ad93ead787527dc1c805b Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 23 Sep 2015 11:10:10 -0400 Subject: [PATCH 036/178] Don't use a local reference to modal -- the intent here was to allow component-isolated modals as in other places, but we can do (or not) that at a later time. --- client/galaxy/scripts/mvc/tools/tools-form-base.js | 10 ++++------ static/maps/mvc/tools/tools-form-base.js.map | 2 +- static/scripts/mvc/tools/tools-form-base.js | 2 +- 3 files changed, 6 insertions(+), 8 deletions(-) diff --git a/client/galaxy/scripts/mvc/tools/tools-form-base.js b/client/galaxy/scripts/mvc/tools/tools-form-base.js index 3fe7b93690c..5f4406d5bc2 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -2,9 +2,8 @@ This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form. */ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', - 'mvc/tools/tools-template', 'mvc/citation/citation-model', 'mvc/citation/citation-view', - 'mvc/ui/ui-modal'], - function(Utils, Deferred, Ui, Form, ToolTemplate, CitationModel, CitationView, Modal) { + 'mvc/tools/tools-template', 'mvc/citation/citation-model', 'mvc/citation/citation-view'], + function(Utils, Deferred, Ui, Form, ToolTemplate, CitationModel, CitationView) { // create form view return Backbone.View.extend({ @@ -12,7 +11,6 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', initialize: function(options) { this.options = Utils.merge(options, {}); this.setElement('
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    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("
    "),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),Galaxy.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){Galaxy.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file From dc0dd6ec4b7a5f47595d43133e5f9d3d999a7e15 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 23 Sep 2015 11:27:41 -0400 Subject: [PATCH 037/178] Simplify logic. --- .../scripts/mvc/dataset/dataset-li-edit.js | 34 +++++++++---------- .../maps/mvc/dataset/dataset-li-edit.js.map | 2 +- static/scripts/mvc/dataset/dataset-li-edit.js | 2 +- 3 files changed, 18 insertions(+), 20 deletions(-) diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js index 85769323fe2..bfa617b86ae 100644 --- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js @@ -159,25 +159,23 @@ var DatasetListItemEdit = _super.extend( /** Render icon-button to re-run the job that created this dataset. */ _renderRerunButton : function(){ var creating_job = this.model.get('creating_job'); - var rerunnable = this.model.get('rerunnable'); - if (!rerunnable){ - return; + if (this.model.get('rerunnable')){ + return faIconButton({ + title : _l( 'Run this job again' ), + href : this.model.urls.rerun, + classes : 'rerun-btn', + target : this.linkTarget, + disabled : !rerunnable, + faIcon : 'fa-refresh', + onclick : function(ev) { + ev.preventDefault(); + var form = new ToolsForm.View({'job_id' : creating_job}); + form.deferred.execute(function(){ + Galaxy.app.display(form.$el); + }); + } + }); } - else return faIconButton({ - title : _l( 'Run this job again' ), - href : this.model.urls.rerun, - classes : 'rerun-btn', - target : this.linkTarget, - disabled : !rerunnable, - faIcon : 'fa-refresh', - onclick : function(ev) { - ev.preventDefault(); - var form = new ToolsForm.View({'job_id' : creating_job}); - form.deferred.execute(function(){ - Galaxy.app.display(form.$el); - }); - } - }); }, /** Render an icon-button or popupmenu of links based on the applicable visualizations */ diff --git a/static/maps/mvc/dataset/dataset-li-edit.js.map b/static/maps/mvc/dataset/dataset-li-edit.js.map index 26c267ad438..73404d4174c 100644 --- a/static/maps/mvc/dataset/dataset-li-edit.js.map +++ b/static/maps/mvc/dataset/dataset-li-edit.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li-edit.js b/static/scripts/mvc/dataset/dataset-li-edit.js index 8bc096ac20f..d44b5fb2b51 100644 --- a/static/scripts/mvc/dataset/dataset-li-edit.js +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this 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b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',h("An error occurred setting the metadata for this dataset"),'
    ',h("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
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    ',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',h("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); +define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var a=this.model.get("creating_job");return this.model.get("rerunnable")?e({title:h("Run this job 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b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === 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    ',h("An error occurred setting the metadata for this dataset"),'
    ',h("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
    ',h("This dataset has been deleted"),'
    ',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
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    ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li-edit.js.map \ No newline at end of file From 15a516b57799e61eaca90a3b7d9dc188a012b808 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 23 Sep 2015 11:30:30 -0400 Subject: [PATCH 038/178] Remove 'disabled' cruft, since we opted to simply not show the button rather than disable it. --- client/galaxy/scripts/mvc/dataset/dataset-li-edit.js | 1 - static/maps/mvc/dataset/dataset-li-edit.js.map | 2 +- static/scripts/mvc/dataset/dataset-li-edit.js | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js index bfa617b86ae..74d8c465913 100644 --- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js @@ -165,7 +165,6 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li-edit.js b/static/scripts/mvc/dataset/dataset-li-edit.js index d44b5fb2b51..031e28ce9fe 100644 --- a/static/scripts/mvc/dataset/dataset-li-edit.js +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this 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b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',h("An error occurred setting the metadata for this dataset"),'
    ',h("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
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    ',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',h("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); +define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var a=this.model.get("creating_job");return this.model.get("rerunnable")?e({title:h("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(b){b.preventDefault();var c=new g.View({job_id:a});c.deferred.execute(function(){Galaxy.app.display(c.$el)})}}):void 0},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',h("An error occurred setting the metadata for this dataset"),'
    ',h("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
    ',h("This dataset has been deleted"),'
    ',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',h("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li-edit.js.map \ No newline at end of file From 52dfd589b986397852d6700a4ca8d8afa7235416 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 10:34:36 -0500 Subject: [PATCH 039/178] Unify the docker command, command_inject, and command_wrapper --- .../ipython/config/ipython.ini.sample | 21 ++++-------- .../rstudio/config/rstudio.ini.sample | 33 ++++++++++++------- .../web/base/interactive_environments.py | 30 +++++++++-------- 3 files changed, 45 insertions(+), 39 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index c8624ca72ec..ec1413aa25e 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -1,5 +1,4 @@ [main] - # Following options are ignored if using the Galaxy dynamic proxy but # are useful if mapping a range of ports for environment consumption. #apache_urls = False @@ -7,26 +6,18 @@ #ssl = False [docker] - -# Command to execute docker. For example `sudo docker` or `docker-lxc`. -command = docker +# Command to launch docker container. For example `sudo docker` or `docker-lxc`. +# If you need to use a command like `sg` you can do that here, just be sure to +# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'` +command = docker run --sig-proxy=true -e DEBUG=false {docker_args} # The docker image name that should be started. image = bgruening/docker-ipython-notebook:dev -# Additional arguments that are passed to the `docker run` command. -command_inject = --sig-proxy=true -e DEBUG=false - -# Command to wrap around the full docker command. -# For example, `sg 'docker' '{cmd}'` where {cmd} will be replaced by the full -# docker command. Make sure to surround the {cmd} with single quotes('). -# Default: empty -#command_wrapper = - # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the # Docker host of the spawned container if that is also not set. -#galaxy_url = +#galaxy_url = # The Docker hostname. It can be useful to run the Docker daemon on a different # host than Galaxy. @@ -35,4 +26,4 @@ command_inject = --sig-proxy=true -e DEBUG=false # Try to set the tempdirectory to world execute - this can fix the issue # where 'sudo docker' is not able to mount the folder otherwise. # "finalize namespace chdir to /import permission denied" -wx_tempdir = False \ No newline at end of file +wx_tempdir = False diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index ed0b64ff7ce..a66e8ebd720 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -1,19 +1,30 @@ [main] # This cannot be changed password_auth = True -# Other -apache_urls = False -ssl = False +# Following options are ignored if using the Galaxy dynamic proxy but +# are useful if mapping a range of ports for environment consumption. +#apache_urls = False +#ssl = False [docker] -command = docker +# Command to launch docker container. For example `sudo docker` or `docker-lxc`. +# If you need to use a command like `sg` you can do that here, just be sure to +# wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'` +command = docker run --sig-proxy=true -e DEBUG=false {docker_args} + +# The docker image name that should be started. image = erasche/docker-rstudio-notebook:dev -# Additional arguments that are passed to the `docker run` command. `-u` -# settings are completely ignored. -command_inject = --sig-proxy=true -e DEBUG=false - -# URL to access the Galaxy API with from the spawned Docker container, if empty +# URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the -# Docker host of the spawned container, if that is also not set. -#galaxy_url= +# Docker host of the spawned container if that is also not set. +#galaxy_url = + +# The Docker hostname. It can be useful to run the Docker daemon on a different +# host than Galaxy. +#docker_hostname = localhost + +# Try to set the tempdirectory to world execute - this can fix the issue +# where 'sudo docker' is not able to mount the folder otherwise. +# "finalize namespace chdir to /import permission denied" +wx_tempdir = False diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index 297ffef099b..315d9c8db27 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -65,7 +65,6 @@ class InteractiveEnviornmentRequest(object): # will need to be recorded here. The ConfigParser doesn't provide a # .get() that will ignore missing sections, so we must make use of # their defaults dictionary instead. - default_dict['command_inject'] = '--sig-proxy=true' default_dict['docker_hostname'] = 'localhost' default_dict['wx_tempdir'] = 'False' default_dict['command_wrapper'] = '' @@ -182,18 +181,23 @@ class InteractiveEnviornmentRequest(object): conf.update(env_override) env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()]) volume_str = ' '.join(['-v "%s"' % volume for volume in volumes]) - cmd = '%s run %s -d %s -p %s:%s -v "%s:/import/" %s %s' % \ - (self.attr.viz_config.get("docker", "command"), - env_str, - self.attr.viz_config.get("docker", "command_inject"), - self.attr.PORT, self.attr.docker_port, - temp_dir, - volume_str, - self.attr.viz_config.get("docker", "image")) - cmd_wrapper = self.attr.viz_config.get("docker", "command_wrapper") - if cmd_wrapper != '' and '{cmd}' in cmd_wrapper: - cmd = cmd_wrapper.format( cmd=cmd ) - return cmd + # This is the basic docker command such as "sudo -u docker docker {docker_args}" + # or just "docker {docker_args}" + command = self.attr.viz_config.get("docker", "command") + # Then we format in the entire docker command in place of + # {docker_args}, so as to let the admin not worry about which args are + # getting passed + command = command.format(docker_args='{environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {volume_str} {image}') + # Once that's available, we format again with all of our arguments + command = command.format( + environment=env_str, + port_ext=self.attr.PORT, + port_int=self.attr.docker_port, + temp_dir=temp_dir, + volume_str=volume_str, + image=self.attr.viz_config.get("docker", "image") + ) + return command def launch(self, raw_cmd=None, env_override={}, volumes=[]): if raw_cmd is None: From 56ac2c0f137523c320ca12c684579b75d4b76dfc Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 10:50:05 -0500 Subject: [PATCH 040/178] Revert command inject and document rationale --- .../ipython/config/ipython.ini.sample | 10 +++++++++- .../rstudio/config/rstudio.ini.sample | 10 +++++++++- lib/galaxy/web/base/interactive_environments.py | 4 +++- 3 files changed, 21 insertions(+), 3 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index ec1413aa25e..4eba7969d9d 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -9,11 +9,19 @@ # Command to launch docker container. For example `sudo docker` or `docker-lxc`. # If you need to use a command like `sg` you can do that here, just be sure to # wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'` -command = docker run --sig-proxy=true -e DEBUG=false {docker_args} +# +# It is recommended that you use command_inject if you need to inject +# additional parameters. This command string is re-used for a `docker inspect` +# command and will likely cause errors if it is extensively modified, past the +# usual group/sudo changes. +command = docker run {docker_args} # The docker image name that should be started. image = bgruening/docker-ipython-notebook:dev +# Additional arguments that are passed to the `docker run` command. +command_inject = --sig-proxy=true -e DEBUG=false + # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the # Docker host of the spawned container if that is also not set. diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index a66e8ebd720..a9da467510a 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -10,11 +10,19 @@ password_auth = True # Command to launch docker container. For example `sudo docker` or `docker-lxc`. # If you need to use a command like `sg` you can do that here, just be sure to # wrap all of the docker portion in single quotes. E.g. `sg 'docker' 'docker {docker_args}'` -command = docker run --sig-proxy=true -e DEBUG=false {docker_args} +# +# It is recommended that you use command_inject if you need to inject +# additional parameters. This command string is re-used for a `docker inspect` +# command and will likely cause errors if it is extensively modified, past the +# usual group/sudo changes. +command = docker run {docker_args} # The docker image name that should be started. image = erasche/docker-rstudio-notebook:dev +# Additional arguments that are passed to the `docker run` command. +command_inject = --sig-proxy=true -e DEBUG=false + # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the # Docker host of the spawned container if that is also not set. diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index 315d9c8db27..b2964e35fbb 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -65,6 +65,7 @@ class InteractiveEnviornmentRequest(object): # will need to be recorded here. The ConfigParser doesn't provide a # .get() that will ignore missing sections, so we must make use of # their defaults dictionary instead. + default_dict['command_inject'] = '--sig-proxy=true' default_dict['docker_hostname'] = 'localhost' default_dict['wx_tempdir'] = 'False' default_dict['command_wrapper'] = '' @@ -187,9 +188,10 @@ class InteractiveEnviornmentRequest(object): # Then we format in the entire docker command in place of # {docker_args}, so as to let the admin not worry about which args are # getting passed - command = command.format(docker_args='{environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {volume_str} {image}') + command = command.format(docker_args='{command_inject} {environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {volume_str} {image}') # Once that's available, we format again with all of our arguments command = command.format( + command_inject=self.attr.viz_config.get("docker", "command_inject"), environment=env_str, port_ext=self.attr.PORT, port_int=self.attr.docker_port, From 484578936bc7ee04c6b28cb848772a4b6ded2b03 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 11:24:37 -0500 Subject: [PATCH 041/178] Refactor to use -P This is a major refactoring to use the -P option of docker which should simplify some of our deployment like running docker containers on another host. In support of #372 --- .../ipython/templates/ipython.mako | 10 +- .../rstudio/templates/rstudio.mako | 17 ++-- .../web/base/interactive_environments.py | 91 +++++++++++++++---- 3 files changed, 86 insertions(+), 32 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/templates/ipython.mako b/config/plugins/interactive_environments/ipython/templates/ipython.mako index 118d72baf2f..8edd23dc423 100644 --- a/config/plugins/interactive_environments/ipython/templates/ipython.mako +++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako @@ -33,18 +33,16 @@ if hda.datatype.__class__.__name__ != "Ipynb": else: shutil.copy( hda.file_name, empty_nb_path ) +# Add all environment variables collected from Galaxy's IE infrastructure +ie_request.launch(env_override={ + 'notebook_password': PASSWORD, +}) ## General IE specific # Access URLs for the notebook from within galaxy. notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/notebooks/ipython_galaxy_notebook.ipynb') notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree') - -# Add all environment variables collected from Galaxy's IE infrastructure -ie_request.launch(env_override={ - 'notebook_password': PASSWORD, -}) - %> diff --git a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako index 0fc4d2a4ba2..c9cdbed7e49 100644 --- a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako +++ b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako @@ -12,14 +12,6 @@ temp_dir = ie_request.temp_dir PASSWORD = ie_request.notebook_pw USERNAME = "galaxy" -## General IE specific -# Access URLs for the notebook from within galaxy. -# TODO: Make this work without pointing directly to IE. Currently does not work -# through proxy. -notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-public-key') -notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/') -notebook_login_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-do-sign-in') - # Did the user give us an RData file? if hda.datatype.__class__.__name__ == "RData": shutil.copy( hda.file_name, os.path.join(temp_dir, '.RData') ) @@ -29,6 +21,15 @@ ie_request.launch(env_override={ 'notebook_password': PASSWORD, 'cors_origin': ie_request.attr.proxy_url, }) + +## General IE specific +# Access URLs for the notebook from within galaxy. +# TODO: Make this work without pointing directly to IE. Currently does not work +# through proxy. +notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-public-key') +notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/') +notebook_login_url = ie_request.url_template('${PROXY_URL}/rstudio/${PORT}/auth-do-sign-in') + %> diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index b2964e35fbb..f81f1ce3e31 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -1,10 +1,11 @@ import ConfigParser import os +import json import stat import random import tempfile -from subprocess import Popen, PIPE +from subprocess import Popen, PIPE, check_output from galaxy.util.bunch import Bunch from galaxy import web @@ -40,11 +41,6 @@ class InteractiveEnviornmentRequest(object): self.load_deploy_config() self.attr.docker_hostname = self.attr.viz_config.get("docker", "docker_hostname") - self.attr.proxy_request = trans.app.proxy_manager.setup_proxy( - trans, host=self.attr.docker_hostname - ) - self.attr.proxy_url = self.attr.proxy_request[ 'proxy_url' ] - self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ] # Generate per-request passwords the IE plugin can use to configure # the destination container. @@ -102,7 +98,7 @@ class InteractiveEnviornmentRequest(object): 'history_id': self.attr.history_id, 'api_key': api_key, 'remote_host': request.remote_addr, - 'docker_port': self.attr.PORT, + # DOCKER_PORT is NO LONGER AVAILABLE. All IEs must update. 'cors_origin': request.host_url, } @@ -144,7 +140,6 @@ class InteractiveEnviornmentRequest(object): There are several variables accessible to the user: - ${PROXY_URL} will be replaced with dynamically create proxy - - ${PORT} will be replaced with the port the docker image is attached to """ # Figure out our substitutions @@ -156,18 +151,12 @@ class InteractiveEnviornmentRequest(object): else: protocol = 'http' - if not self.attr.APACHE_URLS: - # If they are not using apache URLs, that implies there's a port attached to the host - # string, thus we replace just the first instance of host that we see. - url_template = url_template.replace('${HOST}', '${HOST}:${PORT}', 1) - url_template = url_template.replace('${PROTO}', protocol) \ .replace('${HOST}', self.attr.HOST) # Only the following replacements are used with Galaxy dynamic proxy # URLs - url = url_template.replace('${PROXY_URL}', str(self.attr.proxy_url)) \ - .replace('${PORT}', str(self.attr.PORT)) + url = url_template.replace('${PROXY_URL}', str(self.attr.proxy_url)) return url def volume(self, host_path, container_path, **kwds): @@ -188,13 +177,11 @@ class InteractiveEnviornmentRequest(object): # Then we format in the entire docker command in place of # {docker_args}, so as to let the admin not worry about which args are # getting passed - command = command.format(docker_args='{command_inject} {environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {volume_str} {image}') + command = command.format(docker_args='{command_inject} {environment} -d -P -v "{temp_dir}:/import/" {volume_str} {image}') # Once that's available, we format again with all of our arguments command = command.format( command_inject=self.attr.viz_config.get("docker", "command_inject"), environment=env_str, - port_ext=self.attr.PORT, - port_int=self.attr.docker_port, temp_dir=temp_dir, volume_str=volume_str, image=self.attr.viz_config.get("docker", "image") @@ -212,5 +199,73 @@ class InteractiveEnviornmentRequest(object): stdout, stderr = p.communicate() if p.returncode != 0 or len(stderr): log.error( "%s\n%s" % (stdout, stderr) ) + return None else: log.debug( "Container id: %s" % stdout) + port_mappings = self.get_proxied_ports(stdout) + if len(port_mappings) > 1: + log.warning("Don't know how to handle proxies to containers with multiple exposed ports. Arbitrarily choosing first") + elif len(port_mappings) == 0: + log.warning("No exposed ports to map! Images MUST EXPOSE") + return None + # Fetch the first port_mapping + (service, host_ip, host_port) = port_mappings[0] + + # Now we configure our proxy_requst object and we manually specify + # the port to map to and ensure the proxy is available. + self.attr.proxy_request = self.trans.app.proxy_manager.setup_proxy( + self.trans, + host=self.attr.docker_hostname, + port=host_port, + ) + # These variables then become available for use in templating URLs + self.attr.proxy_url = self.attr.proxy_request[ 'proxy_url' ] + # Commented out because it needs to be documented and visible that + # this variable was moved here. Usually would remove commented + # code, but again, needs to be clear where this went. Remove at a + # later time. + # + # PORT is no longer exposed internally. All requests are forced to + # go through the proxy we ship. + # self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ] + + def get_proxied_ports(self, container_id): + """Run docker inspect on a container to figure out which ports were + mapped where. + + :type container_id: str + :param container_id: a docker container ID + + :returns: a list of triples containing (internal_port, external_ip, + external_port), of which the ports are probably the only + useful information. + + Someday code that calls this should be refactored whenever we get + containers with multiple ports working. + """ + command = self.attr.viz_config.get("docker", "command") + command.replace( + "run {docker_args}", + "inspect %s" % container_id + ) + output = check_output(command) + inspect_data = json.loads(output) + # [{ + # "NetworkSettings" : { + # "Ports" : { + # "3306/tcp" : [ + # { + # "HostIp" : "127.0.0.1", + # "HostPort" : "3306" + # } + # ] + mappings = [] + port_mappings = inspect_data[0]['NetworkSettings']['Ports'] + for port_name in port_mappings: + for binding in port_mappings[port_name]: + mappings.append(( + port_name.replace('/tcp', '').replace('/udp', ''), + port_mappings[port_name][binding]['HostIp'], + port_mappings[port_name][binding]['HostPort'] + )) + return mappings From 175f89bdc8df1550d34bc5084df45185ef633057 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 11:27:52 -0500 Subject: [PATCH 042/178] Hardcode defaults, per @jmchilton's comments --- .../ipython/config/ipython.ini.sample | 6 +++--- .../rstudio/config/rstudio.ini.sample | 8 ++++---- lib/galaxy/web/base/interactive_environments.py | 10 ++++++---- 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index 4eba7969d9d..1db0a5bafe8 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -14,13 +14,13 @@ # additional parameters. This command string is re-used for a `docker inspect` # command and will likely cause errors if it is extensively modified, past the # usual group/sudo changes. -command = docker run {docker_args} +#command = docker run {docker_args} # The docker image name that should be started. image = bgruening/docker-ipython-notebook:dev # Additional arguments that are passed to the `docker run` command. -command_inject = --sig-proxy=true -e DEBUG=false +#command_inject = --sig-proxy=true -e DEBUG=false # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the @@ -34,4 +34,4 @@ command_inject = --sig-proxy=true -e DEBUG=false # Try to set the tempdirectory to world execute - this can fix the issue # where 'sudo docker' is not able to mount the folder otherwise. # "finalize namespace chdir to /import permission denied" -wx_tempdir = False +#wx_tempdir = False diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index a9da467510a..248ea2f1e51 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -1,5 +1,5 @@ [main] -# This cannot be changed +# This CANNOT be changed. Eventually will be deprecated password_auth = True # Following options are ignored if using the Galaxy dynamic proxy but # are useful if mapping a range of ports for environment consumption. @@ -15,13 +15,13 @@ password_auth = True # additional parameters. This command string is re-used for a `docker inspect` # command and will likely cause errors if it is extensively modified, past the # usual group/sudo changes. -command = docker run {docker_args} +#command = docker run {docker_args} # The docker image name that should be started. image = erasche/docker-rstudio-notebook:dev # Additional arguments that are passed to the `docker run` command. -command_inject = --sig-proxy=true -e DEBUG=false +#command_inject = --sig-proxy=true -e DEBUG=false # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the @@ -35,4 +35,4 @@ command_inject = --sig-proxy=true -e DEBUG=false # Try to set the tempdirectory to world execute - this can fix the issue # where 'sudo docker' is not able to mount the folder otherwise. # "finalize namespace chdir to /import permission denied" -wx_tempdir = False +#wx_tempdir = False diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index b2964e35fbb..d42e1e0e0be 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -65,10 +65,12 @@ class InteractiveEnviornmentRequest(object): # will need to be recorded here. The ConfigParser doesn't provide a # .get() that will ignore missing sections, so we must make use of # their defaults dictionary instead. - default_dict['command_inject'] = '--sig-proxy=true' - default_dict['docker_hostname'] = 'localhost' - default_dict['wx_tempdir'] = 'False' - default_dict['command_wrapper'] = '' + default_dict = { + 'command': 'docker run {docker_args}', + 'command_inject': '--sig-proxy=true -e DEBUG=false', + 'docker_hostname': 'localhost', + 'wx_tempdir': 'False', + } viz_config = ConfigParser.SafeConfigParser(default_dict) conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" ) if not os.path.exists( conf_path ): From bab1e3b562814c4091200e27ff579c6c54502a13 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Wed, 23 Sep 2015 13:15:50 -0400 Subject: [PATCH 043/178] add update method to folder manager; update root folder name when lib name is updated; refactor exception imports --- lib/galaxy/managers/folders.py | 46 +++++++++++++++++++++++++------- lib/galaxy/managers/libraries.py | 4 +++ 2 files changed, 41 insertions(+), 9 deletions(-) diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py index 7968048bdcd..a588795301d 100644 --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -2,7 +2,13 @@ Manager and Serializer for Library Folders. """ -import galaxy.exceptions +from galaxy.exceptions import ItemAccessibilityException +from galaxy.exceptions import InconsistentDatabase +from galaxy.exceptions import RequestParameterInvalidException +from galaxy.exceptions import InternalServerError +from galaxy.exceptions import AuthenticationRequired +from galaxy.exceptions import InsufficientPermissionsException +from galaxy.exceptions import MalformedId from sqlalchemy.orm.exc import MultipleResultsFound from sqlalchemy.orm.exc import NoResultFound import logging @@ -34,11 +40,11 @@ class FolderManager( object ): try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one() except MultipleResultsFound: - raise galaxy.exceptions.InconsistentDatabase( 'Multiple folders found with the same id.' ) + raise InconsistentDatabase( 'Multiple folders found with the same id.' ) except NoResultFound: - raise galaxy.exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' ) + raise RequestParameterInvalidException( 'No folder found with the id provided.' ) except Exception, e: - raise galaxy.exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) + raise InternalServerError( 'Error loading from the database.' + str( e ) ) folder = self.secure( trans, folder, check_manageable, check_accessible ) return folder @@ -75,10 +81,10 @@ class FolderManager( object ): :raises: AuthenticationRequired, InsufficientPermissionsException """ if not trans.user: - raise galaxy.exceptions.AuthenticationRequired( "Must be logged in to manage Galaxy items.", type='error' ) + raise AuthenticationRequired( "Must be logged in to manage Galaxy items.", type='error' ) current_user_roles = trans.get_current_user_roles() if not trans.app.security_agent.can_manage_library_item( current_user_roles, folder ): - raise galaxy.exceptions.InsufficientPermissionsException( "You don't have permissions to manage this folder.", type='error' ) + raise InsufficientPermissionsException( "You don't have permissions to manage this folder.", type='error' ) else: return folder @@ -126,7 +132,7 @@ class FolderManager( object ): parent_folder = self.get( trans, parent_folder_id ) current_user_roles = trans.get_current_user_roles() if not ( trans.user_is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, parent_folder ) ): - raise galaxy.exceptions.InsufficientPermissionsException( 'You do not have proper permission to create folders under given folder.' ) + raise InsufficientPermissionsException( 'You do not have proper permission to create folders under given folder.' ) new_folder = trans.app.model.LibraryFolder( name=new_folder_name, description=new_folder_description ) # We are associating the last used genome build with folders, so we will always # initialize a new folder with the first dbkey in genome builds list which is currently @@ -139,6 +145,28 @@ class FolderManager( object ): trans.app.security_agent.copy_library_permissions( trans, parent_folder, new_folder ) return new_folder + def update( self, trans, folder, name=None, description=None): + """ + Update the given folder's name or description. + """ + changed = False + if not trans.user_is_admin(): + if not self.check_manageable( trans, folder ): + raise InsufficientPermissionsException( "Only admins can update library folders." ) + if folder.deleted == True: + raise ItemAccessibilityException( "You cannot update deleted library folder. Undelete it first." ) + if name is not None: + folder.name = name + changed = True + if description is not None: + folder.description = description + changed = True + if changed: + trans.sa_session.add( folder ) + trans.sa_session.flush() + return folder + + def delete( self, trans, folder, undelete=False ): """ Mark given folder deleted/undeleted based on the flag. @@ -214,7 +242,7 @@ class FolderManager( object ): if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): cut_id = encoded_folder_id[ 1: ] else: - raise galaxy.exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) + raise MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) return cut_id def decode_folder_id( self, trans, encoded_folder_id ): @@ -232,7 +260,7 @@ class FolderManager( object ): try: decoded_id = trans.security.decode_id( encoded_folder_id ) except ValueError: - raise galaxy.exceptions.MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( encoded_folder_id ) ) ) + raise MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( encoded_folder_id ) ) ) return decoded_id def cut_and_decode( self, trans, encoded_folder_id ): diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py index 3092ded845d..fe83f399382 100644 --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -10,6 +10,7 @@ from sqlalchemy.orm.exc import MultipleResultsFound from sqlalchemy.orm.exc import NoResultFound from galaxy import exceptions +from galaxy.managers import folders from galaxy.util import pretty_print_time_interval log = logging.getLogger( __name__ ) @@ -73,6 +74,9 @@ class LibraryManager( object ): if name is not None: library.name = name changed = True + # When library is renamed the root folder has to be renamed too. + folder_manager = folders.FolderManager() + folder_manager.update( trans, library.root_folder, name=name ) if description is not None: library.description = description changed = True From c9e9c95514e50f9a260b5ed342a715d2846fd4fe Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 12:35:00 -0500 Subject: [PATCH 044/178] Correct small logic bugs, add logging --- lib/galaxy/web/base/interactive_environments.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index 2c1b3c3b71d..fb906fd67d2 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -246,11 +246,15 @@ class InteractiveEnviornmentRequest(object): containers with multiple ports working. """ command = self.attr.viz_config.get("docker", "command") - command.replace( + command = command.replace( "run {docker_args}", "inspect %s" % container_id ) - output = check_output(command) + log.info("Inspecting docker container {0} with command [{1}]".format( + container_id, + command + )) + output = check_output(command, shell=True) inspect_data = json.loads(output) # [{ # "NetworkSettings" : { @@ -267,7 +271,7 @@ class InteractiveEnviornmentRequest(object): for binding in port_mappings[port_name]: mappings.append(( port_name.replace('/tcp', '').replace('/udp', ''), - port_mappings[port_name][binding]['HostIp'], - port_mappings[port_name][binding]['HostPort'] + binding['HostIp'], + binding['HostPort'] )) return mappings From a02df53f3356a03f3784070a4c50accfbc00187f Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 12:51:37 -0500 Subject: [PATCH 045/178] Correct IPython notebooks to new URL --- .../interactive_environments/ipython/templates/ipython.mako | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/templates/ipython.mako b/config/plugins/interactive_environments/ipython/templates/ipython.mako index 8edd23dc423..4d8f780592f 100644 --- a/config/plugins/interactive_environments/ipython/templates/ipython.mako +++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako @@ -40,8 +40,8 @@ ie_request.launch(env_override={ ## General IE specific # Access URLs for the notebook from within galaxy. -notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/notebooks/ipython_galaxy_notebook.ipynb') -notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree') +notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/notebooks/ipython_galaxy_notebook.ipynb') +notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/login?next=%2Fipython%2Ftree') %> From a5b296b8ecd262d58a17049f5a9aeeecb7649621 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 12:52:13 -0500 Subject: [PATCH 046/178] Include user email Fixes bgruening/docker-ipython-notebook#51 --- lib/galaxy/web/base/interactive_environments.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index fb906fd67d2..772037993e5 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -102,6 +102,7 @@ class InteractiveEnviornmentRequest(object): 'remote_host': request.remote_addr, # DOCKER_PORT is NO LONGER AVAILABLE. All IEs must update. 'cors_origin': request.host_url, + 'user_email': self.trans.user.email, } if self.attr.viz_config.has_option("docker", "galaxy_url"): From 3f3c1b679bfef5dbd75d7c267d25fd2979f362d1 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 13:05:37 -0500 Subject: [PATCH 047/178] Pin IE versions --- .../interactive_environments/ipython/config/ipython.ini.sample | 2 +- .../interactive_environments/rstudio/config/rstudio.ini.sample | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index ca488a1d594..01fbc73e8e1 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -12,7 +12,7 @@ command = docker # The docker image name that should be started. -image = bgruening/docker-ipython-notebook:dev +image = bgruening/docker-ipython-notebook:15.07 # Additional arguments that are passed to the `docker run` command. command_inject = --sig-proxy=true -e DEBUG=false diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index ed0b64ff7ce..e314254c385 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -7,7 +7,7 @@ ssl = False [docker] command = docker -image = erasche/docker-rstudio-notebook:dev +image = erasche/docker-rstudio-notebook:15.07 # Additional arguments that are passed to the `docker run` command. `-u` # settings are completely ignored. From b28810444d60dabccee8239a8bff0febc3fc8876 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Wed, 23 Sep 2015 14:14:42 -0400 Subject: [PATCH 048/178] expose API to update lib folder; make manager not update when nothing changes --- lib/galaxy/managers/folders.py | 6 ++-- lib/galaxy/webapps/galaxy/api/folders.py | 36 ++++++++++++++++++++++-- lib/galaxy/webapps/galaxy/buildapp.py | 6 ++++ 3 files changed, 42 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py index a588795301d..572a4eb90a9 100644 --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -152,13 +152,13 @@ class FolderManager( object ): changed = False if not trans.user_is_admin(): if not self.check_manageable( trans, folder ): - raise InsufficientPermissionsException( "Only admins can update library folders." ) + raise InsufficientPermissionsException( "You do not have proper permission to update library folders." ) if folder.deleted == True: raise ItemAccessibilityException( "You cannot update deleted library folder. Undelete it first." ) - if name is not None: + if name is not None and name != folder.name: folder.name = name changed = True - if description is not None: + if description is not None and description != folder.description: folder.description = description changed = True if changed: diff --git a/lib/galaxy/webapps/galaxy/api/folders.py b/lib/galaxy/webapps/galaxy/api/folders.py index 8671bdd336f..74b9ed084f5 100644 --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -246,7 +246,6 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt :returns: detailed folder information :rtype: dictionary - :raises: ItemAccessibilityException, MalformedId, ObjectNotFound """ folder = self.folder_manager.get( trans, self.folder_manager.cut_and_decode( trans, id ), True ) undelete = util.string_as_bool( kwd.get( 'undelete', False ) ) @@ -255,11 +254,42 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt return folder_dict @expose_api - def update( self, trans, id, library_id, payload, **kwd ): + def update( self, trans, encoded_folder_id, **kwd ): """ - PUT /api/folders/{encoded_folder_id} + * PATCH /api/folders/{encoded_folder_id} + Updates the folder defined by an ``encoded_folder_id`` with the data in the payload. + .. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`. + + :param id: the encoded id of the folder + :type id: an encoded id string + + :param payload: (required) dictionary structure containing:: + 'name': new folder's name, cannot be empty + 'description': new folder's description + :type payload: dict + + :returns: detailed folder information + :rtype: dict + + :raises: RequestParameterMissingException """ + decoded_folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id ) + folder = self.folder_manager.get( trans, decoded_folder_id ) + + payload = kwd.get( 'payload', None ) + if payload: + name = payload.get( 'name', None ) + if not name: + raise exceptions.RequestParameterMissingException( "Parameter 'name' of folder is required. You cannot remove it." ) + if payload.get( 'description', None ) or payload.get( 'description', None ) == '': + description = payload.get( 'description', None ) + else: + raise exceptions.RequestParameterMissingException( "You did not specify any payload." ) + updated_folder = self.folder_manager.update( trans, folder, name, description ) + folder_dict = self.folder_manager.get_folder_dict( trans, updated_folder ) + return folder_dict + raise exceptions.NotImplemented( 'Updating folder through this endpoint is not implemented yet.' ) # TODO move to Role manager diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index ef1ca2e96f1..ab9490e066c 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -487,6 +487,12 @@ def populate_api_routes( webapp, app ): action='create', conditions=dict( method=[ "POST" ] ) ) + webapp.mapper.connect( 'update_folder', + '/api/folders/{encoded_folder_id}', + controller='folders', + action='update', + conditions=dict( method=[ "PATCH", "PUT" ] ) ) + webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) From 10af45012735603385ac076f7b517dfe70314484 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 14:22:32 -0500 Subject: [PATCH 049/178] Move run into python from template --- .../interactive_environments/ipython/config/ipython.ini.sample | 2 +- .../interactive_environments/rstudio/config/rstudio.ini.sample | 2 +- lib/galaxy/web/base/interactive_environments.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index 1db0a5bafe8..3af2bd39e7c 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -14,7 +14,7 @@ # additional parameters. This command string is re-used for a `docker inspect` # command and will likely cause errors if it is extensively modified, past the # usual group/sudo changes. -#command = docker run {docker_args} +#command = docker {docker_args} # The docker image name that should be started. image = bgruening/docker-ipython-notebook:dev diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index 248ea2f1e51..f8ed8c8027f 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -15,7 +15,7 @@ password_auth = True # additional parameters. This command string is re-used for a `docker inspect` # command and will likely cause errors if it is extensively modified, past the # usual group/sudo changes. -#command = docker run {docker_args} +#command = docker {docker_args} # The docker image name that should be started. image = erasche/docker-rstudio-notebook:dev diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index d42e1e0e0be..a7719296d21 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -190,7 +190,7 @@ class InteractiveEnviornmentRequest(object): # Then we format in the entire docker command in place of # {docker_args}, so as to let the admin not worry about which args are # getting passed - command = command.format(docker_args='{command_inject} {environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {volume_str} {image}') + command = command.format(docker_args='run {command_inject} {environment} -d -p {port_ext}:{port_int} -v "{temp_dir}:/import/" {volume_str} {image}') # Once that's available, we format again with all of our arguments command = command.format( command_inject=self.attr.viz_config.get("docker", "command_inject"), From d7bff96778b11a3ed2838103aea6cceca43bdfb4 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 15:02:40 -0500 Subject: [PATCH 050/178] Correct stupid mistake from lack of testing --- lib/galaxy/web/base/interactive_environments.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index a7719296d21..a3614639f9f 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -66,7 +66,7 @@ class InteractiveEnviornmentRequest(object): # .get() that will ignore missing sections, so we must make use of # their defaults dictionary instead. default_dict = { - 'command': 'docker run {docker_args}', + 'command': 'docker {docker_args}', 'command_inject': '--sig-proxy=true -e DEBUG=false', 'docker_hostname': 'localhost', 'wx_tempdir': 'False', From 06a67c8c109dcf59425b53b80dcb5419f5e814af Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 15:02:02 -0500 Subject: [PATCH 051/178] Add dynamic_proxy_prefix configuration Normally the proxy binds to :8800 and runs containers under :8800/ipython/... which is great... until you have an upstream proxy like apache wrapping that at the url FQDN/ipython and suddenly your cookies aren't available because they're specific to /galaxy. Thus, when an upstream proxy is in use, we correct the proxy's path to: with :8800/{cookie_path}/gie_proxy/ipython/... which behaves much more nicely with upstraem proxies. --- config/galaxy.ini.sample | 6 ++++++ lib/galaxy/config.py | 1 + lib/galaxy/web/proxy/__init__.py | 8 +++++--- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 5dadaaa29b4..787962d2f95 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -574,6 +574,12 @@ nglims_config_file = tool-data/nglims.yaml # nodejs to wrap connections in SSL). #dynamic_proxy_external_proxy=False +# Additionally, when the dynamic proxy is proxied by an upstream server, you'll +# want to specify a prefixed URL so both Galaxy and the proxy reside under the +# same path that your cookies are under. This will result in a url like +# https://FQDN/galaxy-prefix/gie_proxy for proxying +#dynamic_proxy_prefix=gie_proxy + # -- Logging and Debugging # If True, Galaxy will attempt to configure a simple root logger if a diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 28acdc42262..286ca8b38ef 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -443,6 +443,7 @@ class Configuration( object ): self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) ) self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" ) self.dynamic_proxy_external_proxy = string_as_bool( kwargs.get( "dynamic_proxy_external_proxy", "False" ) ) + self.dynamic_proxy_prefix = kwargs.get( "dynamic_proxy_prefix", "gie_proxy" ) # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) diff --git a/lib/galaxy/web/proxy/__init__.py b/lib/galaxy/web/proxy/__init__.py index 30738ad6c11..fda64907c60 100644 --- a/lib/galaxy/web/proxy/__init__.py +++ b/lib/galaxy/web/proxy/__init__.py @@ -17,7 +17,9 @@ SECURE_COOKIE = "galaxysession" class ProxyManager(object): def __init__( self, config ): - for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug", "dynamic_proxy_external_proxy" ]: + for option in ["manage_dynamic_proxy", "dynamic_proxy_bind_port", + "dynamic_proxy_bind_ip", "dynamic_proxy_debug", + "dynamic_proxy_external_proxy", "dynamic_proxy_prefix"]: setattr( self, option, getattr( config, option ) ) self.launch_by = "node" # TODO: Support docker if self.manage_dynamic_proxy: @@ -44,9 +46,9 @@ class ProxyManager(object): host = host[0:host.index(':')] scheme = trans.request.scheme if not self.dynamic_proxy_external_proxy: - proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + proxy_url = '%s://%s:%d/%s' % (scheme, host, self.dynamic_proxy_bind_port, self.dynamic_proxy_prefix) else: - proxy_url = '%s://%s' % (scheme, host) + proxy_url = '%s://%s/%s' % (scheme, host, self.dynamic_proxy_prefix) return { 'proxy_url': proxy_url, 'proxied_port': proxy_requests.port, From 1ad3308b49a6f5a25ef357300b47791987acbb22 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Wed, 23 Sep 2015 15:09:03 -0500 Subject: [PATCH 052/178] Remove small formatting issue --- .../interactive_environments/ipython/config/ipython.ini.sample | 2 +- .../interactive_environments/rstudio/config/rstudio.ini.sample | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index 3af2bd39e7c..fc29f539d85 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -32,6 +32,6 @@ image = bgruening/docker-ipython-notebook:dev #docker_hostname = localhost # Try to set the tempdirectory to world execute - this can fix the issue -# where 'sudo docker' is not able to mount the folder otherwise. +# where 'sudo docker' is not able to mount the folder otherwise. # "finalize namespace chdir to /import permission denied" #wx_tempdir = False diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index f8ed8c8027f..3f86bca63ba 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -33,6 +33,6 @@ image = erasche/docker-rstudio-notebook:dev #docker_hostname = localhost # Try to set the tempdirectory to world execute - this can fix the issue -# where 'sudo docker' is not able to mount the folder otherwise. +# where 'sudo docker' is not able to mount the folder otherwise. # "finalize namespace chdir to /import permission denied" #wx_tempdir = False From 57f023529aef13723cb1555dc3ad5ea59aef009c Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 23 Sep 2015 14:36:18 -0400 Subject: [PATCH 053/178] Remove tool form mako Fix new-line --- client/galaxy/scripts/mvc/app/app-analysis.js | 42 ++-- client/galaxy/scripts/mvc/app/app-view.js | 9 +- client/galaxy/scripts/mvc/form/form-input.js | 15 +- .../galaxy/scripts/mvc/form/form-section.js | 3 +- client/galaxy/scripts/mvc/form/form-view.js | 10 +- .../scripts/mvc/tools/tools-form-base.js | 51 ++-- client/galaxy/scripts/mvc/tools/tools-form.js | 79 +++---- lib/galaxy/tools/__init__.py | 41 +--- lib/galaxy/webapps/galaxy/api/jobs.py | 8 +- .../webapps/galaxy/controllers/tool_runner.py | 223 +----------------- static/maps/mvc/app/app-analysis.js.map | 2 +- static/maps/mvc/app/app-view.js.map | 2 +- static/maps/mvc/form/form-input.js.map | 2 +- static/maps/mvc/form/form-section.js.map | 2 +- static/maps/mvc/form/form-view.js.map | 2 +- static/maps/mvc/tools/tools-form-base.js.map | 2 +- static/maps/mvc/tools/tools-form.js.map | 2 +- static/scripts/mvc/app/app-analysis.js | 2 +- static/scripts/mvc/app/app-view.js | 2 +- static/scripts/mvc/form/form-input.js | 2 +- static/scripts/mvc/form/form-section.js | 2 +- static/scripts/mvc/form/form-view.js | 2 +- static/scripts/mvc/tools/tools-form-base.js | 2 +- static/scripts/mvc/tools/tools-form.js | 2 +- templates/webapps/galaxy/tool_form.mako | 26 -- test/unit/tools/test_execution.py | 6 +- 26 files changed, 140 insertions(+), 401 deletions(-) delete mode 100644 templates/webapps/galaxy/tool_form.mako diff --git a/client/galaxy/scripts/mvc/app/app-analysis.js b/client/galaxy/scripts/mvc/app/app-analysis.js index 97abe312d96..d8f73312b10 100644 --- a/client/galaxy/scripts/mvc/app/app-analysis.js +++ b/client/galaxy/scripts/mvc/app/app-analysis.js @@ -1,34 +1,38 @@ define(['utils/utils', 'mvc/tools', 'mvc/upload/upload-view', 'mvc/ui/ui-misc', - 'mvc/history/options-menu', 'mvc/history/history-panel-edit-current'], - function( Utils, Tools, Upload, Ui, optionsMenu, HistoryPanel ) { + 'mvc/history/options-menu', 'mvc/history/history-panel-edit-current', 'mvc/tools/tools-form'], + function( Utils, Tools, Upload, Ui, optionsMenu, HistoryPanel, ToolsForm ) { /* Builds the center panel */ var CenterPanel = Backbone.View.extend({ initialize: function( options ) { this.options = Utils.merge( options, {} ); this.setElement( this._template() ); - var params = this.options.params; - this.$( '#galaxy_main' ).prop( 'src', Galaxy.root + ( - ( params.tool_id && ( 'tool_runner?' + $.param( params ) ) ) || - ( params.workflow_id && ( 'workflow/run?id=' + params.workflow_id ) ) || - ( params.m_c && ( params.m_c + '/' + params.m_a ) ) || - ( Galaxy.config.require_login && !Galaxy.user.id && 'user/login') || - 'root/welcome' - )); var self = this; this.$( '#galaxy_main' ).on( 'load', function() { - $( this ).show(); - self.$( '#center-panel' ).empty().hide(); - var galaxy_main = this.contentWindow; - if ( galaxy_main ) { + var location = this.contentWindow && this.contentWindow.location; + if ( location && location.host ) { + $( this ).show(); + self.$( '#center-panel' ).empty().hide(); Galaxy.trigger( 'galaxy_main:load', { - fullpath: galaxy_main.location.pathname + galaxy_main.location.search + galaxy_main.location.hash, - pathname: galaxy_main.location.pathname, - search : galaxy_main.location.search, - hash : galaxy_main.location.hash + fullpath: location.pathname + location.search + location.hash, + pathname: location.pathname, + search : location.search, + hash : location.hash }); } }); + var params = $.extend( {}, Galaxy.params ); + if ( params.tool_id || params.job_id ) { + params.tool_id && ( params.id = params.tool_id ); + this.display( ( new ToolsForm.View( params ) ).$el ); + } else { + this.$( '#galaxy_main' ).prop( 'src', Galaxy.root + ( + ( params.workflow_id && ( 'workflow/run?id=' + params.workflow_id ) ) || + ( params.m_c && ( params.m_c + '/' + params.m_a ) ) || + ( Galaxy.config.require_login && !Galaxy.user.id && 'user/login') || + 'root/welcome' + )); + } }, display: function( $el ) { this.$( '#galaxy_main' ).hide(); @@ -206,4 +210,4 @@ define(['utils/utils', 'mvc/tools', 'mvc/upload/upload-view', 'mvc/ui/ui-misc', center : CenterPanel, right : RightPanel } -}); +}); \ No newline at end of file diff --git a/client/galaxy/scripts/mvc/app/app-view.js b/client/galaxy/scripts/mvc/app/app-view.js index a67e1818eb2..f735b289ac6 100644 --- a/client/galaxy/scripts/mvc/app/app-view.js +++ b/client/galaxy/scripts/mvc/app/app-view.js @@ -8,12 +8,17 @@ define(['utils/utils', 'galaxy.masthead', 'galaxy.menu', 'galaxy.frame', return Backbone.View.extend({ initialize: function( options ) { this.options = Utils.merge( options, {} ); - this.params = this.options.params; this.setElement( this._template( options ) ); // register this view Galaxy.app = this; + // url request parameters + Galaxy.params = this.options.params; + + // shared backbone router + Galaxy.router = new Backbone.Router(); + // configure body $( 'body' ).append( this.$el ); ensure_dd_helper(); @@ -131,4 +136,4 @@ define(['utils/utils', 'galaxy.masthead', 'galaxy.menu', 'galaxy.frame', '
    '; } }); -}); +}); \ No newline at end of file diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js index f62a2fbe616..ae2ab755e2f 100644 --- a/client/galaxy/scripts/mvc/form/form-input.js +++ b/client/galaxy/scripts/mvc/form/form-input.js @@ -100,14 +100,11 @@ define([], function() { /** Main Template */ _template: function(options) { - // create table element - var tmp = '
    ' + + var tmp = '
    ' + '
    ' + '' + '
    ' + '
    '; - - // is optional if (options.collapsible) { tmp += '
    ' + '' + options.label + @@ -115,12 +112,8 @@ define([], function() { } else { tmp += options.label; } - - // finalize title tmp += '
    ' + '
    '; - - // add help tmp += '
    '; if (options.help) { tmp += options.help; @@ -129,13 +122,9 @@ define([], function() { } } tmp += '
    '; - - // finalize tmp += '
    ' + '
    '; - - // return input element return tmp; } }); -}); +}); \ No newline at end of file diff --git a/client/galaxy/scripts/mvc/form/form-section.js b/client/galaxy/scripts/mvc/form/form-section.js index c4a344e58ca..f306604d0ca 100644 --- a/client/galaxy/scripts/mvc/form/form-section.js +++ b/client/galaxy/scripts/mvc/form/form-section.js @@ -316,6 +316,7 @@ define(['utils/utils', // create input field wrapper var input_element = new InputElement(this.app, { + name : input_def.name, label : input_def.label || input_def.name, value : input_def.value, default_value : input_def.default_value, @@ -348,4 +349,4 @@ define(['utils/utils', return { View: View }; -}); +}); \ No newline at end of file diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js index c6ea1a61624..add567a665c 100644 --- a/client/galaxy/scripts/mvc/form/form-view.js +++ b/client/galaxy/scripts/mvc/form/form-view.js @@ -206,12 +206,8 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', inputs : this.options.inputs }); - // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible) { - this.$el.hide(); - $('#tool-form-classic').show(); - return; - } + // remove tooltips + $( '.tooltip' ).remove(); // create portlet this.portlet = new Portlet.View({ @@ -245,4 +241,4 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', console.debug('tools-form-base::initialize() - Completed.'); } }); -}); +}); \ No newline at end of file diff --git a/client/galaxy/scripts/mvc/tools/tools-form-base.js b/client/galaxy/scripts/mvc/tools/tools-form-base.js index 5f4406d5bc2..1dd7002d314 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -44,6 +44,9 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', } }, this.options); + // allow option customization + this.options.customize && this.options.customize( this.options ); + // create form this.form = new Form(this.options); @@ -65,20 +68,19 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', this.options.id = options.id; this.options.version = options.version; - if (options.job_id) { + if ( options.job_id ) { build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun'; } else { - // construct url var build_url = Galaxy.root + 'api/tools/' + options.id + '/build?'; - if (options.dataset_id) { - build_url += 'dataset_id=' + options.dataset_id; - } else { + if ( options.version ) { build_url += 'tool_version=' + options.version + '&'; - var loc = top.location.href; - var pos = loc.indexOf('?'); - if (loc.indexOf('tool_id=') != -1 && pos !== -1) { - build_url += loc.slice(pos + 1); - } + } + if ( Galaxy.params && Galaxy.params.tool_id == options.id ) { + _.each( Galaxy.params, function ( item, key ) { + if ( [ 'tool_version', 'tool_id' ].indexOf( key ) == -1 ) { + build_url += key + '=' + item + '&'; + } + } ); } } @@ -117,18 +119,23 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', // show error var error_message = response.error || response.err_msg || 'Uncaught error.'; - if (self.form == undefined){ - self.form = new Form(); - } - Galaxy.modal.show({ - title : 'Tool cannot be executed', - body : error_message, - buttons : { - 'Close' : function() { - Galaxy.modal.hide(); + if ( self.$el.is(':empty') ) { + self.$el.prepend((new Ui.Message({ + message : error_message, + status : 'danger', + persistent : true + })).$el); + } else { + Galaxy.modal.show({ + title : 'Tool request failed', + body : error_message, + buttons : { + 'Close' : function() { + Galaxy.modal.hide(); + } } - } - }); + }); + } } }); }, @@ -350,4 +357,4 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', } } }); -}); +}); \ No newline at end of file diff --git a/client/galaxy/scripts/mvc/tools/tools-form.js b/client/galaxy/scripts/mvc/tools/tools-form.js index f678789dc26..745c6e2ff26 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -2,53 +2,50 @@ This is the regular tool form. */ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tools/tools-form-base', 'mvc/tools/tools-jobs'], - function(Utils, Ui, ToolFormBase, ToolJobs) { - - // create form view + function( Utils, Ui, ToolFormBase, ToolJobs ) { var View = ToolFormBase.extend({ - // initialize - initialize: function(options) { - // execute button + initialize: function( options ) { var self = this; - var execute = new Ui.Button({ - icon : 'fa-check', - tooltip : 'Execute: ' + options.name, - title : 'Execute', - cls : 'btn btn-primary', - floating : 'clear', - onclick : function() { - execute.wait(); - self.form.portlet.disable(); - ToolJobs.submit(self.form, self.options, function() { - execute.unwait(); - self.form.portlet.enable(); - }); + ToolFormBase.prototype.initialize.call( this, Utils.merge({ + customize: function( options ) { + // build execute button + options.buttons = { + execute : execute_btn = new Ui.Button({ + icon : 'fa-check', + tooltip : 'Execute: ' + options.name + ' (' + options.version + ')', + title : 'Execute', + cls : 'btn btn-primary', + floating : 'clear', + onclick : function() { + execute_btn.wait(); + self.form.portlet.disable(); + ToolJobs.submit( self.form, options, function() { + execute_btn.unwait(); + self.form.portlet.enable(); + } ); + } + }) + }; + + // remap feature + if ( options.job_id && options.job_remap ) { + options.inputs[ 'rerun_remap_job_id' ] = { + label : 'Resume dependencies from this job', + name : 'rerun_remap_job_id', + type : 'select', + display : 'radio', + ignore : '__ignore__', + value : '__ignore__', + options : [ [ 'Yes', options.job_id ], [ 'No', '__ignore__' ] ], + help : 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.' + } + } } - }); - // add remap button - if (options.job_id && options.job_remap) { - options.inputs['rerun_remap_job_id'] = { - label : 'Resume dependencies from this job', - name : 'rerun_remap_job_id', - type : 'select', - display : 'radio', - ignore : '__ignore__', - value : '__ignore__', - options : [['Yes', options.job_id], ['No', '__ignore__']], - help : 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.' - } - } - // create options dictionary - options = Utils.merge(options, { - buttons : { - execute : execute - } - }); - ToolFormBase.prototype.initialize.call(this, options); + }, options ) ); } }); return { View: View }; -}); +}); \ No newline at end of file diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 8c9ab61ffd5..081a289791c 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -451,7 +451,7 @@ class Tool( object, Dictifiable ): requires_setting_metadata = True default_tool_action = DefaultToolAction dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) - default_template = 'tool_form.mako' + default_template = '' def __init__( self, config_file, tool_source, app, guid=None, repository_id=None, allow_code_files=True ): """Load a tool from the config named by `config_file`""" @@ -2328,15 +2328,11 @@ class Tool( object, Dictifiable ): return tool_dict - def to_json(self, trans, kwd={}, is_workflow=False): + def to_json(self, trans, kwd={}, job=None, is_workflow=False): """ Recursively creates a tool dictionary containing repeats, dynamic options and updated states. """ - job_id = kwd.get('__job_id__', None) - dataset_id = kwd.get('__dataset_id__', None) history_id = kwd.get('history_id', None) - - # history id history = None try: if history_id is not None: @@ -2351,34 +2347,6 @@ class Tool( object, Dictifiable ): log.exception('tools::to_json - %s.' % error) return { 'error': error } - # load job details if provided - job = None - if job_id: - try: - job_id = trans.security.decode_id( job_id ) - job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) - except Exception, exception: - trans.response.status = 500 - log.error('Failed to retrieve job.') - return { 'error': 'Failed to retrieve job.' } - elif dataset_id: - try: - dataset_id = trans.security.decode_id( dataset_id ) - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) - if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ): - trans.response.status = 500 - log.error('User has no access to dataset.') - return { 'error': 'User has no access to dataset.' } - job = data.creating_job - if not job: - trans.response.status = 500 - log.error('Creating job not found.') - return { 'error': 'Creating job not found.' } - except Exception, exception: - trans.response.status = 500 - log.error('Failed to get job information.') - return { 'error': 'Failed to get job information.' } - # load job parameters into incoming tool_message = '' if job: @@ -2668,6 +2636,7 @@ class Tool( object, Dictifiable ): # add additional properties tool_model.update({ + 'id' : self.id, 'help' : tool_help, 'citations' : tool_citations, 'biostar_url' : trans.app.config.biostar_url, @@ -2677,7 +2646,9 @@ class Tool( object, Dictifiable ): 'requirements' : tool_requirements, 'errors' : state_errors, 'state_inputs' : state_inputs, - 'job_remap' : self._get_job_remap(job) + 'job_id' : trans.security.encode_id( job.id ) if job else None, + 'job_remap' : self._get_job_remap( job ), + 'history_id' : trans.security.encode_id( history.id ) }) # check for errors diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py index 0bb5c690fa6..f7ac3c2431b 100644 --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -204,12 +204,10 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ): job = self.__get_job(trans, id) if not job: raise exceptions.ObjectNotFound("Could not access job with id '%s'" % id) - tool_id = job.tool_id - tool_version = job.tool_version - tool = self.app.toolbox.get_tool( tool_id, tool_version ) + tool = self.app.toolbox.get_tool( job.tool_id, job.tool_version ) if not tool.is_workflow_compatible: - raise exceptions.ConfigDoesNotAllowException( "Tool '%s' cannot be rerun." % ( tool_id ) ) - return tool.to_json(trans, kwd={'__job_id__' : id}) + raise exceptions.ConfigDoesNotAllowException( "Tool '%s' cannot be rerun." % ( job.tool_id ) ) + return tool.to_json(trans, {}, job=job) def __dictify_associations( self, trans, *association_lists ): rval = [] diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py index 63c2d478611..0231f02750c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -12,13 +12,7 @@ from galaxy import web from galaxy.tools import DefaultToolState from galaxy.tools import DataSourceTool from galaxy.tools.actions import upload_common -from galaxy.tools.parameters import params_to_incoming -from galaxy.tools.parameters import visit_input_values -from galaxy.tools.parameters.basic import DataToolParameter -from galaxy.tools.parameters.basic import DataCollectionToolParameter -from galaxy.tools.parameters.basic import UnvalidatedValue from galaxy.util.bunch import Bunch -from galaxy.util.hash_util import is_hashable from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController @@ -55,94 +49,21 @@ class ToolRunner( BaseUIController ): return self.get_toolbox().get_tool_components( tool_id, tool_version, get_loaded_tools_by_lineage, set_selected ) @web.expose - def index( self, trans, tool_id=None, from_noframe=None, **kwd ): - # No tool id passed, redirect to main page + def index( self, trans, tool_id=None, **kwd ): if tool_id is None: return trans.response.send_redirect( url_for( controller="root", action="welcome" ) ) - # When the tool form is initially loaded, the received kwd will not include a 'refresh' - # entry (which only is included when another option is selected in the tool_version_select_field), - # so the default selected option should be the most recent version of the tool. The following - # check will mae sure this occurs. - refreshed_on_change = kwd.get( 'refresh', False ) - tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, - tool_version=None, - get_loaded_tools_by_lineage=False, - set_selected=refreshed_on_change ) - # No tool matching the tool id, display an error (shouldn't happen) - if not tool or not tool.allow_user_access( trans.user ): - log.error( "index called with tool id '%s' but no such tool exists", tool_id ) - trans.log_event( "Tool id '%s' does not exist" % tool_id ) - trans.response.status = 404 - return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) )) - if tool.require_login and not trans.user: - message = "You must be logged in to use this tool." - status = "info" - redirect = url_for( controller='tool_runner', action='index', tool_id=tool_id, **kwd ) - return trans.response.send_redirect( url_for( controller='user', - action='login', - cntrller='user', - message=message, - status=status, - redirect=redirect ) ) - - def _validated_params_for( kwd ): - params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers - # do param translation here, used by datasource tools - if tool.input_translator: - tool.input_translator.translate( params ) - return params - - params = _validated_params_for( kwd ) - # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), - # so make sure to create a new history if we've never had one before. - history = tool.get_default_history_by_trans( trans, create=True ) - try: - template, vars = tool.handle_input( trans, params.__dict__ ) - except KeyError: - # This error indicates (or at least can indicate) there was a - # problem with the stored tool_state - it is incompatible with - # this variant of the tool - possibly because the tool changed - # or because the tool version changed. - del kwd[ "tool_state" ] - params = _validated_params_for( kwd ) - template, vars = tool.handle_input( trans, params.__dict__ ) - if len( params ) > 0: - trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) - add_frame = AddFrameData() - add_frame.debug = trans.debug - if from_noframe is not None: - add_frame.wiki_url = trans.app.config.wiki_url - add_frame.from_noframe = True - return trans.fill_template( template, - history=history, - toolbox=self.get_toolbox(), - tool_version_select_field=tool_version_select_field, - tool=tool, - util=galaxy.util, - add_frame=add_frame, - form_input_auto_focus=True, - **vars ) + else: + return trans.response.send_redirect( url_for( controller="root", tool_id=tool_id ) ) @web.expose - def rerun( self, trans, id=None, from_noframe=None, job_id=None, **kwd ): + def rerun( self, trans, id=None, job_id=None, **kwd ): """ Given a HistoryDatasetAssociation id, find the job and that created the dataset, extract the parameters, and display the appropriate tool form with parameters already filled in. """ - if job_id: - try: - job_id = trans.security.decode_id( job_id ) - job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) - except: - error( "Invalid value for 'job_id' parameter" ) - if not trans.user_is_admin(): - for data_assoc in job.output_datasets: - # only allow rerunning if user is allowed access to the dataset. - if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data_assoc.dataset.dataset ): - error( "You are not allowed to rerun this job" ) - param_error_text = "Failed to get parameters for job id %d " % job_id - else: + + if job_id is None: if not id: error( "'id' parameter is required" ) try: @@ -160,135 +81,11 @@ class ToolRunner( BaseUIController ): error( "You are not allowed to access this dataset" ) # Get the associated job, if any. job = data.creating_job - if not job: - raise Exception("Failed to get job information for dataset hid %d" % data.hid) - param_error_text = "Failed to get parameters for dataset id %d " % data.id - # Get the tool object - tool_id = job.tool_id - tool_version = job.tool_version - try: - tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, - tool_version=tool_version, - get_loaded_tools_by_lineage=False, - set_selected=True ) - if ( tool.id == job.tool_id or tool.old_id == job.tool_id ) and tool.version == job.tool_version: - tool_id_version_message = '' - elif tool.id == job.tool_id: - if job.tool_version is None: - # For some reason jobs don't always keep track of the tool version. - tool_id_version_message = '' - else: - tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version - if len( tools ) > 1: - tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.' - else: - tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.' + if job: + job_id = trans.security.encode_id( job.id ) else: - if len( tools ) > 1: - tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version - tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.' - else: - tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % ( job.tool_id, job.tool_version ) - tool_id_version_message += 'currently available. You can rerun the job with this tool, which is a derivation of the original tool.' - assert tool is not None, 'Requested tool has not been loaded.' - except: - # This is expected so not an exception. - tool_id_version_message = '' - error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) - if not tool.allow_user_access( trans.user ): - error( "The requested tool is unknown." ) - # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now - if not tool.is_workflow_compatible: - error( "The '%s' tool does not currently support rerunning." % tool.name ) - # Get the job's parameters - try: - params_objects = job.get_param_values( trans.app, ignore_errors=True ) - except: - raise Exception( param_error_text ) - upgrade_messages = tool.check_and_update_param_values( params_objects, trans, update_values=False ) - # Need to remap dataset parameters. Job parameters point to original - # dataset used; parameter should be the analygous dataset in the - # current history. - history = trans.get_history() - hda_source_dict = {} # Mapping from HDA in history to source HDAs. - for hda in history.datasets: - source_hda = hda.copied_from_history_dataset_association - while source_hda: # should this check library datasets as well? - # FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories, - # but is still less than perfect when eg individual datasets are copied between histories - if source_hda not in hda_source_dict or source_hda.hid == hda.hid: - hda_source_dict[ source_hda ] = hda - source_hda = source_hda.copied_from_history_dataset_association - # Ditto for dataset collections. - hdca_source_dict = {} - for hdca in history.dataset_collections: - source_hdca = hdca.copied_from_history_dataset_collection_association - while source_hdca: - if source_hdca not in hdca_source_dict or source_hdca.hid == hdca.hid: - hdca_source_dict[ source_hdca ] = hdca - source_hdca = source_hdca.copied_from_history_dataset_collection_association - - # Unpack unvalidated values to strings, they'll be validated when the - # form is submitted (this happens when re-running a job that was - # initially run by a workflow) - # This needs to be done recursively through grouping parameters - def rerun_callback( input, value, prefixed_name, prefixed_label ): - if isinstance( value, UnvalidatedValue ): - try: - return input.to_html_value( value.value, trans.app ) - except Exception, e: - # Need to determine when (if ever) the to_html_value call could fail. - log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) ) - return str( value ) - if isinstance( input, DataToolParameter ): - if isinstance(value, list): - values = [] - for val in value: - if is_hashable( val ): - if val in history.datasets: - values.append( val ) - elif val in hda_source_dict: - values.append( hda_source_dict[ val ]) - return values - if is_hashable( value ) and value not in history.datasets and value in hda_source_dict: - return hda_source_dict[ value ] - elif isinstance( input, DataCollectionToolParameter ): - if is_hashable( value ) and value not in history.dataset_collections and value in hdca_source_dict: - return hdca_source_dict[ value ] - - visit_input_values( tool.inputs, params_objects, rerun_callback ) - # Create a fake tool_state for the tool, with the parameters values - state = tool.new_state( trans ) - state.inputs = params_objects - # If the job failed and has dependencies, allow dependency remap - if job.state == job.states.ERROR: - try: - if [ hda.dependent_jobs for hda in [ jtod.dataset for jtod in job.output_datasets ] if hda.dependent_jobs ]: - state.rerun_remap_job_id = trans.app.security.encode_id(job.id) - except: - # Job has no outputs? - pass - # create an incoming object from the original job's dataset-modified param objects - incoming = {} - params_to_incoming( incoming, tool.inputs, params_objects, trans.app ) - incoming[ "tool_state" ] = galaxy.util.object_to_string( state.encode( tool, trans.app ) ) - template, vars = tool.handle_input( trans, incoming, old_errors=upgrade_messages ) # update new state with old parameters - # Is the "add frame" stuff neccesary here? - add_frame = AddFrameData() - add_frame.debug = trans.debug - if from_noframe is not None: - add_frame.wiki_url = trans.app.config.wiki_url - add_frame.from_noframe = True - return trans.fill_template( template, - history=history, - toolbox=self.get_toolbox(), - tool_version_select_field=tool_version_select_field, - tool=tool, - job=job, - util=galaxy.util, - add_frame=add_frame, - tool_id_version_message=tool_id_version_message, - **vars ) + raise Exception("Failed to get job information for dataset hid %d" % data.hid) + return trans.response.send_redirect( url_for( controller="root", job_id=job_id ) ) 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    '].join("")}),i.$(".modal-header").remove(),i.$(".modal-footer").css("margin-top","0px"),j=new b.DatasetList({title:g.title,subtitle:g.subtitle||e(["Click the checkboxes on the right to select datasets. ","Click the datasets names to see their details. "].join("")),el:i.$body.find(".list-panel"),selecting:!0,selected:g.selected,collection:new a.DatasetAssociationCollection(d)}),j.once("rendered:initial",function(){i.show(),i.$el.addClass("dataset-choice-modal")}),g.multiselect||(j.on("rendered",function(){j.$(".list-actions").hide()}),j.on("view:selected",function(a){l.resolve([a.model.toJSON()])})),j.render(0),l.always(function(){i.hide()})):l.reject("No matches found")},h=Backbone.View.extend(d.LoggableMixin).extend({className:"dataset-choice",initialize:function(a){this.debug(this+"(DatasetChoice).initialize:",a),this.label=void 0!==a.label?e(a.label):"",this.where=a.where,this.datasetsOnly=void 0!==a.datasetsOnly?a.datasetsOnly:!0,this.datasetJSON=a.datasetJSON||[],this.selected=a.selected||[],this._setUpListeners()},_setUpListeners:function(){},render:function(){var a=this.toJSON();return this.$el.html(this._template(a)),this.$(".selected").replaceWith(this._renderSelected(a)),this},_template:function(a){return _.template([""].join(""))(a)},_renderSelected:function(a){return $(a.selected.length?_.template(['
    ','<%= selected.hid %>: <%= selected.name %>','',"<%= selected.misc_blurb %>","",e("format")+": ","<%= selected.file_ext %>","<%= selected.misc_info %>","","
    "].join(""),{variable:"selected"})(a.selected[0]):['(',e("click to select a dataset"),")"].join(""))},toJSON:function(){var a=this;return{label:a.label,datasets:a.datasetJSON,selected:_.compact(_.map(a.selected,function(b){return _.findWhere(a.datasetJSON,{id:b})}))}},events:{click:"chooseWithModal"},chooseWithModal:function(){var a=this;return this._createModal().done(function(b){b?(a.selected=_.pluck(b,"id"),a.trigger("selected",a,b),a.render()):a.trigger("cancelled",a)}).fail(function(){a.trigger("error",a,arguments)})},_createModal:function(){return new g(this.datasetJSON,this._getModalOptions())},_getModalOptions:function(){return{title:this.label,multiselect:!1,selected:this.selected,where:this.where,datasetsOnly:this.datasetsOnly}},toString:function(){return"DatasetChoice("+this.selected+")"}}),i=h.extend({className:h.prototype.className+" multi",cells:{hid:e("History #"),name:e("Name"),misc_blurb:e("Summary"),file_ext:e("Format"),genome_build:e("Genome"),tags:e("Tags"),annotation:e("Annotation")},initialize:function(a){this.showHeaders=void 0!==a.showHeaders?a.showHeaders:!0,this.cells=a.cells||this.cells,h.prototype.initialize.call(this,a)},_renderSelected:function(a){return $(a.selected.length?_.template(['',"<% if( json.showHeaders ){ %>","","<% _.map( json.cells, function( val, key ){ %>","","<% }); %>","","<% } %>","","<% _.map( json.selected, function( selected ){ %>","","<% _.map( json.cells, function( val, key ){ %>",'',"<% }) %>","","<% }); %>","","
    <%= val %>
    <%= selected[ key ] %>
    "].join(""),{variable:"json"})(a):['(',e("click to select a dataset"),")"].join(""))},toJSON:function(){return _.extend(h.prototype.toJSON.call(this),{showHeaders:this.showHeaders,cells:this.cells})},_getModalOptions:function(){return _.extend(h.prototype._getModalOptions.call(this),{multiselect:!0})},toString:function(){return"DatasetChoice("+this.selected+")"}});return{DatasetChoiceModal:g,DatasetChoice:h,MultiDatasetChoice:i}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-choice.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-parameters.js b/static/scripts/mvc/form/form-parameters.js index 5de13400b68..dedf7bdee81 100644 --- a/static/scripts/mvc/form/form-parameters.js +++ b/static/scripts/mvc/form/form-parameters.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a)),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new f({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})},_fieldFtp:function(a){var b=this;return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})}); +define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new f({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})},_fieldFtp:function(a){var b=this;return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})}); //# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-repeat.js b/static/scripts/mvc/form/form-repeat.js index 684fa01f19c..cda21f7fb8d 100644 --- a/static/scripts/mvc/form/form-repeat.js +++ b/static/scripts/mvc/form/form-repeat.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("
    ");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("
    ").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(a.id&&!this.list[a.id]){this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()}},del:function(a){if(this.list[a]){this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()}},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}}); +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("
    ");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("
    ").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(!a.id||this.list[a.id])return void console.debug("form-repeat::add - Duplicate repeat block id.");this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(a){if(!this.list[a])return void console.debug("form-repeat::del - Invalid repeat block id.");this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}}); //# sourceMappingURL=../../../maps/mvc/form/form-repeat.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-select-content.js b/static/scripts/mvc/form/form-select-content.js index af94968aee6..b071f73ba0a 100644 --- a/static/scripts/mvc/form/form-select-content.js +++ b/static/scripts/mvc/form/form-select-content.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d,this.history={};var e=this;this.setElement('
    '),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var d=[];for(var e in b){var f=b[e];d.push({label:f.hid+": "+f.name,value:f.id}),c.history[f.id+"_"+f.src]=f}a.update(d)}}var c=this;b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=this.history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=this.history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});return{View:c}}); +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d,this.history={};var e=this;this.setElement('
    '),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var d=[];for(var e in b){var f=b[e];d.push({label:f.hid+": "+f.name,value:f.id}),c.history[f.id+"_"+f.src]=f}a.update(d)}}var c=this;b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){console.debug("tools-select-content::value() - Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=this.history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=this.history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/form/form-select-content.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-view.js b/static/scripts/mvc/form/form-view.js index 4e0ca52caac..b9aec0a30c1 100644 --- a/static/scripts/mvc/form/form-view.js +++ b/static/scripts/mvc/form/form-view.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("
    "),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change")}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),void(this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message})))}})}); +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("
    "),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),void console.debug("tools-form-base::initialize() - Completed."))}})}); //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map \ No newline at end of file diff --git a/static/scripts/mvc/history/options-menu.js b/static/scripts/mvc/history/options-menu.js index 5f1886aecb8..5271f818597 100644 --- a/static/scripts/mvc/history/options-menu.js +++ b/static/scripts/mvc/history/options-menu.js @@ -1,2 +1,2 @@ -define(["mvc/ui/popup-menu","mvc/base-mvc","utils/localization"],function(a,b,c){function d(a,b,c){return _.clone(e).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var e=[{html:c("History Lists"),header:!0},{html:c("Saved Histories"),href:"history/list"},{html:c("Histories Shared with Me"),href:"history/list_shared"},{html:c("Current History"),header:!0,anon:!0},{html:c("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:c("Copy History"),href:"history/copy"},{html:c("Copy Datasets"),href:"dataset/copy_datasets"},{html:c("Share or Publish"),href:"history/sharing"},{html:c("Extract Workflow"),href:"workflow/build_from_current_history"},{html:c("Dataset Security"),href:"root/history_set_default_permissions"},{html:c("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:c("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:c("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really unhide all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets")})}}},{html:c("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really delete all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets")})}}},{html:c("Purge Deleted Datasets"),confirm:c("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:c("Show Structure"),href:"history/display_structured",anon:!0},{html:c("Export Citations"),href:"history/citations",anon:!0},{html:c("Export to File"),href:"history/export_archive?preview=True",anon:!0},{html:c("Delete"),confirm:c("Really delete the current history?"),href:"history/delete_current"},{html:c("Delete Permanently"),confirm:c("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:!0,anon:!0},{html:c("Other Actions"),header:!0},{html:c("Import from File"),href:"history/import_archive"}],f=function(b,c){c=c||{};var e=void 0===c.anonymous?!0:c.anonymous,f=c.purgeAllowed||!1,g=c.root||(Galaxy&&Galaxy.options?Galaxy.options.root:"/"),h=d(e,f,g);return new a(b,h)};return f}); +define(["mvc/ui/popup-menu","mvc/base-mvc","utils/localization"],function(a,b,c){function d(a,b,c){return _.clone(e).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var e=[{html:c("History Lists"),header:!0},{html:c("Saved Histories"),href:"history/list"},{html:c("Histories Shared with Me"),href:"history/list_shared"},{html:c("Current History"),header:!0,anon:!0},{html:c("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:c("Copy History"),href:"history/copy"},{html:c("Copy Datasets"),href:"dataset/copy_datasets"},{html:c("Share or Publish"),href:"history/sharing"},{html:c("Extract Workflow"),href:"workflow/build_from_current_history"},{html:c("Dataset Security"),href:"root/history_set_default_permissions"},{html:c("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:c("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:c("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really unhide all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets"),console.error(arguments)})}}},{html:c("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really delete all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets"),console.error(arguments)})}}},{html:c("Purge Deleted Datasets"),confirm:c("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:c("Show Structure"),href:"history/display_structured",anon:!0},{html:c("Export Citations"),href:"history/citations",anon:!0},{html:c("Export to File"),href:"history/export_archive?preview=True",anon:!0},{html:c("Delete"),confirm:c("Really delete the current history?"),href:"history/delete_current"},{html:c("Delete Permanently"),confirm:c("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:!0,anon:!0},{html:c("Other Actions"),header:!0},{html:c("Import from File"),href:"history/import_archive"}],f=function(b,c){c=c||{};var e=void 0===c.anonymous?!0:c.anonymous,f=c.purgeAllowed||!1,g=c.root||(Galaxy&&Galaxy.options?Galaxy.options.root:"/"),h=d(e,f,g);return new a(b,h)};return f}); //# sourceMappingURL=../../../maps/mvc/history/options-menu.js.map \ No newline at end of file diff --git a/static/scripts/mvc/job/job-model.js b/static/scripts/mvc/job/job-model.js index fb4e6186f95..0d227e1a694 100644 --- a/static/scripts/mvc/job/job-model.js +++ b/static/scripts/mvc/job/job-model.js @@ -1,2 +1,2 @@ -define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}}); +define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){console.debug(a,b)},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){console.debug(this);var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}}); //# sourceMappingURL=../../../maps/mvc/job/job-model.js.map \ No newline at end of file diff --git a/static/scripts/mvc/library/library-foldertoolbar-view.js b/static/scripts/mvc/library/library-foldertoolbar-view.js index 918c7bd46eb..398c985becf 100644 --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -1,3 +1,3 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file_or_folder===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+"/"+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[],e=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&e.push(this.parentElement.parentElement.id)});for(var f=[],g=c.length-1;g>=0;g--){var h=c[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=h,i.source="library",f.push(i)}for(var g=e.length-1;g>=0;g--){var j=e[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=j,i.source="library_folder",f.push(i)}this.initChainCallControl({length:f.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(f,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[],d=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&d.push(this.parentElement.parentElement.id)});var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+b,f={ld_ids:c,folder_ids:d};this.processDownload(e,f,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+=''}),$('
    '+e+"
    ").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.idb.id?1:a.id=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}))}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url=(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;g--){var h=new d.Item({id:e[g]});f.push(h)}this.options.chain_call_control.total_number=e.length,this.chainCallDeletingHdas(f)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push('
    '),tmpl_array.push(" DATA LIBRARIES"),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push(' "),tmpl_array.push("<% } else { %>"),tmpl_array.push(' '),tmpl_array.push("<% } %>"),tmpl_array.push(' '),tmpl_array.push(' "),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(" "),tmpl_array.push("
    "),tmpl_array.push('
    '),tmpl_array.push("
    "),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push("

    Library name:

    "),tmpl_array.push('

    <%- library.get("name") %>

    '),tmpl_array.push("

    Library description:

    "),tmpl_array.push('

    <%- library.get("description") %>

    '),tmpl_array.push("

    Library synopsis:

    "),tmpl_array.push('

    <%- library.get("synopsis") %>

    '),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push("
    "),tmpl_array.push(''),tmpl_array.push(''),tmpl_array.push("
    "),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push(''),a.push("Select history: "),a.push('"),a.push(""),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('
    '),a.push("Importing selected datasets to history <%= _.escape(history_name) %>"),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('
    '),a.push("Adding selected datasets to library folder <%= _.escape(folder_name) %>"),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('
    '),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('
    '),a.push('
    All files you select will be imported into the current folder.
    '),a.push(''),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push('
    '),a.push("
    "),a.push("
    "),a.push("

    You can set extension type and genome for all imported datasets at once:

    "),a.push("
    "),a.push('Type: '),a.push(' Genome: '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('
    '),a.push('
    All files within the given folders and their subfolders will be imported into the current folder.
    '),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push(''),a.push("
    "),a.push("

    You can set extension type and genome for all imported datasets at once:

    "),a.push("
    "),a.push('Type: '),a.push(' Genome: '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('
    '),a.push('
    '),a.push("Select history: "),a.push('"),a.push("
    "),a.push("
    "),a.push('
    '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateHistoryContents:function(){var a=[];return a.push("Choose the datasets to import:"),a.push("
      "),a.push(" <% _.each(history_contents, function(history_item) { %>"),a.push('
    • ">'),a.push(' <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'),a.push("
      • "),a.push(" <% }); %>"),a.push("
    "),_.template(a.join(""))},templatePaginator:function(){return tmpl_array=[],tmpl_array.push('
      '), -tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>"),tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push('
    • '),tmpl_array.push(' <% print( show_page ) %>'),tmpl_array.push("
      • "),tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>"),tmpl_array.push('
    • <% print( show_page + 1 ) %>
      • '),tmpl_array.push('
      • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
    • <% print( show_page + 1 ) %>
      • '),tmpl_array.push('
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push("
    "),tmpl_array.push(" "),tmpl_array.push(' showing <%- items_shown %> of <%- total_items_count %> items'),tmpl_array.push(" "),_.template(tmpl_array.join(""))}});return{FolderToolbarView:f}}); +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file_or_folder===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+"/"+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[],e=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&e.push(this.parentElement.parentElement.id)});for(var f=[],g=c.length-1;g>=0;g--){var h=c[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=h,i.source="library",f.push(i)}for(var g=e.length-1;g>=0;g--){var j=e[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=j,i.source="library_folder",f.push(i)}this.initChainCallControl({length:f.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(f,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[],d=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&d.push(this.parentElement.parentElement.id)});var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+b,f={ld_ids:c,folder_ids:d};this.processDownload(e,f,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+=''}),$('
    '+e+"
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Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;g--){var h=new d.Item({id:e[g]});f.push(h)}this.options.chain_call_control.total_number=e.length,this.chainCallDeletingHdas(f)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push('
    '),tmpl_array.push(" DATA LIBRARIES"),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push(' "),tmpl_array.push("<% } else { %>"),tmpl_array.push(' '),tmpl_array.push("<% } %>"),tmpl_array.push(' '),tmpl_array.push(' "),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(" "),tmpl_array.push("
    "),tmpl_array.push('
    '),tmpl_array.push("
    "),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push("

    Library name:

    "),tmpl_array.push('

    <%- library.get("name") %>

    '),tmpl_array.push("

    Library description:

    "),tmpl_array.push('

    <%- library.get("description") %>

    '),tmpl_array.push("

    Library synopsis:

    "),tmpl_array.push('

    <%- library.get("synopsis") %>

    '),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push("
    "),tmpl_array.push(''),tmpl_array.push(''),tmpl_array.push("
    "),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push(''),a.push("Select history: "),a.push('"),a.push(""),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('
    '),a.push("Importing selected datasets to history <%= _.escape(history_name) %>"),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('
    '),a.push("Adding selected datasets to library folder <%= _.escape(folder_name) %>"),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('
    '),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('
    '),a.push('
    All files you select will be imported into the current folder.
    '),a.push(''),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push('
    '),a.push("
    "),a.push("
    "),a.push("

    You can set extension type and genome for all imported datasets at once:

    "),a.push("
    "),a.push('Type: '),a.push(' Genome: '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('
    '),a.push('
    All files within the given folders and their subfolders will be imported into the current folder.
    '),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push(''),a.push("
    "),a.push("

    You can set extension type and genome for all imported datasets at once:

    "),a.push("
    "),a.push('Type: '),a.push(' Genome: '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('
    '),a.push('
    '),a.push("Select history: "),a.push('"),a.push("
    "),a.push("
    "),a.push('
    '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateHistoryContents:function(){var a=[];return a.push("Choose the datasets to import:"),a.push("
      "),a.push(" <% _.each(history_contents, function(history_item) { %>"),a.push('
    • ">'),a.push(' <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'),a.push("
      • "),a.push(" <% }); %>"),a.push("
    "),_.template(a.join(""))},templatePaginator:function(){ +return tmpl_array=[],tmpl_array.push('
      '),tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>"),tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push('
    • '),tmpl_array.push(' <% print( show_page ) %>'),tmpl_array.push("
      • "),tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>"),tmpl_array.push('
    • <% print( show_page + 1 ) %>
      • '),tmpl_array.push('
      • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
    • <% print( show_page + 1 ) %>
      • '),tmpl_array.push('
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push("
    "),tmpl_array.push(" "),tmpl_array.push(' showing <%- items_shown %> of <%- total_items_count %> items'),tmpl_array.push(" "),_.template(tmpl_array.join(""))}});return{FolderToolbarView:f}}); //# sourceMappingURL=../../../maps/mvc/library/library-foldertoolbar-view.js.map \ No newline at end of file diff --git a/static/scripts/mvc/list/list-panel.js b/static/scripts/mvc/list/list-panel.js index 62d34d8da22..6c717e19ed7 100644 --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -1,2 +1,2 @@ -define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d){var e=Backbone.View.extend(c.LoggableMixin).extend({viewClass:a.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:d("This list is empty"),noneFoundMsg:d("No matching items found"),searchPlaceholder:d("search"),initialize:function(a){a=a||{},a.logger&&(this.logger=a.logger),this.log(this+".initialize:",a),this.fxSpeed=_.has(a,"fxSpeed")?a.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=a.searchFor||"",this.indicator=new b(this.$el),this.selecting=void 0!==a.selecting?a.selecting:!0,this.selected=a.selected||[],this.lastSelected=null,this.dragItems=a.dragItems||!1,this.viewClass=a.viewClass||this.viewClass,this.views=[],this.collection=a.collection||new this.collectionClass([]),this.filters=a.filters||[],this.$scrollContainer=a.$scrollContainer||this.$scrollContainer,this.title=a.title||"",this.subtitle=a.subtitle||"",this._setUpListeners()},freeViews:function(){return _.each(this.views,function(a){a.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on("error",function(a,b,c,d,e){},this),this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this),this.on("loading-done",function(){this._hideLoadingIndicator(40)},this),this.once("rendered",function(){this.trigger("rendered:initial",this)},this),this.logger&&this.on("all",function(){this.log(this+"",arguments)},this),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.collection.on("error",function(a,b,c,d,e){this.trigger("error",a,b,c,d,e)},this),this.collection.on("reset",function(){this.renderItems()},this),this.collection.on("add",this.addItemView,this),this.collection.on("remove",this.removeItemView,this),this.logger&&this.collection.on("all",function(){this.info(this+"(collection)",arguments)},this),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on("view:selected",function(a,b){if(b&&b.shiftKey&&this.lastSelected){var c=this.viewFromModelId(this.lastSelected);c&&this.selectRange(a,c)}else b&&b.altKey&&!this.selecting&&this.showSelectors();this.selected.push(a.model.id),this.lastSelected=a.model.id},this),this.on("view:de-selected",function(a){this.selected=_.without(this.selected,a.model.id)},this)},render:function(a){this.log(this+".render",a);var b=this._buildNewRender();return this._setUpBehaviors(b),this._queueNewRender(b,a),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var a=$(this.templates.el({},this));return this._renderControls(a),this._renderTitle(a),this._renderSubtitle(a),this._renderSearch(a),this.renderItems(a),a},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=$(this.templates.controls({},this));return a.find(".controls").replaceWith(b),b},_renderTitle:function(){},_renderSubtitle:function(){},_queueNewRender:function(a,b){b=void 0===b?this.fxSpeed:b;var c=this;c.log("_queueNewRender:",a,b),$(c).queue("fx",[function(a){this.$el.fadeOut(b,a)},function(b){c._swapNewRender(a),b()},function(a){this.$el.fadeIn(b,a)},function(a){c.trigger("rendered",c),a()}])},_swapNewRender:function(a){return this.$el.empty().attr("class",this.className).append(a.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(a){return a=a||this.$el,a.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(a),this},_renderMultiselectActionMenu:function(a){a=a||this.$el;var b=a.find(".list-action-menu"),c=this.multiselectActions();if(!c.length)return b.empty();var e=$(['
    ','",'","
    "].join("")),f=c.map(function(a){var b=['
  • ',a.html,"
    • "].join("");return $(b).click(function(b){return b.preventDefault(),a.func(b)})});return e.find("ul").append(f),b.replaceWith(e),e},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(a){return(a||this.$el).find("> .list-items")},$messages:function(a){return(a||this.$el).find("> .controls .messages")},$emptyMessage:function(a){return(a||this.$el).find("> .empty-message")},renderItems:function(a){a=a||this.$el;var b=this;b.log(this+".renderItems",a);var c=b.$list(a);return b.views=b._filterCollection().map(function(a){return b._createItemView(a).render(0)}),c.empty(),b.views.length?(b._attachItems(a),b.$emptyMessage(a).hide()):b._renderEmptyMessage(a).show(),b.trigger("views:ready",b.views),b.views},_filterCollection:function(){var a=this;return a.collection.filter(_.bind(a._filterItem,a))},_filterItem:function(a){var b=this;return _.every(b.filters.map(function(b){return b.call(a)}))&&(!b.searchFor||a.matchesAll(b.searchFor))},_createItemView:function(a){var b=this._getItemViewClass(a),c=_.extend(this._getItemViewOptions(a),{model:a}),d=new b(c);return this._setUpItemViewListeners(d),d},_getItemViewClass:function(){return this.viewClass},_getItemViewOptions:function(a){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:_.contains(this.selected,a.id),draggable:this.dragItems}},_setUpItemViewListeners:function(a){var b=this;return a.on("all",function(){var a=Array.prototype.slice.call(arguments,0);a[0]="view:"+a[0],b.trigger.apply(b,a)}),a.on("draggable:dragstart",function(a,b){var c={},d=this.getSelectedModels();c=d.length?d.toJSON():[b.model.toJSON()],a.dataTransfer.setData("text",JSON.stringify(c))},this),b},_attachItems:function(a){return this.$list(a).append(this.views.map(function(a){return a.$el})),this},_renderEmptyMessage:function(a){this.debug("_renderEmptyMessage",a,this.searchFor);var b=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(a).text(b)},expandAll:function(){_.each(this.views,function(a){a.expand()})},collapseAll:function(){_.each(this.views,function(a){a.collapse()})},addItemView:function(a){this.log(this+".addItemView:",a);var b=this;if(!b._filterItem(a))return void 0;var c=b._createItemView(a);return $(c).queue("fx",[function(a){b.$emptyMessage().fadeOut(b.fxSpeed,a)},function(a){b._attachView(c),a()}]),c},_attachView:function(a){var b=this;b.views.push(a),b.$list().append(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},removeItemView:function(a){this.log(this+".removeItemView:",a);var b=this,c=b.viewFromModel(a);return c?(b.views=_.without(b.views,c),b.trigger("view:removed",c),$({}).queue("fx",[function(a){c.$el.fadeOut(b.fxSpeed,a)},function(a){c.remove(),b.trigger("view:removed:rendered"),b.views.length?a():b._renderEmptyMessage().fadeIn(b.fxSpeed,a)}]),c):void 0},viewFromModelId:function(a){for(var b=0;bc?this.views.slice(c,d+1):this.views.slice(d,c+1)},_renderSearch:function(a){return a.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)}),a},_firstSearch:function(a){return this.log("onFirstSearch",a),this.searchItems(a)},searchItems:function(a){return this.searchFor=a,this.trigger("search:searching",a,this),this.renderItems(),this.$("> .controls .search-query").val(a),this},clearSearch:function(){return this.searchFor="",this.trigger("search:clear",this),this.renderItems(),this.$("> .controls .search-query").val(""),this},showSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(a),_.each(this.views,function(b){b.showSelector(a)})},hideSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(a),_.each(this.views,function(b){b.hideSelector(a)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(a){_.each(this.views,function(b){b.select(a)})},deselectAll:function(a){this.lastSelected=null,_.each(this.views,function(b){b.deselect(a)})},selectRange:function(a,b){var c=this.viewRange(a,b);return _.each(c,function(a){a.select()}),c},getSelectedViews:function(){return _.filter(this.views,function(a){return a.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(a){return a.model}))},_showLoadingIndicator:function(a,c,d){this.debug("_showLoadingIndicator",this.indicator,a,c,d),c=void 0!==c?c:this.fxSpeed,this.indicator||(this.indicator=new b(this.$el,this.$el.parent()),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(c),this.indicator.show(a,c,d)):this.indicator.show(0,d)},_hideLoadingIndicator:function(a,b){this.debug("_hideLoadingIndicator",this.indicator,a,b),a=void 0!==a?a:this.fxSpeed,this.indicator&&this.indicator.hide(a,b)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(a,b){return b=b||0,this.$scrollContainer().animate({scrollTop:a},b),this},scrollToTop:function(a){return this.scrollTo(0,a)},scrollToItem:function(a,b){if(!a)return this;var c=a.$el.position().top;return this.scrollTo(c,b)},scrollToId:function(a,b){return this.scrollToItem(this.viewFromModelId(a),b)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=function(){var a=c.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),b=c.wrapTemplate(['
    ','
    ','
    <%= view.title %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return{el:a,controls:b}}();var f=e.extend({modelCollectionKey:"contents",initialize:function(a){e.prototype.initialize.call(this,a),this.selecting=void 0!==a.selecting?a.selecting:!1,this.setModel(this.model,a)},setModel:function(a,b){if(b=b||{},this.debug(this+".setModel:",a,b),this.freeModel(),this.freeViews(),a){var c=this.model?this.model.get("id"):null;this.model=a,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:b.collection||new this.collectionClass([]),this._setUpCollectionListeners(),c&&a.get("id")!==c&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.model.on("error",function(){var a=Array.prototype.slice.call(arguments,0);a.unshift("error"),this.trigger.apply(this,a)},this),this},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=this.model?this.model.toJSON():{},c=$(this.templates.controls(b,this));return a.find(".controls").replaceWith(c),c},toString:function(){return"ModelListPanel("+this.model+")"}});return f.prototype.templates=function(){var a=c.wrapTemplate(['
    ','
    ','
    <%= model.name %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return _.extend(_.clone(e.prototype.templates),{controls:a})}(),{ListPanel:e,ModelListPanel:f}}); +define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d){var e=Backbone.View.extend(c.LoggableMixin).extend({viewClass:a.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:d("This list is empty"),noneFoundMsg:d("No matching items found"),searchPlaceholder:d("search"),initialize:function(a){a=a||{},a.logger&&(this.logger=a.logger),this.log(this+".initialize:",a),this.fxSpeed=_.has(a,"fxSpeed")?a.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=a.searchFor||"",this.indicator=new b(this.$el),this.selecting=void 0!==a.selecting?a.selecting:!0,this.selected=a.selected||[],this.lastSelected=null,this.dragItems=a.dragItems||!1,this.viewClass=a.viewClass||this.viewClass,this.views=[],this.collection=a.collection||new this.collectionClass([]),this.filters=a.filters||[],this.$scrollContainer=a.$scrollContainer||this.$scrollContainer,this.title=a.title||"",this.subtitle=a.subtitle||"",this._setUpListeners()},freeViews:function(){return _.each(this.views,function(a){a.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on("error",function(a,b,c,d,e){console.error(a,b,c,d,e)},this),this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this),this.on("loading-done",function(){this._hideLoadingIndicator(40)},this),this.once("rendered",function(){this.trigger("rendered:initial",this)},this),this.logger&&this.on("all",function(){this.log(this+"",arguments)},this),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.collection.on("error",function(a,b,c,d,e){this.trigger("error",a,b,c,d,e)},this),this.collection.on("reset",function(){this.renderItems()},this),this.collection.on("add",this.addItemView,this),this.collection.on("remove",this.removeItemView,this),this.logger&&this.collection.on("all",function(){this.info(this+"(collection)",arguments)},this),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on("view:selected",function(a,b){if(b&&b.shiftKey&&this.lastSelected){var c=this.viewFromModelId(this.lastSelected);c&&this.selectRange(a,c)}else b&&b.altKey&&!this.selecting&&this.showSelectors();this.selected.push(a.model.id),this.lastSelected=a.model.id},this),this.on("view:de-selected",function(a){this.selected=_.without(this.selected,a.model.id)},this)},render:function(a){this.log(this+".render",a);var b=this._buildNewRender();return this._setUpBehaviors(b),this._queueNewRender(b,a),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var a=$(this.templates.el({},this));return this._renderControls(a),this._renderTitle(a),this._renderSubtitle(a),this._renderSearch(a),this.renderItems(a),a},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=$(this.templates.controls({},this));return a.find(".controls").replaceWith(b),b},_renderTitle:function(){},_renderSubtitle:function(){},_queueNewRender:function(a,b){b=void 0===b?this.fxSpeed:b;var c=this;c.log("_queueNewRender:",a,b),$(c).queue("fx",[function(a){this.$el.fadeOut(b,a)},function(b){c._swapNewRender(a),b()},function(a){this.$el.fadeIn(b,a)},function(a){c.trigger("rendered",c),a()}])},_swapNewRender:function(a){return this.$el.empty().attr("class",this.className).append(a.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(a){return a=a||this.$el,a.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(a),this},_renderMultiselectActionMenu:function(a){a=a||this.$el;var b=a.find(".list-action-menu"),c=this.multiselectActions();if(!c.length)return b.empty();var e=$(['
    ','",'","
    "].join("")),f=c.map(function(a){var b=['
  • ',a.html,"
    • "].join("");return $(b).click(function(b){return b.preventDefault(),a.func(b)})});return e.find("ul").append(f),b.replaceWith(e),e},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(a){return(a||this.$el).find("> .list-items")},$messages:function(a){return(a||this.$el).find("> .controls .messages")},$emptyMessage:function(a){return(a||this.$el).find("> .empty-message")},renderItems:function(a){a=a||this.$el;var b=this;b.log(this+".renderItems",a);var c=b.$list(a);return b.views=b._filterCollection().map(function(a){return b._createItemView(a).render(0)}),c.empty(),b.views.length?(b._attachItems(a),b.$emptyMessage(a).hide()):b._renderEmptyMessage(a).show(),b.trigger("views:ready",b.views),b.views},_filterCollection:function(){var a=this;return a.collection.filter(_.bind(a._filterItem,a))},_filterItem:function(a){var b=this;return _.every(b.filters.map(function(b){return b.call(a)}))&&(!b.searchFor||a.matchesAll(b.searchFor))},_createItemView:function(a){var b=this._getItemViewClass(a),c=_.extend(this._getItemViewOptions(a),{model:a}),d=new b(c);return this._setUpItemViewListeners(d),d},_getItemViewClass:function(){return this.viewClass},_getItemViewOptions:function(a){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:_.contains(this.selected,a.id),draggable:this.dragItems}},_setUpItemViewListeners:function(a){var b=this;return a.on("all",function(){var a=Array.prototype.slice.call(arguments,0);a[0]="view:"+a[0],b.trigger.apply(b,a)}),a.on("draggable:dragstart",function(a,b){var c={},d=this.getSelectedModels();c=d.length?d.toJSON():[b.model.toJSON()],a.dataTransfer.setData("text",JSON.stringify(c))},this),b},_attachItems:function(a){return this.$list(a).append(this.views.map(function(a){return a.$el})),this},_renderEmptyMessage:function(a){this.debug("_renderEmptyMessage",a,this.searchFor);var b=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(a).text(b)},expandAll:function(){_.each(this.views,function(a){a.expand()})},collapseAll:function(){_.each(this.views,function(a){a.collapse()})},addItemView:function(a){this.log(this+".addItemView:",a);var b=this;if(!b._filterItem(a))return void 0;var c=b._createItemView(a);return $(c).queue("fx",[function(a){b.$emptyMessage().fadeOut(b.fxSpeed,a)},function(a){b._attachView(c),a()}]),c},_attachView:function(a){var b=this;b.views.push(a),b.$list().append(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},removeItemView:function(a){this.log(this+".removeItemView:",a);var b=this,c=b.viewFromModel(a);return c?(b.views=_.without(b.views,c),b.trigger("view:removed",c),$({}).queue("fx",[function(a){c.$el.fadeOut(b.fxSpeed,a)},function(a){c.remove(),b.trigger("view:removed:rendered"),b.views.length?a():b._renderEmptyMessage().fadeIn(b.fxSpeed,a)}]),c):void 0},viewFromModelId:function(a){for(var b=0;bc?this.views.slice(c,d+1):this.views.slice(d,c+1)},_renderSearch:function(a){return a.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)}),a},_firstSearch:function(a){return this.log("onFirstSearch",a),this.searchItems(a)},searchItems:function(a){return this.searchFor=a,this.trigger("search:searching",a,this),this.renderItems(),this.$("> .controls .search-query").val(a),this},clearSearch:function(){return this.searchFor="",this.trigger("search:clear",this),this.renderItems(),this.$("> .controls .search-query").val(""),this},showSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(a),_.each(this.views,function(b){b.showSelector(a)})},hideSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(a),_.each(this.views,function(b){b.hideSelector(a)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(a){_.each(this.views,function(b){b.select(a)})},deselectAll:function(a){this.lastSelected=null,_.each(this.views,function(b){b.deselect(a)})},selectRange:function(a,b){var c=this.viewRange(a,b);return _.each(c,function(a){a.select()}),c},getSelectedViews:function(){return _.filter(this.views,function(a){return a.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(a){return a.model}))},_showLoadingIndicator:function(a,c,d){this.debug("_showLoadingIndicator",this.indicator,a,c,d),c=void 0!==c?c:this.fxSpeed,this.indicator||(this.indicator=new b(this.$el,this.$el.parent()),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(c),this.indicator.show(a,c,d)):this.indicator.show(0,d)},_hideLoadingIndicator:function(a,b){this.debug("_hideLoadingIndicator",this.indicator,a,b),a=void 0!==a?a:this.fxSpeed,this.indicator&&this.indicator.hide(a,b)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(a,b){return b=b||0,this.$scrollContainer().animate({scrollTop:a},b),this},scrollToTop:function(a){return this.scrollTo(0,a)},scrollToItem:function(a,b){if(!a)return this;var c=a.$el.position().top;return this.scrollTo(c,b)},scrollToId:function(a,b){return this.scrollToItem(this.viewFromModelId(a),b)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=function(){var a=c.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),b=c.wrapTemplate(['
    ','
    ','
    <%= view.title %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return{el:a,controls:b}}();var f=e.extend({modelCollectionKey:"contents",initialize:function(a){e.prototype.initialize.call(this,a),this.selecting=void 0!==a.selecting?a.selecting:!1,this.setModel(this.model,a)},setModel:function(a,b){if(b=b||{},this.debug(this+".setModel:",a,b),this.freeModel(),this.freeViews(),a){var c=this.model?this.model.get("id"):null;this.model=a,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:b.collection||new this.collectionClass([]),this._setUpCollectionListeners(),c&&a.get("id")!==c&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.model.on("error",function(){var a=Array.prototype.slice.call(arguments,0);a.unshift("error"),this.trigger.apply(this,a)},this),this},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=this.model?this.model.toJSON():{},c=$(this.templates.controls(b,this));return a.find(".controls").replaceWith(c),c},toString:function(){return"ModelListPanel("+this.model+")"}});return f.prototype.templates=function(){var a=c.wrapTemplate(['
    ','
    ','
    <%= model.name %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return _.extend(_.clone(e.prototype.templates),{controls:a})}(),{ListPanel:e,ModelListPanel:f}}); //# sourceMappingURL=../../../maps/mvc/list/list-panel.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-base.js b/static/scripts/mvc/tools/tools-form-base.js index 426dc006318..329e2ed656e 100644 --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -1,2 +1,2 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("
    "),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this;this.options.id=b.id,this.options.version=b.version;var d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g)},error:function(a){c.deferred.done(g);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||galaxy_config.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("
    "),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this;this.options.id=b.id,this.options.version=b.version;var d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||galaxy_config.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-workflow.js b/static/scripts/mvc/tools/tools-form-workflow.js index 798ea86de9e..4bf7c67bbea 100644 --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;this.node=c.node,this.node&&(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),b.prototype.initialize.call(this,c))},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var g=b.inputs[e];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=f.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expanded=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&c(g,d.slice(0))}}var d=[];for(key in b)d.push({0:b[key],1:b[key]});d.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},f=this;return c(e),e}});return{View:c}}); +define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=c.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var g=b.inputs[e];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=f.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expanded=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&c(g,d.slice(0))}}var d=[];for(key in b)d.push({0:b[key],1:b[key]});d.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},f=this;return c(e),e}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-jobs.js b/static/scripts/mvc/tools/tools-jobs.js index f6926c6c383..d4b1708c3a3 100644 --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}}); +define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map \ No newline at end of file diff --git a/static/scripts/mvc/ui/ui-frames.js b/static/scripts/mvc/ui/ui-frames.js index aea84c96ad5..b9e78655ec1 100644 --- a/static/scripts/mvc/ui/ui-frames.js +++ b/static/scripts/mvc/ui/ui-frames.js @@ -1,2 +1,2 @@ -define([],function(){var a=Backbone.View.extend({options:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0,onchange:null},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:null,initialize:function(a){var b=this;a&&(this.options=_.defaults(a,this.options)),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(this._template()),$(this.el).append(this._templateBackground()),$(this.el).append(this._templateMenu()),$(this.el_main).append($(this.el));var c="#frame-shadow";$(this.el).append(this._templateShadow(c.substring(1))),this.frame_shadow={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1},this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list[c]=this.frame_shadow,this._panelRefresh(),this.visible?this.show():this.hide();var b=this;$(window).resize(function(){b.visible&&b._panelRefresh()})},add:function(a){var b={title:"",content:null,target:"",type:null};if(a=a?_.defaults(a,b):b,a.content){if(this.frame_counter>=this.options.frame_max)return void alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");var c="#frame-"+this.frame_counter_id++;if(0!==$(c).length)return void alert("This frame already exists. This page might contain multiple frame managers.");this.top=this.options.top_min;var d=null;if("url"===a.type)d=$(this._templateFrameUrl(c.substring(1),a.title,a.content));else if("other"===a.type){d=$(this._templateFrame(c.substring(1),a.title));var e=d.find(".f-content");_.isFunction(a.content)?a.content(e):e.append(a.content)}$(this.el).append(d);var f={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1};a.width=this._toPixelCoord("width",this.options.frame.cols),a.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt($(f.id).css("z-index")),this.frame_list[c]=f,this.frame_counter++,this._frameResize(f,{width:a.width,height:a.height}),this._frameInsert(f,{top:0,left:0},!0),this.visible||this.show()}},show:function(){this.visible=!0,this.$el.find(".frame").fadeIn("fast"),this.$el.find(this.frame_shadow.id).hide(),this.$el.find(".frame-background").show(),this._panelRefresh(),this._menuRefresh()},hide:function(){null===this.event.type&&(this.visible=!1,this.$el.find(".frame").fadeOut("fast"),this.$el.find(".frame-background").hide(),this.$el.find(".frame-menu").hide(),this._menuRefresh())},length:function(){return this.frame_counter},setOnChange:function(a){this.options.onchange=a},event:{type:null,target:null,xy:null},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose","mousedown .f-pin":"_eventFrameLock"},_eventFrameMouseDown:function(a){if(null===this.event.type&&(($(a.target).hasClass("f-header")||$(a.target).hasClass("f-title"))&&(this.event.type="drag"),$(a.target).hasClass("f-resize")&&(this.event.type="resize"),null!==this.event.type)){if(a.preventDefault(),this.event.target=this._frameIdentify(a.target),this.event.target.grid_lock)return void(this.event.type=null);this.event.xy={x:a.originalEvent.pageX,y:a.originalEvent.pageY},this._frameDragStart(this.event.target)}},_eventFrameMouseMove:function(a){if("drag"==this.event.type||"resize"==this.event.type){var b={x:a.originalEvent.pageX,y:a.originalEvent.pageY},c={x:b.x-this.event.xy.x,y:b.y-this.event.xy.y};this.event.xy=b;var d=this._frameScreen(this.event.target);if("resize"==this.event.type){d.width+=c.x,d.height+=c.y;var e=this.options.cell-this.options.margin-1;d.width=Math.max(d.width,e),d.height=Math.max(d.height,e),this._frameResize(this.event.target,d),d.width=this._toGridCoord("width",d.width)+1,d.height=this._toGridCoord("height",d.height)+1,d.width=this._toPixelCoord("width",d.width),d.height=this._toPixelCoord("height",d.height),this._frameResize(this.frame_shadow,d),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)})}if("drag"==this.event.type){d.left+=c.x,d.top+=c.y,this._frameOffset(this.event.target,d);var f={top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)};0!==f.left&&f.left++,this._frameInsert(this.frame_shadow,f)}}},_eventFrameMouseUp:function(){("drag"==this.event.type||"resize"==this.event.type)&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target),c=this;$(b.id).fadeOut("fast",function(){$(b.id).remove(),delete c.frame_list[b.id],c.frame_counter--,c._panelRefresh(!0),c._panelAnimationComplete(),c.visible&&0==c.frame_counter&&c.hide()})}},_eventFrameLock:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target);b.grid_lock?(b.grid_lock=!1,$(b.id).find(".f-pin").removeClass("toggle"),$(b.id).find(".f-header").removeClass("f-not-allowed"),$(b.id).find(".f-title").removeClass("f-not-allowed"),$(b.id).find(".f-resize").show(),$(b.id).find(".f-close").show()):(b.grid_lock=!0,$(b.id).find(".f-pin").addClass("toggle"),$(b.id).find(".f-header").addClass("f-not-allowed"),$(b.id).find(".f-title").addClass("f-not-allowed"),$(b.id).find(".f-resize").hide(),$(b.id).find(".f-close").hide())}},_eventHide:function(){null===this.event.type&&this.hide()},_eventPanelScroll:function(a){if(null===this.event.type&&this.visible){var b=$(a.srcElement).parents(".frame");if(0!==b.length)return void a.stopPropagation();a.preventDefault();var c=a.originalEvent.detail?a.originalEvent.detail:a.originalEvent.wheelDelta/-3;this._panelScroll(c)}},_eventPanelScroll_up:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(a){return this.frame_list["#"+$(a).closest(".frame").attr("id")]},_frameDragStart:function(a){this._frameFocus(a,!0);var b=this._frameScreen(a);this._frameResize(this.frame_shadow,b),this._frameGrid(this.frame_shadow,a.grid_location),a.grid_location=null,$(this.frame_shadow.id).show(),$(".f-cover").show()},_frameDragStop:function(a){this._frameFocus(a,!1);var b=this._frameScreen(this.frame_shadow);this._frameResize(a,b),this._frameGrid(a,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,$(this.frame_shadow.id).hide(),$(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(a,b){var c="width"==a||"height"==a?1:-1;return"top"==a&&(b-=this.top),parseInt((b+c*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(a,b){var c="width"==a||"height"==a?1:-1,d=b*this.options.cell-c*this.options.margin;return"top"==a&&(d+=this.top),d},_toGrid:function(a){return{top:this._toGridCoord("top",a.top),left:this._toGridCoord("left",a.left),width:this._toGridCoord("width",a.width),height:this._toGridCoord("height",a.height)}},_toPixel:function(a){return{top:this._toPixelCoord("top",a.top),left:this._toPixelCoord("left",a.left),width:this._toPixelCoord("width",a.width),height:this._toPixelCoord("height",a.height)}},_isCollision:function(a){function b(a,b){return!(a.left>b.left+b.width-1||a.left+a.width-1b.top+b.height-1||a.top+a.height-1c?-1:c>d?1:0}),e=0;e
    '},_templateFrame:function(a,b){return b||(b=""),'
    '+b+'
    '},_templateFrameUrl:function(a,b,c){c+=-1==c.indexOf("?")?"?":"&",c+="widget=True";var d=$(this._templateFrame(a,b));return d.find(".f-content").append(''),d},_templateShadow:function(a){return'
    '},_templateBackground:function(){return'
    '},_templateMenu:function(){return'
    '}});return{View:a}}); +define([],function(){var a=Backbone.View.extend({options:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0,onchange:null},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:null,initialize:function(a){var b=this;a&&(this.options=_.defaults(a,this.options)),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(this._template()),$(this.el).append(this._templateBackground()),$(this.el).append(this._templateMenu()),$(this.el_main).append($(this.el));var c="#frame-shadow";$(this.el).append(this._templateShadow(c.substring(1))),this.frame_shadow={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1},this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list[c]=this.frame_shadow,this._panelRefresh(),this.visible?this.show():this.hide();var b=this;$(window).resize(function(){b.visible&&b._panelRefresh()})},add:function(a){var b={title:"",content:null,target:"",type:null};if(a=a?_.defaults(a,b):b,a.content){if(this.frame_counter>=this.options.frame_max)return void alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");var c="#frame-"+this.frame_counter_id++;if(0!==$(c).length)return void alert("This frame already exists. This page might contain multiple frame managers.");this.top=this.options.top_min;var d=null;if("url"===a.type)d=$(this._templateFrameUrl(c.substring(1),a.title,a.content));else if("other"===a.type){d=$(this._templateFrame(c.substring(1),a.title));var e=d.find(".f-content");_.isFunction(a.content)?a.content(e):e.append(a.content)}$(this.el).append(d);var f={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1};a.width=this._toPixelCoord("width",this.options.frame.cols),a.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt($(f.id).css("z-index")),this.frame_list[c]=f,this.frame_counter++,this._frameResize(f,{width:a.width,height:a.height}),this._frameInsert(f,{top:0,left:0},!0),this.visible||this.show()}},show:function(){this.visible=!0,this.$el.find(".frame").fadeIn("fast"),this.$el.find(this.frame_shadow.id).hide(),this.$el.find(".frame-background").show(),this._panelRefresh(),this._menuRefresh()},hide:function(){null===this.event.type&&(this.visible=!1,this.$el.find(".frame").fadeOut("fast"),this.$el.find(".frame-background").hide(),this.$el.find(".frame-menu").hide(),this._menuRefresh())},length:function(){return this.frame_counter},setOnChange:function(a){this.options.onchange=a},event:{type:null,target:null,xy:null},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose","mousedown .f-pin":"_eventFrameLock"},_eventFrameMouseDown:function(a){if(null===this.event.type&&(($(a.target).hasClass("f-header")||$(a.target).hasClass("f-title"))&&(this.event.type="drag"),$(a.target).hasClass("f-resize")&&(this.event.type="resize"),null!==this.event.type)){if(a.preventDefault(),this.event.target=this._frameIdentify(a.target),this.event.target.grid_lock)return void(this.event.type=null);this.event.xy={x:a.originalEvent.pageX,y:a.originalEvent.pageY},this._frameDragStart(this.event.target)}},_eventFrameMouseMove:function(a){if("drag"==this.event.type||"resize"==this.event.type){var b={x:a.originalEvent.pageX,y:a.originalEvent.pageY},c={x:b.x-this.event.xy.x,y:b.y-this.event.xy.y};this.event.xy=b;var d=this._frameScreen(this.event.target);if("resize"==this.event.type){d.width+=c.x,d.height+=c.y;var e=this.options.cell-this.options.margin-1;d.width=Math.max(d.width,e),d.height=Math.max(d.height,e),this._frameResize(this.event.target,d),d.width=this._toGridCoord("width",d.width)+1,d.height=this._toGridCoord("height",d.height)+1,d.width=this._toPixelCoord("width",d.width),d.height=this._toPixelCoord("height",d.height),this._frameResize(this.frame_shadow,d),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)})}if("drag"==this.event.type){d.left+=c.x,d.top+=c.y,this._frameOffset(this.event.target,d);var f={top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)};0!==f.left&&f.left++,this._frameInsert(this.frame_shadow,f)}}},_eventFrameMouseUp:function(){("drag"==this.event.type||"resize"==this.event.type)&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target),c=this;$(b.id).fadeOut("fast",function(){$(b.id).remove(),delete c.frame_list[b.id],c.frame_counter--,c._panelRefresh(!0),c._panelAnimationComplete(),c.visible&&0==c.frame_counter&&c.hide()})}},_eventFrameLock:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target);b.grid_lock?(b.grid_lock=!1,$(b.id).find(".f-pin").removeClass("toggle"),$(b.id).find(".f-header").removeClass("f-not-allowed"),$(b.id).find(".f-title").removeClass("f-not-allowed"),$(b.id).find(".f-resize").show(),$(b.id).find(".f-close").show()):(b.grid_lock=!0,$(b.id).find(".f-pin").addClass("toggle"),$(b.id).find(".f-header").addClass("f-not-allowed"),$(b.id).find(".f-title").addClass("f-not-allowed"),$(b.id).find(".f-resize").hide(),$(b.id).find(".f-close").hide())}},_eventHide:function(){null===this.event.type&&this.hide()},_eventPanelScroll:function(a){if(null===this.event.type&&this.visible){var b=$(a.srcElement).parents(".frame");if(0!==b.length)return void a.stopPropagation();a.preventDefault();var c=a.originalEvent.detail?a.originalEvent.detail:a.originalEvent.wheelDelta/-3;this._panelScroll(c)}},_eventPanelScroll_up:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(a){return this.frame_list["#"+$(a).closest(".frame").attr("id")]},_frameDragStart:function(a){this._frameFocus(a,!0);var b=this._frameScreen(a);this._frameResize(this.frame_shadow,b),this._frameGrid(this.frame_shadow,a.grid_location),a.grid_location=null,$(this.frame_shadow.id).show(),$(".f-cover").show()},_frameDragStop:function(a){this._frameFocus(a,!1);var b=this._frameScreen(this.frame_shadow);this._frameResize(a,b),this._frameGrid(a,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,$(this.frame_shadow.id).hide(),$(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(a,b){var c="width"==a||"height"==a?1:-1;return"top"==a&&(b-=this.top),parseInt((b+c*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(a,b){var c="width"==a||"height"==a?1:-1,d=b*this.options.cell-c*this.options.margin;return"top"==a&&(d+=this.top),d},_toGrid:function(a){return{top:this._toGridCoord("top",a.top),left:this._toGridCoord("left",a.left),width:this._toGridCoord("width",a.width),height:this._toGridCoord("height",a.height)}},_toPixel:function(a){return{top:this._toPixelCoord("top",a.top),left:this._toPixelCoord("left",a.left),width:this._toPixelCoord("width",a.width),height:this._toPixelCoord("height",a.height)}},_isCollision:function(a){function b(a,b){return!(a.left>b.left+b.width-1||a.left+a.width-1b.top+b.height-1||a.top+a.height-1c?-1:c>d?1:0}),e=0;e
    '},_templateFrame:function(a,b){return b||(b=""),'
    '+b+'
    '},_templateFrameUrl:function(a,b,c){c+=-1==c.indexOf("?")?"?":"&",c+="widget=True";var d=$(this._templateFrame(a,b));return d.find(".f-content").append(''),d},_templateShadow:function(a){return'
    '},_templateBackground:function(){return'
    '},_templateMenu:function(){return'
    '}});return{View:a}}); //# sourceMappingURL=../../../maps/mvc/ui/ui-frames.js.map \ No newline at end of file diff --git a/static/scripts/mvc/ui/ui-select.js b/static/scripts/mvc/ui/ui-select.js index 2cba7b6fa99..f7ec2b55fd9 100644 --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -1,2 +1,2 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.options.container&&(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple)){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return''}});return{View:b}}); +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),!this.options.container)return void console.log("ui-select::initialize() : container not specified.");if(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return''}});return{View:b}}); //# sourceMappingURL=../../../maps/mvc/ui/ui-select.js.map \ No newline at end of file diff --git a/static/scripts/utils/deferred.js b/static/scripts/utils/deferred.js index e4249d15900..8d93e813da1 100644 --- a/static/scripts/utils/deferred.js +++ b/static/scripts/utils/deferred.js @@ -1,2 +1,2 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})}); +define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,console.debug("Deferred:register() - Register "+b),b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,console.debug("Deferred:done() - Unregister "+a),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})}); //# sourceMappingURL=../../maps/utils/deferred.js.map \ No newline at end of file diff --git a/static/scripts/utils/graph.js b/static/scripts/utils/graph.js index 4224fea67e8..5d5a8839b45 100644 --- a/static/scripts/utils/graph.js +++ b/static/scripts/utils/graph.js @@ -1,2 +1,2 @@ -define([],function(){function a(a,b){for(var c in b)if(b.hasOwnProperty(c)&&(!a.hasOwnProperty(c)||a[c]!==b[c]))return!1;return!0}function b(b,c){var d="function"==typeof c?c:void 0,e="object"==typeof c?c:void 0,f=[],g=0;for(var h in b)if(b.hasOwnProperty(h)){var i=b[h];d?f.push(d.call(i,i,h,g)):e?"object"==typeof i&&a(i,e)&&f.push(i):f.push(i),g+=1}return f}function c(a,b,c){var d=this;return d.source=void 0!==a?a:null,d.target=void 0!==b?b:null,d.data=c||null,d}function d(a,b){var c=this;return c.name=void 0!==a?a:"(unnamed)",c.data=b||null,c.edges={},c.degree=0,c}function e(a,b,c){return this.directed=a||!1,this.init(c).read(b)}function f(a,b,c){function d(a){return Math.floor(Math.random()*a)}for(var f={nodes:[],links:[]},g=0;b>g;g++)f.nodes.push({name:g});for(g=0;c>g;g++)f.links.push({source:d(b),target:d(b)});return new e(a,f)}c.prototype.toString=function(){return this.source+"->"+this.target},c.prototype.toJSON=function(){var a={source:this.source,target:this.target};return this.data&&(a.data=this.data),a},d.prototype.toString=function(){return"Vertex("+this.name+")"},d.prototype.eachEdge=function(a){return b(this.edges,a)},d.prototype.toJSON=function(){return{name:this.name,data:this.data}};var g=function(a,b){var c=this;return c.graph=a,c.processFns=b||{vertexEarly:function(){},edge:function(){},vertexLate:function(){}},c._cache={},c};g.prototype.search=function(a){var b=this;return a in b._cache?b._cache[a]:(a instanceof d||(a=b.graph.vertices[a]),b._cache[a.name]=b._search(a))},g.prototype._search=function(a,b){return b=b||{discovered:{},edges:[]}},g.prototype.searchTree=function(a){return this._searchTree(this.search(a))},g.prototype._searchTree=function(a){var b=this;return new e(!0,{edges:a.edges,vertices:Object.keys(a.discovered).map(function(a){return b.graph.vertices[a].toJSON()})})};var h=function(a,b){var c=this;return g.call(this,a,b),c};h.prototype=new g,h.prototype.constructor=h,h.prototype._search=function(a,b){function c(a,c){var f=this;d.processFns.edge&&d.processFns.edge.call(d,f,c,b),b.discovered[a.name]||(b.discovered[a.name]=!0,b.edges.push({source:f.name,target:a.name}),e.push(a))}b=b||{discovered:{},edges:[]};var d=this,e=[];for(b.discovered[a.name]=!0,e.push(a);e.length;){var f=e.shift();d.processFns.vertexEarly&&d.processFns.vertexEarly.call(d,f,b),d.graph.eachAdjacent(f,c),d.processFns.vertexLate&&d.processFns.vertexLate.call(d,f,b)}return b};var i=function(a,b){var c=this;return g.call(this,a,b),c};return i.prototype=new g,i.prototype.constructor=i,i.prototype._search=function(a,b){function c(a,c){var f=this;e.processFns.edge&&e.processFns.edge.call(e,f,c,b),b.discovered[a.name]||(b.edges.push({source:f.name,target:a.name}),d(a))}function d(a){b.discovered[a.name]=!0,e.processFns.vertexEarly&&e.processFns.vertexEarly.call(e,a,b),b.entryTimes[a.name]=f++,e.graph.eachAdjacent(a,c),e.processFns.vertexLate&&e.processFns.vertexLate.call(e,a,b),b.exitTimes[a.name]=f++}b=b||{discovered:{},edges:[],entryTimes:{},exitTimes:{}};var e=this,f=0;return d(a),b},window.Graph=e,e.prototype.init=function(a){a=a||{};var b=this;return b.allowReflexiveEdges=a.allowReflexiveEdges||!1,b.vertices={},b.numEdges=0,b},e.prototype.read=function(a){if(!a)return this;var b=this;return a.hasOwnProperty("nodes")?b.readNodesAndLinks(a):a.hasOwnProperty("vertices")?b.readVerticesAndEdges(a):b},e.prototype.readNodesAndLinks=function(a){if(!a||!a.hasOwnProperty("nodes"))return this;var b=this;return a.nodes.forEach(function(a){b.createVertex(a.name,a.data)}),(a.links||[]).forEach(function(c){var 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a=this;return this.weakComponents().map(function(b){return new e(a.directed,b)})},{Vertex:d,Edge:c,BreadthFirstSearch:h,DepthFirstSearch:i,Graph:e,randGraph:f}}); +define([],function(){function a(a,b){for(var c in b)if(b.hasOwnProperty(c)&&(!a.hasOwnProperty(c)||a[c]!==b[c]))return!1;return!0}function b(b,c){var d="function"==typeof c?c:void 0,e="object"==typeof c?c:void 0,f=[],g=0;for(var h in b)if(b.hasOwnProperty(h)){var i=b[h];d?f.push(d.call(i,i,h,g)):e?"object"==typeof i&&a(i,e)&&f.push(i):f.push(i),g+=1}return f}function c(a,b,c){var d=this;return d.source=void 0!==a?a:null,d.target=void 0!==b?b:null,d.data=c||null,d}function d(a,b){var c=this;return c.name=void 0!==a?a:"(unnamed)",c.data=b||null,c.edges={},c.degree=0,c}function e(a,b,c){return this.directed=a||!1,this.init(c).read(b)}function f(a,b,c){function d(a){return Math.floor(Math.random()*a)}for(var f={nodes:[],links:[]},g=0;b>g;g++)f.nodes.push({name:g});for(g=0;c>g;g++)f.links.push({source:d(b),target:d(b)});return 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d=a.nodes[c.source].name,e=a.nodes[c.target].name;b.createEdge(d,e,b.directed)}),b},e.prototype.readVerticesAndEdges=function(a){if(!a||!a.hasOwnProperty("vertices"))return this;var b=this;return a.vertices.forEach(function(a){b.createVertex(a.name,a.data)}),(a.edges||[]).forEach(function(a){b.createEdge(a.source,a.target,b.directed)}),b},e.prototype.createVertex=function(a,b){return this.vertices[a]?this.vertices[a]:this.vertices[a]=new d(a,b)},e.prototype.createEdge=function(a,b,d,e){var f=a===b;if(!this.allowReflexiveEdges&&f)return null;if(sourceVertex=this.vertices[a],targetVertex=this.vertices[b],!sourceVertex||!targetVertex)return null;var g=this,h=new c(a,b,e);return sourceVertex.edges[b]=h,sourceVertex.degree+=1,g.numEdges+=1,f||d||g.createEdge(b,a,!0),h},e.prototype.edges=function(a){return Array.prototype.concat.apply([],this.eachVertex(function(b){return b.eachEdge(a)}))},e.prototype.eachVertex=function(a){return b(this.vertices,a)},e.prototype.adjacent=function(a){var 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    Is the build not listed here? Add a Custom Build
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    • or create a new session with this dataset as the only track

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    ").addClass("filters").hide(),this.parent_div.bind("drag",function(a){a.stopPropagation()}).click(function(a){a.stopPropagation()}).bind("dblclick",function(a){a.stopPropagation()}).bind("keydown",function(a){a.stopPropagation()}),b&&"filters"in b){for(var c,d=("alpha_filter"in b?b.alpha_filter:null),f=("height_filter"in b?b.height_filter:null),g=b.filters,h=0;h").addClass("param-row").appendTo(this.parent_div),j=$("").attr("value","Run on complete dataset").appendTo(i),k=this;j.click(function(){k.run_on_dataset()})}};return b(f.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var a,b={},c=[],d=0;d= "+a.low),a.max!==a.high&&(b=c(d,a.tool_id,[]),b[b.length]=a.tool_exp_name+" <= "+a.high));var f=[];for(var g in d)f[f.length]=[g,d[g]];!function a(b,c){var d=c[0],e=d[0],f=d[1],g="("+f.join(") and (")+")",h={cond:g,input:b,target_dataset_id:b,tool_id:e};c=c.slice(1),$.getJSON(run_tool_url,h,function(b){b.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+e,buttons:{Close:Galaxy.modal.hide()}}):0===c.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):a(b.dataset_id,c)})}(this.track.dataset_id,f)}}),{FiltersManager:f,NumberFilter:e}}); //# sourceMappingURL=../../../maps/viz/trackster/filters.js.map \ No newline at end of file diff --git a/static/scripts/viz/visualization.js b/static/scripts/viz/visualization.js index 9b6c5179a10..6376a8e4bc4 100644 --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,2 +1,2 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(a,b,c,d){var e={toJSON:function(){var b=this,c={};return a.each(b.constructor.to_json_keys,function(a){var d=b.get(a);a in b.constructor.to_json_mappers&&(d=b.constructor.to_json_mappers[a](d,b)),c[a]=d}),c}},f=function(a,b,c,d){$.ajax({url:a,data:c,error:function(){alert("Grid failed")},success:function(a){Galaxy.modal.show({title:"Select datasets for new tracks",body:a,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var a=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var c={data_type:"track_config",hda_ldda:"hda"},d=$(this).val();"id"!==$(this).attr("name")&&(c.hda_ldda="ldda"),a[a.length]=$.ajax({url:b+"/"+d,data:c,dataType:"json"})}),$.when.apply($,a).then(function(){var a=arguments[0]instanceof Array?$.map(arguments,function(a){return a[0]}):[arguments[0]];d(a)}),Galaxy.modal.hide()}}})}})},g=function(a){this.default_font=void 0!==a?a:"9px Monaco, Lucida Console, 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h=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=b.toString(),f=a.indexOf(d,function(a){return a.toString()===e});return-1!==f&&(c[e].stale?(d.splice(f,1),delete c[e]):this.move_key_to_end(b,f)),c[e]},set_elt:function(a,b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=a.toString(),f=this.attributes.num_elements;if(!c[e]){if(d.length>=f){var g=d.shift();delete c[g.toString()]}d.push(a)}return c[e]=b,b},move_key_to_end:function(a,b){this.attributes.key_ary.splice(b,1),this.attributes.key_ary.push(a)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),i=h.extend({defaults:a.extend({},h.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(){return!0},can_subset:function(){return!1}}),initialize:function(){h.prototype.initialize.call(this);var a=this.get("init_data");a&&this.add_data(a)},add_data:function(b){this.get("num_elements")m.get("start")?a.set("end",a.get("start")+this.attributes.min_region_size):a.set("start",a.get("end")-this.attributes.min_region_size),a.set("genome",this.attributes.genome),a.trim()}return this.load_data(a,b,d,e)},set_data:function(a,b){this.set_elt(a,b)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(a,b,c,d,e){var f=this._mark_stale(a);if(f&&this.get("data_mode_compatible")(f,b)){var g=a.get("start");e===this.DEEP_DATA_REQ?$.extend(d,{start_val:f.data.length+1}):e===this.BROAD_DATA_REQ&&(g=(f.max_high?f.max_high:f.data[f.data.length-1][2])+1);var h=a.copy().set("start",g),i=this,j=this.load_data(h,b,c,d),k=$.Deferred();return this.set_data(a,k),$.when(j).then(function(b){b.data&&(b.data=f.data.concat(b.data),b.max_low&&(b.max_low=f.max_low),b.message&&(b.message=b.message.replace(/[0-9]+/,b.data.length))),i.set_data(a,b),k.resolve(b)}),k}},can_get_more_detailed_data:function(a){var b=this.get_elt(a);return"bigwig"===b.dataset_type&&b.data.length<8e3},get_more_detailed_data:function(a,b,c,d,e){var f=this._mark_stale(a);if(f)return e||(e={}),"bigwig"===f.dataset_type&&(e.num_samples=1e3*d),this.load_data(a,b,c,e)},_mark_stale:function(a){var b=this.get_elt(a);return b.stale=!0,b},get_genome_wide_data:function(b){var c=this,d=!0,e=a.map(b.get("chroms_info").chrom_info,function(a){var b=c.get_elt(new l({chrom:a.chrom,start:0,end:a.len}));return b||(d=!1),b});if(d)return e;var f=$.Deferred();return $.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(a){c.add_data(a.data),f.resolve(a.data)}),f},subset_entry:function(b,c){var d={bigwig:function(b,c){return a.filter(b,function(a){return a[0]>=c.get("start")&&a[0]<=c.get("end")})},refseq:function(a,c){var d=c.get("start")-b.region.get("start");return b.data.slice(d,d+c.length())}},e=b.data;return!b.region.same(c)&&b.dataset_type in d&&(e=d[b.dataset_type](b.data,c)),{region:c,data:e,dataset_type:b.dataset_type}}}),j=i.extend({initialize:function(a){var b=new Backbone.Model;b.urlRoot=a.data_url,this.set("dataset",b)},load_data:function(a,b,c,d){return a.length()<=1e5?i.prototype.load_data.call(this,a,b,c,d):{data:null,region:a}}}),k=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(a){this.id=a.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(b){var c=a.find(this.get_chroms_info(),function(a){return a.chrom===b});return new l({chrom:c.chrom,end:c.len})},get_chrom_len:function(b){return a.find(this.get_chroms_info(),function(a){return a.chrom===b}).len}}),l=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(a){return this.attributes.chrom===a.get("chrom")&&this.attributes.start===a.get("start")&&this.attributes.end===a.get("end")},initialize:function(a){if(a.from_str){var b=a.from_str.split(":"),c=b[0],d=b[1].split("-");this.set({chrom:c,start:parseInt(d[0],10),end:parseInt(d[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new l({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(a){var b,c=this.get("chrom"),d=a.get("chrom"),e=this.get("start"),f=a.get("start"),g=this.get("end"),h=a.get("end");return c&&d&&c!==d?l.overlap_results.DIF_CHROMS:b=f>e?f>g?l.overlap_results.BEFORE:h>g?l.overlap_results.OVERLAP_START:l.overlap_results.CONTAINS:e>f?e>h?l.overlap_results.AFTER:h>=g?l.overlap_results.CONTAINED_BY:l.overlap_results.OVERLAP_END:g>=h?l.overlap_results.CONTAINS:l.overlap_results.CONTAINED_BY},trim:function(){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var a=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>a&&(this.attributes.end=a-1)}return this},contains:function(a){return this.compute_overlap(a)===l.overlap_results.CONTAINS},overlaps:function(b){return 0===a.intersection([this.compute_overlap(b)],[l.overlap_results.DIF_CHROMS,l.overlap_results.BEFORE,l.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),m=Backbone.Collection.extend({model:l}),n=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(a){this.set("region",new l(a.region))}}),o=Backbone.Collection.extend({model:n}),p=Backbone.Model.extend(e).extend({defaults:{mode:"Auto"},initialize:function(a){this.set("dataset",new b.Dataset(a.dataset));var c=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(c,a.prefs));var e=this.get("preloaded_data");e=e?e.data:[],this.set("data_manager",new i({dataset:this.get("dataset"),init_data:e}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(b,c){return 0===a.size(b)&&(b={name:c.get("config").get("name").get("value"),color:c.get("config").get("color").get("value")}),b},dataset:function(a){return{id:a.id,hda_ldda:a.get("hda_ldda")}}}}),q=Backbone.Collection.extend({model:p}),r=Backbone.Model.extend({defaults:{title:"",type:""},urlRoot:galaxy_config.root+"api/visualizations",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),s=r.extend(e).extend({defaults:a.extend({},r.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(a){this.set("drawables",new q(a.tracks));var b=[];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(b,a.prefs)),this.unset("tracks"),this.get("drawables").each(function(a){a.unset("preloaded_data")})},add_tracks:function(a){this.get("drawables").add(a)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(a,b){return{obj_type:"View",prefs:{name:b.get("title"),content_visible:!0},drawables:b.get("drawables")}}}}),t=Backbone.Router.extend({initialize:function(a){this.view=a.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var b=this;b.view.on("navigate",function(a){b.navigate(a)})},change_location:function(a){this.view.go_to(a)}});return{BackboneTrack:p,BrowserBookmark:n,BrowserBookmarkCollection:o,Cache:h,CanvasManager:g,Genome:k,GenomeDataManager:i,GenomeRegion:l,GenomeRegionCollection:m,GenomeVisualization:s,GenomeReferenceDataManager:j,TrackBrowserRouter:t,Visualization:r,select_datasets:f}}); +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(a,b,c,d){var e={toJSON:function(){var b=this,c={};return a.each(b.constructor.to_json_keys,function(a){var d=b.get(a);a in b.constructor.to_json_mappers&&(d=b.constructor.to_json_mappers[a](d,b)),c[a]=d}),c}},f=function(a,b,c,d){$.ajax({url:a,data:c,error:function(){alert("Grid failed")},success:function(a){Galaxy.modal.show({title:"Select datasets for new tracks",body:a,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var a=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var c={data_type:"track_config",hda_ldda:"hda"},d=$(this).val();"id"!==$(this).attr("name")&&(c.hda_ldda="ldda"),a[a.length]=$.ajax({url:b+"/"+d,data:c,dataType:"json"})}),$.when.apply($,a).then(function(){var a=arguments[0]instanceof Array?$.map(arguments,function(a){return a[0]}):[arguments[0]];d(a)}),Galaxy.modal.hide()}}})}})},g=function(a){this.default_font=void 0!==a?a:"9px Monaco, Lucida 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h=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=b.toString(),f=a.indexOf(d,function(a){return a.toString()===e});return-1!==f&&(c[e].stale?(d.splice(f,1),delete c[e]):this.move_key_to_end(b,f)),c[e]},set_elt:function(a,b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=a.toString(),f=this.attributes.num_elements;if(!c[e]){if(d.length>=f){var g=d.shift();delete c[g.toString()]}d.push(a)}return c[e]=b,b},move_key_to_end:function(a,b){this.attributes.key_ary.splice(b,1),this.attributes.key_ary.push(a)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),i=h.extend({defaults:a.extend({},h.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(){return!0},can_subset:function(){return!1}}),initialize:function(){h.prototype.initialize.call(this);var a=this.get("init_data");a&&this.add_data(a)},add_data:function(b){this.get("num_elements")m.get("start")?a.set("end",a.get("start")+this.attributes.min_region_size):a.set("start",a.get("end")-this.attributes.min_region_size),a.set("genome",this.attributes.genome),a.trim()}return this.load_data(a,b,d,e)},set_data:function(a,b){this.set_elt(a,b)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(a,b,c,d,e){var f=this._mark_stale(a);if(!f||!this.get("data_mode_compatible")(f,b))return void console.log("ERROR: problem with getting more data: current data is not compatible");var g=a.get("start");e===this.DEEP_DATA_REQ?$.extend(d,{start_val:f.data.length+1}):e===this.BROAD_DATA_REQ&&(g=(f.max_high?f.max_high:f.data[f.data.length-1][2])+1);var h=a.copy().set("start",g),i=this,j=this.load_data(h,b,c,d),k=$.Deferred();return this.set_data(a,k),$.when(j).then(function(b){b.data&&(b.data=f.data.concat(b.data),b.max_low&&(b.max_low=f.max_low),b.message&&(b.message=b.message.replace(/[0-9]+/,b.data.length))),i.set_data(a,b),k.resolve(b)}),k},can_get_more_detailed_data:function(a){var b=this.get_elt(a);return"bigwig"===b.dataset_type&&b.data.length<8e3},get_more_detailed_data:function(a,b,c,d,e){var f=this._mark_stale(a);return f?(e||(e={}),"bigwig"===f.dataset_type&&(e.num_samples=1e3*d),this.load_data(a,b,c,e)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(a){var b=this.get_elt(a);return b||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),a.toString()),b.stale=!0,b},get_genome_wide_data:function(b){var c=this,d=!0,e=a.map(b.get("chroms_info").chrom_info,function(a){var b=c.get_elt(new l({chrom:a.chrom,start:0,end:a.len}));return b||(d=!1),b});if(d)return e;var f=$.Deferred();return $.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(a){c.add_data(a.data),f.resolve(a.data)}),f},subset_entry:function(b,c){var d={bigwig:function(b,c){return a.filter(b,function(a){return a[0]>=c.get("start")&&a[0]<=c.get("end")})},refseq:function(a,c){var d=c.get("start")-b.region.get("start");return b.data.slice(d,d+c.length())}},e=b.data;return!b.region.same(c)&&b.dataset_type in d&&(e=d[b.dataset_type](b.data,c)),{region:c,data:e,dataset_type:b.dataset_type}}}),j=i.extend({initialize:function(a){var b=new Backbone.Model;b.urlRoot=a.data_url,this.set("dataset",b)},load_data:function(a,b,c,d){return a.length()<=1e5?i.prototype.load_data.call(this,a,b,c,d):{data:null,region:a}}}),k=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(a){this.id=a.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(b){var c=a.find(this.get_chroms_info(),function(a){return a.chrom===b});return new l({chrom:c.chrom,end:c.len})},get_chrom_len:function(b){return a.find(this.get_chroms_info(),function(a){return a.chrom===b}).len}}),l=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(a){return this.attributes.chrom===a.get("chrom")&&this.attributes.start===a.get("start")&&this.attributes.end===a.get("end")},initialize:function(a){if(a.from_str){var b=a.from_str.split(":"),c=b[0],d=b[1].split("-");this.set({chrom:c,start:parseInt(d[0],10),end:parseInt(d[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new l({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(a){var b,c=this.get("chrom"),d=a.get("chrom"),e=this.get("start"),f=a.get("start"),g=this.get("end"),h=a.get("end");return c&&d&&c!==d?l.overlap_results.DIF_CHROMS:b=f>e?f>g?l.overlap_results.BEFORE:h>g?l.overlap_results.OVERLAP_START:l.overlap_results.CONTAINS:e>f?e>h?l.overlap_results.AFTER:h>=g?l.overlap_results.CONTAINED_BY:l.overlap_results.OVERLAP_END:g>=h?l.overlap_results.CONTAINS:l.overlap_results.CONTAINED_BY},trim:function(){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var a=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>a&&(this.attributes.end=a-1)}return this},contains:function(a){return this.compute_overlap(a)===l.overlap_results.CONTAINS},overlaps:function(b){return 0===a.intersection([this.compute_overlap(b)],[l.overlap_results.DIF_CHROMS,l.overlap_results.BEFORE,l.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),m=Backbone.Collection.extend({model:l}),n=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(a){this.set("region",new l(a.region))}}),o=Backbone.Collection.extend({model:n}),p=Backbone.Model.extend(e).extend({defaults:{mode:"Auto"},initialize:function(a){this.set("dataset",new b.Dataset(a.dataset));var c=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(c,a.prefs));var e=this.get("preloaded_data");e=e?e.data:[],this.set("data_manager",new i({dataset:this.get("dataset"),init_data:e}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(b,c){return 0===a.size(b)&&(b={name:c.get("config").get("name").get("value"),color:c.get("config").get("color").get("value")}),b},dataset:function(a){return{id:a.id,hda_ldda:a.get("hda_ldda")}}}}),q=Backbone.Collection.extend({model:p}),r=Backbone.Model.extend({defaults:{title:"",type:""},urlRoot:galaxy_config.root+"api/visualizations",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),s=r.extend(e).extend({defaults:a.extend({},r.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(a){this.set("drawables",new q(a.tracks));var b=[];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(b,a.prefs)),this.unset("tracks"),this.get("drawables").each(function(a){a.unset("preloaded_data")})},add_tracks:function(a){this.get("drawables").add(a)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(a,b){return{obj_type:"View",prefs:{name:b.get("title"),content_visible:!0},drawables:b.get("drawables")}}}}),t=Backbone.Router.extend({initialize:function(a){this.view=a.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var b=this;b.view.on("navigate",function(a){b.navigate(a)})},change_location:function(a){this.view.go_to(a)}});return{BackboneTrack:p,BrowserBookmark:n,BrowserBookmarkCollection:o,Cache:h,CanvasManager:g,Genome:k,GenomeDataManager:i,GenomeRegion:l,GenomeRegionCollection:m,GenomeVisualization:s,GenomeReferenceDataManager:j,TrackBrowserRouter:t,Visualization:r,select_datasets:f}}); //# sourceMappingURL=../../maps/viz/visualization.js.map \ No newline at end of file From 84b5726ca99bb681b6883bd42093c3a58e036d24 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 17 Sep 2015 14:55:08 +0100 Subject: [PATCH 009/178] Extend tool API to allow cross product mapping over collections. By default if single data parameters are mapped over by collections, the collections are matched up (e.g. for two collections the items are paired off and two collections of dimension (N) will result in running N jobs and producing an (N) dimensional output for each define output). In the parameter meta value wrapper (where batch mode can be set with the ``batch`` flag), the linked flag is now respected for collection operations. If ``linked`` is ``False``, then the cross product of the inputs will be used to map over the tool. In the above simplest case, this would cause an NxN (``list:list``) collection to be created for each tool output. This operation was previously available for individual datasets, but when supplied a collection it would not create an implicit collection pulling together all the relevant datasets with the correct structure - it would just run the jobs and leave the datasets uncollected. Now a collection with the correct structure and identifiers is created. Limitations: ----------------- This does not enable tool form support but the API for collections matches that for doing cross product operations over sets of individual datasets, so once support is added to the tool form for that collection support should be trivial. Testing: ----------------- The following test case has been extended to now ensure that an implicit collection is created and that it has the right dimensionality/structure and contents. ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_map_over_two_collections_unlinked --- lib/galaxy/dataset_collections/matching.py | 37 +++++++++++++----- lib/galaxy/dataset_collections/structure.py | 36 +++++++++++++++--- .../dataset_collections/type_description.py | 4 ++ lib/galaxy/tools/parameters/meta.py | 6 +-- test/api/test_tools.py | 38 +++++++++++++++++-- 5 files changed, 100 insertions(+), 21 deletions(-) diff --git a/lib/galaxy/dataset_collections/matching.py b/lib/galaxy/dataset_collections/matching.py index 88763df069c..3398aec4a65 100644 --- a/lib/galaxy/dataset_collections/matching.py +++ b/lib/galaxy/dataset_collections/matching.py @@ -1,6 +1,6 @@ from galaxy.util import bunch from galaxy import exceptions -from .structure import get_structure +from .structure import get_structure, leaf CANNOT_MATCH_ERROR_MESSAGE = "Cannot match collection types." @@ -13,10 +13,11 @@ class CollectionsToMatch( object ): def __init__( self ): self.collections = {} - def add( self, input_name, hdca, subcollection_type=None ): + def add( self, input_name, hdca, subcollection_type=None, linked=True ): self.collections[ input_name ] = bunch.Bunch( hdca=hdca, subcollection_type=subcollection_type, + linked=linked, ) def has_collections( self ): @@ -37,21 +38,32 @@ class MatchingCollections( object ): """ def __init__( self ): - self.structure = None + self.linked_structure = None + self.unlinked_structures = [] self.collections = {} - def __attempt_add_to_match( self, input_name, hdca, collection_type_description, subcollection_type ): + def __attempt_add_to_linked_match( self, input_name, hdca, collection_type_description, subcollection_type ): structure = get_structure( hdca, collection_type_description, leaf_subcollection_type=subcollection_type ) - if not self.structure: - self.structure = structure + if not self.linked_structure: + self.linked_structure = structure self.collections[ input_name ] = hdca else: - if not self.structure.can_match( structure ): + if not self.linked_structure.can_match( structure ): raise exceptions.MessageException( CANNOT_MATCH_ERROR_MESSAGE ) self.collections[ input_name ] = hdca def slice_collections( self ): - return self.structure.walk_collections( self.collections ) + return self.linked_structure.walk_collections( self.collections ) + + @property + def structure( self ): + """Yield cross product of all unlinked datasets to linked dataset.""" + effective_structure = leaf + for unlinked_structure in self.unlinked_structures: + effective_structure = effective_structure.multiply( unlinked_structure ) + linked_structure = self.linked_structure or leaf + effective_structure = effective_structure.multiply( linked_structure ) + return None if effective_structure.is_leaf else effective_structure @staticmethod def for_collections( collections_to_match, collection_type_descriptions ): @@ -61,8 +73,13 @@ class MatchingCollections( object ): matching_collections = MatchingCollections() for input_key, to_match in collections_to_match.iteritems(): hdca = to_match.hdca - subcollection_type = to_match.subcollection_type collection_type_description = collection_type_descriptions.for_collection_type( hdca.collection.collection_type ) - matching_collections.__attempt_add_to_match( input_key, hdca, collection_type_description, subcollection_type ) + subcollection_type = to_match.subcollection_type + + if to_match.linked: + matching_collections.__attempt_add_to_linked_match( input_key, hdca, collection_type_description, subcollection_type ) + else: + structure = get_structure( hdca, collection_type_description, leaf_subcollection_type=subcollection_type ) + matching_collections.unlinked_structures.append( structure ) return matching_collections diff --git a/lib/galaxy/dataset_collections/structure.py b/lib/galaxy/dataset_collections/structure.py index b08d62748bc..8f1eab5a020 100644 --- a/lib/galaxy/dataset_collections/structure.py +++ b/lib/galaxy/dataset_collections/structure.py @@ -15,23 +15,34 @@ class Leaf( object ): def is_leaf( self ): return True + def clone( self ): + return self + + def multiply( self, other_structure ): + return other_structure.clone() + + leaf = Leaf() class Tree( object ): - def __init__( self, dataset_collection, collection_type_description ): + def __init__( self, children, collection_type_description ): + self.children = children self.collection_type_description = collection_type_description + + @staticmethod + def for_dataset_collection( dataset_collection, collection_type_description ): children = [] for element in dataset_collection.elements: if collection_type_description.has_subcollections(): child_collection = element.child_collection subcollection_type_description = collection_type_description.subcollection_type_description() # Type description of children - children.append( ( element.element_identifier, Tree( child_collection, collection_type_description=subcollection_type_description ) ) ) + tree = Tree.for_dataset_collection( child_collection, collection_type_description=subcollection_type_description ) + children.append( ( element.element_identifier, tree ) ) else: children.append( ( element.element_identifier, leaf ) ) - - self.children = children + return Tree( children, collection_type_description ) def walk_collections( self, hdca_dict ): return self._walk_collections( dict_map( lambda hdca: hdca.collection, hdca_dict ) ) @@ -96,6 +107,21 @@ class Tree( object ): element_identifiers=element_identifiers, ) + def multiply( self, other_structure ): + if other_structure.is_leaf: + return self.clone() + + new_collection_type = self.collection_type_description.multiply( other_structure.collection_type_description ) + new_children = [] + for (identifier, structure) in self.children: + new_children.append( (identifier, structure.multiply( other_structure ) ) ) + + return Tree( new_children, new_collection_type ) + + def clone( self ): + cloned_children = map( lambda (identifier, element): (identifier, element.clone()), self.children ) + return Tree( cloned_children, self.collection_type_description ) + def dict_map( func, input_dict ): return dict( [ ( k, func(v) ) for k, v in input_dict.iteritems() ] ) @@ -105,4 +131,4 @@ def get_structure( dataset_collection_instance, collection_type_description, lea if leaf_subcollection_type: collection_type_description = collection_type_description.effective_collection_type_description( leaf_subcollection_type ) - return Tree( dataset_collection_instance.collection, collection_type_description ) + return Tree.for_dataset_collection( dataset_collection_instance.collection, collection_type_description ) diff --git a/lib/galaxy/dataset_collections/type_description.py b/lib/galaxy/dataset_collections/type_description.py index 8d0aa8cbbb3..0bf85b3e367 100644 --- a/lib/galaxy/dataset_collections/type_description.py +++ b/lib/galaxy/dataset_collections/type_description.py @@ -102,6 +102,10 @@ class CollectionTypeDescription( object ): def rank_type_plugin( self ): return self.collection_type_description_factory.type_registry.get( self.rank_collection_type() ) + def multiply( self, other_collection_type ): + collection_type = map_over_collection_type( self, other_collection_type ) + return self.collection_type_description_factory.for_collection_type( collection_type ) + def __str__( self ): return "CollectionTypeDescription[%s]" % self.collection_type diff --git a/lib/galaxy/tools/parameters/meta.py b/lib/galaxy/tools/parameters/meta.py index 2c91a702224..77076a76bae 100644 --- a/lib/galaxy/tools/parameters/meta.py +++ b/lib/galaxy/tools/parameters/meta.py @@ -35,7 +35,7 @@ def expand_meta_parameters( trans, tool, incoming ): classification = permutations.input_classification.SINGLE if __collection_multirun_parameter( value ): collection_value = value[ 'values' ][ 0 ] - values = __expand_collection_parameter( trans, input_key, collection_value, collections_to_match ) + values = __expand_collection_parameter( trans, input_key, collection_value, collections_to_match, linked=is_linked ) else: values = value[ 'values' ] else: @@ -102,7 +102,7 @@ def expand_meta_parameters( trans, tool, incoming ): return expanded_incomings, collection_info -def __expand_collection_parameter( trans, input_key, incoming_val, collections_to_match ): +def __expand_collection_parameter( trans, input_key, incoming_val, collections_to_match, linked=False ): # If subcollectin multirun of data_collection param - value will # be "hdca_id|subcollection_type" else it will just be hdca_id if "|" in incoming_val: @@ -119,7 +119,7 @@ def __expand_collection_parameter( trans, input_key, incoming_val, collections_t subcollection_type = None hdc_id = trans.app.security.decode_id( encoded_hdc_id ) hdc = trans.sa_session.query( model.HistoryDatasetCollectionAssociation ).get( hdc_id ) - collections_to_match.add( input_key, hdc, subcollection_type=subcollection_type ) + collections_to_match.add( input_key, hdc, subcollection_type=subcollection_type, linked=linked ) if subcollection_type is not None: from galaxy.dataset_collections import subcollections subcollection_elements = subcollections.split_dataset_collection_instance( hdc, subcollection_type ) diff --git a/test/api/test_tools.py b/test/api/test_tools.py index b7507c37414..9bb837ccc62 100644 --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -804,9 +804,41 @@ class ToolsTestCase( api.ApiTestCase ): self.assertEquals( len( outputs ), 4 ) self.assertEquals( len( response_object[ 'jobs' ] ), 4 ) - # Implicit collections not created with unlinked inputs yet - this may - # be problematic. - self.assertEquals( len( response_object[ 'implicit_collections' ] ), 0 ) + implicit_collections = response_object[ 'implicit_collections' ] + self.assertEquals( len( implicit_collections ), 1 ) + implicit_collection = implicit_collections[ 0 ] + self.assertEquals( implicit_collection[ "collection_type" ], "paired:paired" ) + + outer_elements = implicit_collection[ "elements" ] + assert len( outer_elements ) == 2 + element0, element1 = outer_elements + assert element0[ "element_identifier" ] == "forward" + assert element1[ "element_identifier" ] == "reverse" + + elements0 = element0[ "object" ][ "elements" ] + elements1 = element1[ "object" ][ "elements" ] + + assert len( elements0 ) == 2 + assert len( elements1 ) == 2 + + element00, element01 = elements0 + assert element00[ "element_identifier" ] == "forward" + assert element01[ "element_identifier" ] == "reverse" + + element10, element11 = elements1 + assert element10[ "element_identifier" ] == "forward" + assert element11[ "element_identifier" ] == "reverse" + + expected_contents_list = [ + (element00, "123\n789\n"), + (element01, "123\n0ab\n"), + (element10, "456\n789\n"), + (element11, "456\n0ab\n"), + ] + for (element, expected_contents) in expected_contents_list: + dataset_id = element["object"]["id"] + contents = self.dataset_populator.get_history_dataset_content( history_id, dataset_id=dataset_id ) + self.assertEquals(expected_contents, contents) @skip_without_tool( "cat1" ) def test_map_over_collected_and_individual_datasets( self ): From ef23abc6df1dfc1b5ca10d380c2e7a840862c76a Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 18 Sep 2015 15:42:07 +0100 Subject: [PATCH 010/178] WIP: Improved state tracking of HDCA in history panel. For tools which dynamically discover datasets for an output collection, keep the collection yellow until the structure of the HDCA has been fully defined. HDCAs still have the problem that they will always be green even if datasets contained within are in error, running, or queued states - but at least the structure is now reflected in the color. --- client/galaxy/scripts/mvc/collection/collection-model.js | 8 +++++--- client/galaxy/scripts/mvc/history/hdca-li.js | 2 +- lib/galaxy/model/__init__.py | 3 +++ static/maps/mvc/collection/collection-model.js.map | 2 +- static/maps/mvc/history/hdca-li.js.map | 2 +- static/scripts/mvc/collection/collection-model.js | 2 +- static/scripts/mvc/history/hdca-li.js | 2 +- test/api/test_dataset_collections.py | 1 + 8 files changed, 14 insertions(+), 8 deletions(-) diff --git a/client/galaxy/scripts/mvc/collection/collection-model.js b/client/galaxy/scripts/mvc/collection/collection-model.js index 844309f6e6e..49da237372c 100644 --- a/client/galaxy/scripts/mvc/collection/collection-model.js +++ b/client/galaxy/scripts/mvc/collection/collection-model.js @@ -241,10 +241,12 @@ var DatasetCollection = Backbone.Model return json; }, - /** is the collection done with updates and ready to be used? (finished running, etc.) */ + /** Is this collection in a 'ready' state no processing (for the collection) is left + * to do on the server. + */ inReadyState : function(){ -//TODO: state currenly unimplemented for collections - return true; + var populated = this.get( 'populated' ); + return ( this.isDeletedOrPurged() || populated ); }, //TODO:?? the following are the same interface as DatasetAssociation - can we combine? diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js index ee633d82e87..c98b5b99527 100644 --- a/client/galaxy/scripts/mvc/history/hdca-li.js +++ b/client/galaxy/scripts/mvc/history/hdca-li.js @@ -46,7 +46,7 @@ var HDCAListItemView = _super.extend( _swapNewRender : function( $newRender ){ _super.prototype._swapNewRender.call( this, $newRender ); //TODO: model currently has no state - var state = this.model.get( 'state' ) || STATES.OK; + var state = !this.model.get( 'populated' ) ? STATES.RUNNING : STATES.OK; //if( this.model.has( 'state' ) ){ this.$el.addClass( 'state-' + state ); //} diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 4811890336f..37a292ea510 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3047,6 +3047,9 @@ class DatasetCollectionInstance( object, HasName ): id=self.id, name=self.name, collection_type=self.collection.collection_type, + populated=self.collection.populated, + populated_state=self.collection.populated_state, + populated_state_message=self.collection.populated_state_message, type="collection", # contents type (distinguished from file or folder (in case of library)) ) diff --git a/static/maps/mvc/collection/collection-model.js.map b/static/maps/mvc/collection/collection-model.js.map index 512f3e27839..534ce4c9de0 100644 --- a/static/maps/mvc/collection/collection-model.js.map +++ b/static/maps/mvc/collection/collection-model.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/collection/collection-model.js b/static/scripts/mvc/collection/collection-model.js index 7616ff85fe5..e2c782fab57 100644 --- a/static/scripts/mvc/collection/collection-model.js +++ b/static/scripts/mvc/collection/collection-model.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/dataset-model","mvc/base-mvc","utils/localization"],function(a,b){var c={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(a){return _.extend(a,a.object,{element_id:a.id}),delete a.object,a},constructor:function(a){a=this._mergeObject(a),this.idAttribute="element_id",Backbone.Model.apply(this,arguments)},parse:function(a){var b=a;return b=this._mergeObject(b)}},d=Backbone.Model.extend(b.LoggableMixin).extend(c),e=Backbone.Collection.extend(b.LoggableMixin).extend({model:d,initialize:function(a,b){this.debug(this+"(DCECollection).initialize:",a,b),b=b||{}},toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),f=a.DatasetAssociation.extend(b.mixin(c,{defaults:_.extend({},a.DatasetAssociation.prototype.defaults,c.defaults),constructor:function(a,b){this.debug(" DatasetDCE.constructor:",a,b),c.constructor.call(this,a,b)},initialize:function(b,c){this.debug(this+"(DatasetDCE).initialize:",b,c),a.DatasetAssociation.prototype.initialize.call(this,b,c)},toString:function(){var a=this.get("element_identifier");return["DatasetDCE(",a,")"].join("")}})),g=e.extend({model:f,initialize:function(a,b){this.debug(this+"(DatasetDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=Backbone.Model.extend(b.LoggableMixin).extend(b.SearchableModelMixin).extend({defaults:{collection_type:null,deleted:!1},collectionClass:e,initialize:function(a,b){this.debug(this+"(DatasetCollection).initialize:",a,b,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var a=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(a),this.elements},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return this.elements&&(a.elements=this.elements.toJSON()),a},inReadyState:function(){return!0},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(){return this.elements},"delete":function(a){return this.get("deleted")?jQuery.when():this.save({deleted:!0},a)},undelete:function(a){return!this.get("deleted")||this.get("purged")?jQuery.when():this.save({deleted:!1},a)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var a=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+a.join(",")+")"}}),i=h.extend({collectionClass:g,initialize:function(a,b){this.debug(this+"(ListDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),j=i.extend({initialize:function(a,b){this.debug(this+"(PairDatasetCollection).initialize:",a,b),i.prototype.initialize.call(this,a,b)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),k=h.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",a,")"].join("")}})),l=e.extend({model:k,initialize:function(a,b){this.debug(this+"(NestedDCDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=j.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedPairDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",a,")"].join("")}})),n=l.extend({model:m,initialize:function(a,b){this.debug(this+"(NestedPairDCDCECollection).initialize:",a,b),l.prototype.initialize.call(this,a,b)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),o=h.extend({collectionClass:n,initialize:function(a,b){this.debug(this+"(ListPairedDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:i,PairDatasetCollection:j,ListPairedDatasetCollection:o}}); +define(["mvc/dataset/dataset-model","mvc/base-mvc","utils/localization"],function(a,b){var c={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(a){return _.extend(a,a.object,{element_id:a.id}),delete a.object,a},constructor:function(a){a=this._mergeObject(a),this.idAttribute="element_id",Backbone.Model.apply(this,arguments)},parse:function(a){var b=a;return b=this._mergeObject(b)}},d=Backbone.Model.extend(b.LoggableMixin).extend(c),e=Backbone.Collection.extend(b.LoggableMixin).extend({model:d,initialize:function(a,b){this.debug(this+"(DCECollection).initialize:",a,b),b=b||{}},toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),f=a.DatasetAssociation.extend(b.mixin(c,{defaults:_.extend({},a.DatasetAssociation.prototype.defaults,c.defaults),constructor:function(a,b){this.debug(" DatasetDCE.constructor:",a,b),c.constructor.call(this,a,b)},initialize:function(b,c){this.debug(this+"(DatasetDCE).initialize:",b,c),a.DatasetAssociation.prototype.initialize.call(this,b,c)},toString:function(){var a=this.get("element_identifier");return["DatasetDCE(",a,")"].join("")}})),g=e.extend({model:f,initialize:function(a,b){this.debug(this+"(DatasetDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=Backbone.Model.extend(b.LoggableMixin).extend(b.SearchableModelMixin).extend({defaults:{collection_type:null,deleted:!1},collectionClass:e,initialize:function(a,b){this.debug(this+"(DatasetCollection).initialize:",a,b,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var a=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(a),this.elements},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return this.elements&&(a.elements=this.elements.toJSON()),a},inReadyState:function(){var a=this.get("populated");return this.isDeletedOrPurged()||a},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(){return this.elements},"delete":function(a){return this.get("deleted")?jQuery.when():this.save({deleted:!0},a)},undelete:function(a){return!this.get("deleted")||this.get("purged")?jQuery.when():this.save({deleted:!1},a)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var a=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+a.join(",")+")"}}),i=h.extend({collectionClass:g,initialize:function(a,b){this.debug(this+"(ListDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),j=i.extend({initialize:function(a,b){this.debug(this+"(PairDatasetCollection).initialize:",a,b),i.prototype.initialize.call(this,a,b)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),k=h.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",a,")"].join("")}})),l=e.extend({model:k,initialize:function(a,b){this.debug(this+"(NestedDCDCECollection).initialize:",a,b),e.prototype.initialize.call(this,a,b)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=j.extend(b.mixin(c,{constructor:function(a,b){this.debug(" NestedPairDCDCE.constructor:",a,b),c.constructor.call(this,a,b)},toString:function(){var a=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",a,")"].join("")}})),n=l.extend({model:m,initialize:function(a,b){this.debug(this+"(NestedPairDCDCECollection).initialize:",a,b),l.prototype.initialize.call(this,a,b)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),o=h.extend({collectionClass:n,initialize:function(a,b){this.debug(this+"(ListPairedDatasetCollection).initialize:",a,b),h.prototype.initialize.call(this,a,b)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:i,PairDatasetCollection:j,ListPairedDatasetCollection:o}}); //# sourceMappingURL=../../../maps/mvc/collection/collection-model.js.map \ No newline at end of file diff --git a/static/scripts/mvc/history/hdca-li.js b/static/scripts/mvc/history/hdca-li.js index aa10e9096d2..422c9f9df06 100644 --- a/static/scripts/mvc/history/hdca-li.js +++ b/static/scripts/mvc/history/hdca-li.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("state")||a.OK;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
    ',e("This collection has been hidden"),"
    ","<% } %>"],"collection")}),b=d.wrapTemplate(['
    ','','
    ','<%- collection.hid %> ','<%- collection.name %>',"
    ",'
    ',"
    "],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); +define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
    ',e("This collection has been hidden"),"
    ","<% } %>"],"collection")}),b=d.wrapTemplate(['
    ','','
    ','<%- collection.hid %> ','<%- collection.name %>',"
    ",'
    ',"
    "],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); //# sourceMappingURL=../../../maps/mvc/history/hdca-li.js.map \ No newline at end of file diff --git a/test/api/test_dataset_collections.py b/test/api/test_dataset_collections.py index 6993d81b305..2e298fe7698 100644 --- a/test/api/test_dataset_collections.py +++ b/test/api/test_dataset_collections.py @@ -87,6 +87,7 @@ class DatasetCollectionApiTestCase( api.ApiTestCase ): pair_1_object = pair_1_element[ "object" ] self._assert_has_keys( pair_1_object, "collection_type", "elements" ) self.assertEquals( pair_1_object[ "collection_type" ], "paired" ) + self.assertEquals( pair_1_object[ "populated" ], True ) pair_elements = pair_1_object[ "elements" ] assert len( pair_elements ) == 2 pair_1_element_1 = pair_elements[ 0 ] From 98f6dcc4dea061db7c04fbe8e2cd86898d10343b Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Fri, 18 Sep 2015 17:03:54 -0400 Subject: [PATCH 011/178] Render HDCAs when their models change --- client/galaxy/scripts/mvc/history/hdca-li.js | 6 ++---- static/maps/mvc/history/hdca-li.js.map | 2 +- static/scripts/mvc/history/hdca-li.js | 2 +- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js index c98b5b99527..b2b9977ef4e 100644 --- a/client/galaxy/scripts/mvc/history/hdca-li.js +++ b/client/galaxy/scripts/mvc/history/hdca-li.js @@ -21,11 +21,9 @@ var HDCAListItemView = _super.extend( /** event listeners */ _setUpListeners : function(){ _super.prototype._setUpListeners.call( this ); - // re-rendering on deletion + this.model.on( 'change', function( model, options ){ - if( _.isEqual( _.keys( model.changed ), [ 'visible' ] ) ){ - this.render(); - } + this.render(); }, this ); }, diff --git a/static/maps/mvc/history/hdca-li.js.map b/static/maps/mvc/history/hdca-li.js.map index 083d56fab03..aa95fa04548 100644 --- a/static/maps/mvc/history/hdca-li.js.map +++ b/static/maps/mvc/history/hdca-li.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/history/hdca-li.js b/static/scripts/mvc/history/hdca-li.js index 422c9f9df06..05eb43b6674 100644 --- a/static/scripts/mvc/history/hdca-li.js +++ b/static/scripts/mvc/history/hdca-li.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["visible"])&&this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
    ',e("This collection has been hidden"),"
    ","<% } %>"],"collection")}),b=d.wrapTemplate(['
    ','','
    ','<%- collection.hid %> ','<%- collection.name %>',"
    ",'
    ',"
    "],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); +define(["mvc/dataset/states","mvc/collection/collection-li","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){var f=b.DCListItemView,g=f.extend({className:f.prototype.className+" history-content",_setUpListeners:function(){f.prototype._setUpListeners.call(this),this.model.on("change",function(){this.render()},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return c.ListCollectionPanel;case"paired":return c.PairCollectionPanel;case"list:paired":return c.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(b){f.prototype._swapNewRender.call(this,b);var c=this.model.get("populated")?a.OK:a.RUNNING;return this.$el.addClass("state-"+c),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDCAListItemView("+a+")"}});return g.prototype.templates=function(){var a=_.extend({},f.prototype.templates.warnings,{hidden:d.wrapTemplate(["<% if( !collection.visible ){ %>",'
    ',e("This collection has been hidden"),"
    ","<% } %>"],"collection")}),b=d.wrapTemplate(['
    ','','
    ','<%- collection.hid %> ','<%- collection.name %>',"
    ",'
    ',"
    "],"collection");return _.extend({},f.prototype.templates,{warnings:a,titleBar:b})}(),{HDCAListItemView:g}}); //# sourceMappingURL=../../../maps/mvc/history/hdca-li.js.map \ No newline at end of file From 07dd69edd5472afef305fb170f18628a0cf3402d Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 21 Sep 2015 14:23:38 +0100 Subject: [PATCH 012/178] Allow discover_datasets tag to use format attribute (instead of ext). https://github.com/TGAC/tgac-galaxytools/commit/93514438cb50fab48d0e211f1e1869b0f591ed66#commitcomment-13349396. --- lib/galaxy/tools/parameters/output_collect.py | 2 ++ test/functional/tools/multi_output_configured.xml | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/tools/parameters/output_collect.py b/lib/galaxy/tools/parameters/output_collect.py index b673e1f787c..7403705d64e 100644 --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -355,6 +355,8 @@ class DatasetCollector( object ): self.pattern = pattern self.default_dbkey = kwargs.get( "dbkey", None ) self.default_ext = kwargs.get( "ext", None ) + if self.default_ext is None and "format" in kwargs: + self.default_ext = kwargs.get( "format" ) self.default_visible = util.asbool( kwargs.get( "visible", None ) ) self.directory = kwargs.get( "directory", None ) self.assign_primary_output = util.asbool( kwargs.get( 'assign_primary_output', False ) ) diff --git a/test/functional/tools/multi_output_configured.xml b/test/functional/tools/multi_output_configured.xml index 354cba05aab..cd5965a049d 100644 --- a/test/functional/tools/multi_output_configured.xml +++ b/test/functional/tools/multi_output_configured.xml @@ -25,7 +25,7 @@ - + From 87d5063a0dff35d6cddda3f17a8cadb6b04ff5e9 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 21 Sep 2015 15:48:56 +0100 Subject: [PATCH 013/178] Implement min/max for multiple data input parameters. --- lib/galaxy/tools/parameters/basic.py | 44 +++++++++++++++++++--- test/api/test_tools.py | 13 +++++++ test/functional/tools/multi_data_param.xml | 2 +- 3 files changed, 53 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index b00cc86c828..d3afd35392a 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1764,6 +1764,22 @@ class DataToolParameter( BaseDataToolParameter ): self.validators.append( validation.MetadataValidator() ) self._parse_formats( trans, tool, input_source ) self.multiple = input_source.get_bool('multiple', False) + self.min = input_source.get( 'min' ) + self.max = input_source.get( 'max' ) + if self.min: + try: + self.min = int( self.min ) + except: + raise ValueError( "An integer is required for min property." ) + if self.max: + try: + self.max = int( self.max ) + except: + raise ValueError( "An integer is required for max property." ) + if not self.multiple and (self.min is not None): + raise ValueError( "Cannot specify min property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name ) + if not self.multiple and (self.max is not None): + raise ValueError( "Cannot specify max property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name ) self.is_dynamic = True self._parse_options( input_source ) # Load conversions required for the dataset input @@ -2052,17 +2068,31 @@ class DataToolParameter( BaseDataToolParameter ): return "No dataset" def validate( self, value, history=None ): + dataset_count = 0 for validator in self.validators: if value and self.multiple: - if isinstance(value, list): - for v in value: - validator.validate( v, history ) - elif isinstance(value, galaxy.model.HistoryDatasetCollectionAssociation): - for v in value.collection.dataset_instances: + if not isinstance( value, list ): + value = [ value ] + for v in value: + if isinstance(v, galaxy.model.HistoryDatasetCollectionAssociation): + for dataset_instance in v.collection.dataset_instances: + dataset_count += 1 + validator.validate( dataset_instance, history ) + else: + dataset_count += 1 validator.validate( v, history ) else: + if value: + dataset_count += 1 validator.validate( value, history ) + if self.min is not None: + if self.min > dataset_count: + raise ValueError( "At least %d datasets are required." % self.min ) + if self.max is not None: + if self.max < dataset_count: + raise ValueError( "At most %d datasets are required." % self.max ) + def get_dependencies( self ): """ Get the *names* of the other params this param depends on. @@ -2124,6 +2154,10 @@ class DataToolParameter( BaseDataToolParameter ): d['extensions'] = extensions d['edam_formats'] = edam_formats d['multiple'] = self.multiple + if self.multiple: + # For consistency, should these just always be in the dict? + d['min'] = self.min + d['max'] = self.max d['options'] = {'hda': [], 'hdca': []} # return default content if context is not available diff --git a/test/api/test_tools.py b/test/api/test_tools.py index 62db749398f..74fa95d743c 100644 --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -62,6 +62,19 @@ class ToolsTestCase( api.ApiTestCase ): self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help', 'argument' ) assert case2_inputs[ 0 ][ "name" ] == "seed" + @skip_without_tool( "multi_data_param" ) + def test_show_multi_data( self ): + tool_info = self._show_valid_tool( "multi_data_param" ) + + f1_info, f2_info = tool_info[ "inputs" ][ 0 ], tool_info[ "inputs" ][ 1 ] + self._assert_has_keys( f1_info, "min", "max" ) + assert f1_info["min"] == 1 + assert f1_info["max"] == 1235 + + self._assert_has_keys( f2_info, "min", "max" ) + assert f2_info["min"] is None + assert f2_info["max"] is None + def _show_valid_tool( self, tool_id ): tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) ) self._assert_status_code_is( tool_show_response, 200 ) diff --git a/test/functional/tools/multi_data_param.xml b/test/functional/tools/multi_data_param.xml index 6fe5de3bc53..1fcec1b9bc6 100644 --- a/test/functional/tools/multi_data_param.xml +++ b/test/functional/tools/multi_data_param.xml @@ -6,7 +6,7 @@ cat ${" ".join(map(str, $f2))} >> $out2 - + From b9913d29316de4058197739b2ae4cfed5c5ae2f3 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Mon, 21 Sep 2015 11:53:29 -0400 Subject: [PATCH 014/178] Swap tool form to use Galaxy.modal --- .../scripts/mvc/tools/tools-form-base.js | 10 +- static/maps/mvc/tools/tools-form-base.js.map | 2 +- static/scripts/mvc/tools/tools-form-base.js | 179 +++++++++++++++++- 3 files changed, 184 insertions(+), 7 deletions(-) diff --git a/client/galaxy/scripts/mvc/tools/tools-form-base.js b/client/galaxy/scripts/mvc/tools/tools-form-base.js index d3fa2cd8b0f..43959ab52bb 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -2,8 +2,9 @@ This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form. */ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', - 'mvc/tools/tools-template', 'mvc/citation/citation-model', 'mvc/citation/citation-view'], - function(Utils, Deferred, Ui, Form, ToolTemplate, CitationModel, CitationView) { + 'mvc/tools/tools-template', 'mvc/citation/citation-model', 'mvc/citation/citation-view', + 'mvc/ui/ui-modal'], + function(Utils, Deferred, Ui, Form, ToolTemplate, CitationModel, CitationView, Modal) { // create form view return Backbone.View.extend({ @@ -11,6 +12,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', initialize: function(options) { this.options = Utils.merge(options, {}); this.setElement('
    '); + this.modal = Galaxy.modal; // create deferred processing queue handler // this handler reduces the number of requests to the api by filtering redundant requests @@ -117,12 +119,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', // show error var error_message = response.error || 'Uncaught error.'; - self.form.modal.show({ + self.modal.show({ title : 'Tool cannot be executed', body : error_message, buttons : { 'Close' : function() { - self.form.modal.hide(); + self.modal.hide(); } } }); diff --git a/static/maps/mvc/tools/tools-form-base.js.map b/static/maps/mvc/tools/tools-form-base.js.map index a79eda9b999..88a72130cf2 100644 --- a/static/maps/mvc/tools/tools-form-base.js.map +++ b/static/maps/mvc/tools/tools-form-base.js.map @@ -1 +1 @@ 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    "),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var d=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)e=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var e=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)e+="dataset_id="+b.dataset_id;else{e+="tool_version="+b.version+"&";var f=top.location.href,g=f.indexOf("?");-1!=f.indexOf("tool_id=")&&-1!==g&&(e+=f.slice(g+1))}}var h=this.deferred.register();a.request({type:"GET",url:e,success:function(a){d._buildForm(a.tool_model||a),!c&&d.form.message.update({status:"success",message:"Now you are using '"+d.options.name+"' version "+d.options.version+".",persistent:!1}),d.deferred.done(h)},error:function(a){d.deferred.done(h);var b=a.error||"Uncaught error.";d.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){d.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); -//# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file +define([ "utils/utils", "utils/deferred", "mvc/ui/ui-misc", "mvc/form/form-view", "mvc/tools/tools-template", "mvc/citation/citation-model", "mvc/citation/citation-view", "mvc/ui/ui-modal" ], function(a, b, c, d, e, f, g) { + return Backbone.View.extend({ + initialize: function(c) { + this.options = a.merge(c, {}), this.setElement("
    "), this.modal = Galaxy.modal, + this.deferred = new b(), c.inputs ? this._buildForm(c) : this._buildModel(c, !0); + }, + _buildForm: function(b) { + var c = this; + this.options = a.merge(b, this.options), this.options = a.merge({ + icon: "fa-wrench", + title: "" + b.name + " " + b.description + " (Galaxy Tool Version " + b.version + ")", + operations: this._operations(), + onchange: function() { + c.deferred.reset(), c.deferred.execute(function() { + c._updateModel(); + }); + } + }, this.options), this.form = new d(this.options), this._footer(), this.$el.empty(), + this.$el.append(this.form.$el); + }, + _buildModel: function(b, c) { + var d = this; + if (this.options.id = b.id, this.options.version = b.version, b.job_id) e = Galaxy.root + "api/jobs/" + b.job_id + "/build_for_rerun"; else { + var e = Galaxy.root + "api/tools/" + b.id + "/build?"; + if (b.dataset_id) e += "dataset_id=" + b.dataset_id; else { + e += "tool_version=" + b.version + "&"; + var f = top.location.href, g = f.indexOf("?"); + -1 != f.indexOf("tool_id=") && -1 !== g && (e += f.slice(g + 1)); + } + } + var h = this.deferred.register(); + a.request({ + type: "GET", + url: e, + success: function(a) { + d._buildForm(a.tool_model || a), !c && d.form.message.update({ + status: "success", + message: "Now you are using '" + d.options.name + "' version " + d.options.version + ".", + persistent: !1 + }), d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model ready."), + console.debug(a); + }, + error: function(a) { + d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model request failed."), + console.debug(a); + var b = a.error || "Uncaught error."; + d.modal.show({ + title: "Tool cannot be executed", + body: b, + buttons: { + Close: function() { + d.modal.hide(); + } + } + }); + } + }); + }, + _updateModel: function() { + var b = this.options.update_url || Galaxy.root + "api/tools/" + this.options.id + "/build", c = this, d = this.form, e = { + tool_id: this.options.id, + tool_version: this.options.version, + inputs: $.extend(!0, {}, c.form.data.create()) + }; + d.wait(!0); + var f = this.deferred.register(); + console.debug("tools-form-base::_updateModel() - Sending current state (see below)."), + console.debug(e), a.request({ + type: "POST", + url: b, + data: e, + success: function(a) { + c.form.update(a.tool_model || a), c.options.update && c.options.update(a), d.wait(!1), + console.debug("tools-form-base::_updateModel() - Received new model (see below)."), + console.debug(a), c.deferred.done(f); + }, + error: function(a) { + c.deferred.done(f), console.debug("tools-form-base::_updateModel() - Refresh request failed."), + console.debug(a); + } + }); + }, + _operations: function() { + var a = this, b = this.options, d = new c.ButtonMenu({ + icon: "fa-cubes", + title: !b.narrow && "Versions" || null, + tooltip: "Select another tool version" + }); + if (!b.is_workflow && b.versions && b.versions.length > 1) for (var f in b.versions) { + var g = b.versions[f]; + g != b.version && d.addMenu({ + title: "Switch to " + g, + version: g, + icon: "fa-cube", + onclick: function() { + var c = b.id.replace(b.version, this.version), d = this.version; + a.deferred.reset(), a.deferred.execute(function() { + a._buildModel({ + id: c, + version: d + }); + }); + } + }); + } else d.$el.hide(); + var h = new c.ButtonMenu({ + icon: "fa-caret-down", + title: !b.narrow && "Options" || null, + tooltip: "View available options" + }); + return b.biostar_url && (h.addMenu({ + icon: "fa-question-circle", + title: "Question?", + tooltip: "Ask a question about this tool (Biostar)", + onclick: function() { + window.open(b.biostar_url + "/p/new/post/"); + } + }), h.addMenu({ + icon: "fa-search", + title: "Search", + tooltip: "Search help for this tool (Biostar)", + onclick: function() { + window.open(b.biostar_url + "/local/search/page/?q=" + b.name); + } + })), h.addMenu({ + icon: "fa-share", + title: "Share", + tooltip: "Share this tool", + onclick: function() { + prompt("Copy to clipboard: Ctrl+C, Enter", window.location.origin + Galaxy.root + "root?tool_id=" + b.id); + } + }), Galaxy.user && Galaxy.user.get("is_admin") && h.addMenu({ + icon: "fa-download", + title: "Download", + tooltip: "Download this tool", + onclick: function() { + window.location.href = Galaxy.root + "api/tools/" + b.id + "/download"; + } + }), b.requirements && b.requirements.length > 0 && h.addMenu({ + icon: "fa-info-circle", + title: "Requirements", + tooltip: "Display tool requirements", + onclick: function() { + this.visible ? (this.visible = !1, a.form.message.update({ + message: "" + })) : (this.visible = !0, a.form.message.update({ + persistent: !0, + message: e.requirements(b), + status: "info" + })); + } + }), b.sharable_url && h.addMenu({ + icon: "fa-external-link", + title: "See in Tool Shed", + tooltip: "Access the repository", + onclick: function() { + window.open(b.sharable_url); + } + }), { + menu: h, + versions: d + }; + }, + _footer: function() { + var a = this.options; + if ("" != a.help && this.form.$el.append(e.help(a)), a.citations) { + var b = $("
    "), c = new f.ToolCitationCollection(); + c.tool_id = a.id; + var d = new g.CitationListView({ + el: b, + collection: c + }); + d.render(), c.fetch(), this.form.$el.append(b); + } + } + }); +}); \ No newline at end of file From 83bd9dd541079f0571b90044e1a64d8318377039 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Mon, 21 Sep 2015 12:01:44 -0400 Subject: [PATCH 015/178] repack without --develop --- static/maps/mvc/tools/tools-form-base.js.map | 2 +- static/scripts/mvc/tools/tools-form-base.js | 179 +------------------ 2 files changed, 3 insertions(+), 178 deletions(-) diff --git a/static/maps/mvc/tools/tools-form-base.js.map b/static/maps/mvc/tools/tools-form-base.js.map index 88a72130cf2..2b4524a0e41 100644 --- a/static/maps/mvc/tools/tools-form-base.js.map +++ b/static/maps/mvc/tools/tools-form-base.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-base.js b/static/scripts/mvc/tools/tools-form-base.js index be0c8292ed4..6c76174b8cd 100644 --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -1,177 +1,2 @@ -define([ "utils/utils", "utils/deferred", "mvc/ui/ui-misc", "mvc/form/form-view", "mvc/tools/tools-template", "mvc/citation/citation-model", "mvc/citation/citation-view", "mvc/ui/ui-modal" ], function(a, b, c, d, e, f, g) { - return Backbone.View.extend({ - initialize: function(c) { - this.options = a.merge(c, {}), this.setElement("
    "), this.modal = Galaxy.modal, - this.deferred = new b(), c.inputs ? this._buildForm(c) : this._buildModel(c, !0); - }, - _buildForm: function(b) { - var c = this; - this.options = a.merge(b, this.options), this.options = a.merge({ - icon: "fa-wrench", - title: "" + b.name + " " + b.description + " (Galaxy Tool Version " + b.version + ")", - operations: this._operations(), - onchange: function() { - c.deferred.reset(), c.deferred.execute(function() { - c._updateModel(); - }); - } - }, this.options), this.form = new d(this.options), this._footer(), this.$el.empty(), - this.$el.append(this.form.$el); - }, - _buildModel: function(b, c) { - var d = this; - if (this.options.id = b.id, this.options.version = b.version, b.job_id) e = Galaxy.root + "api/jobs/" + b.job_id + "/build_for_rerun"; else { - var e = Galaxy.root + "api/tools/" + b.id + "/build?"; - if (b.dataset_id) e += "dataset_id=" + b.dataset_id; else { - e += "tool_version=" + b.version + "&"; - var f = top.location.href, g = f.indexOf("?"); - -1 != f.indexOf("tool_id=") && -1 !== g && (e += f.slice(g + 1)); - } - } - var h = this.deferred.register(); - a.request({ - type: "GET", - url: e, - success: function(a) { - d._buildForm(a.tool_model || a), !c && d.form.message.update({ - status: "success", - message: "Now you are using '" + d.options.name + "' version " + d.options.version + ".", - persistent: !1 - }), d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model ready."), - console.debug(a); - }, - error: function(a) { - d.deferred.done(h), console.debug("tools-form::initialize() - Initial tool model request failed."), - console.debug(a); - var b = a.error || "Uncaught error."; - d.modal.show({ - title: "Tool cannot be executed", - body: b, - buttons: { - Close: function() { - d.modal.hide(); - } - } - }); - } - }); - }, - _updateModel: function() { - var b = this.options.update_url || Galaxy.root + "api/tools/" + this.options.id + "/build", c = this, d = this.form, e = { - tool_id: this.options.id, - tool_version: this.options.version, - inputs: $.extend(!0, {}, c.form.data.create()) - }; - d.wait(!0); - var f = this.deferred.register(); - console.debug("tools-form-base::_updateModel() - Sending current state (see below)."), - console.debug(e), a.request({ - type: "POST", - url: b, - data: e, - success: function(a) { - c.form.update(a.tool_model || a), c.options.update && c.options.update(a), d.wait(!1), - console.debug("tools-form-base::_updateModel() - Received new model (see below)."), - console.debug(a), c.deferred.done(f); - }, - error: function(a) { - c.deferred.done(f), console.debug("tools-form-base::_updateModel() - Refresh request failed."), - console.debug(a); - } - }); - }, - _operations: function() { - var a = this, b = this.options, d = new c.ButtonMenu({ - icon: "fa-cubes", - title: !b.narrow && "Versions" || null, - tooltip: "Select another tool version" - }); - if (!b.is_workflow && b.versions && b.versions.length > 1) for (var f in b.versions) { - var g = b.versions[f]; - g != b.version && d.addMenu({ - title: "Switch to " + g, - version: g, - icon: "fa-cube", - onclick: function() { - var c = b.id.replace(b.version, this.version), d = this.version; - a.deferred.reset(), a.deferred.execute(function() { - a._buildModel({ - id: c, - version: d - }); - }); - } - }); - } else d.$el.hide(); - var h = new c.ButtonMenu({ - icon: "fa-caret-down", - title: !b.narrow && "Options" || null, - tooltip: "View available options" - }); - return b.biostar_url && (h.addMenu({ - icon: "fa-question-circle", - title: "Question?", - tooltip: "Ask a question about this tool (Biostar)", - onclick: function() { - window.open(b.biostar_url + "/p/new/post/"); - } - }), h.addMenu({ - icon: "fa-search", - title: "Search", - tooltip: "Search help for this tool (Biostar)", - onclick: function() { - window.open(b.biostar_url + "/local/search/page/?q=" + b.name); - } - })), h.addMenu({ - icon: "fa-share", - title: "Share", - tooltip: "Share this tool", - onclick: function() { - prompt("Copy to clipboard: Ctrl+C, Enter", window.location.origin + Galaxy.root + "root?tool_id=" + b.id); - } - }), Galaxy.user && Galaxy.user.get("is_admin") && h.addMenu({ - icon: "fa-download", - title: "Download", - tooltip: "Download this tool", - onclick: function() { - window.location.href = Galaxy.root + "api/tools/" + b.id + "/download"; - } - }), b.requirements && b.requirements.length > 0 && h.addMenu({ - icon: "fa-info-circle", - title: "Requirements", - tooltip: "Display tool requirements", - onclick: function() { - this.visible ? (this.visible = !1, a.form.message.update({ - message: "" - })) : (this.visible = !0, a.form.message.update({ - persistent: !0, - message: e.requirements(b), - status: "info" - })); - } - }), b.sharable_url && h.addMenu({ - icon: "fa-external-link", - title: "See in Tool Shed", - tooltip: "Access the repository", - onclick: function() { - window.open(b.sharable_url); - } - }), { - menu: h, - versions: d - }; - }, - _footer: function() { - var a = this.options; - if ("" != a.help && this.form.$el.append(e.help(a)), a.citations) { - var b = $("
    "), c = new f.ToolCitationCollection(); - c.tool_id = a.id; - var d = new g.CitationListView({ - el: b, - collection: c - }); - d.render(), c.fetch(), this.form.$el.append(b); - } - } - }); -}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("
    "),this.modal=Galaxy.modal,this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var d=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)e=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var e=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)e+="dataset_id="+b.dataset_id;else{e+="tool_version="+b.version+"&";var f=top.location.href,g=f.indexOf("?");-1!=f.indexOf("tool_id=")&&-1!==g&&(e+=f.slice(g+1))}}var h=this.deferred.register();a.request({type:"GET",url:e,success:function(a){d._buildForm(a.tool_model||a),!c&&d.form.message.update({status:"success",message:"Now you are using '"+d.options.name+"' version "+d.options.version+".",persistent:!1}),d.deferred.done(h)},error:function(a){d.deferred.done(h);var b=a.error||"Uncaught error.";d.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){d.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); +//# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file From 56f10c9a1d7fa984aa1c286abaf4fadd26f1746a Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 21 Sep 2015 13:51:41 -0400 Subject: [PATCH 016/178] make except catch just Exceptions, not everything I am not sure when these are hapenning (error initialized with encoded id & tool without id) but this should be safe fix --- lib/galaxy/tools/errors.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/errors.py b/lib/galaxy/tools/errors.py index c9b8f40feb5..60313d72ed1 100644 --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -60,7 +60,7 @@ class ErrorReporter( object ): try: hda = sa_session.query( model.HistoryDatasetAssociation ).get( hda_id ) assert hda is not None, ValueError( "No HDA yet" ) - except: + except Exception: hda = sa_session.query( model.HistoryDatasetAssociation ).get( app.security.decode_id( hda_id ) ) assert isinstance( hda, model.HistoryDatasetAssociation ), ValueError( "Bad value provided for HDA (%s)." % ( hda ) ) self.hda = hda @@ -135,7 +135,7 @@ class EmailErrorReporter( ErrorReporter ): subject = "Galaxy tool error report from %s" % email try: subject = "%s (%s)" % ( subject, self.app.toolbox.get_tool( self.job.tool_id, self.job.tool_version ).old_id ) - except: + except Exception: pass # Send it return util.send_mail( frm, to, subject, self.report, self.app.config ) From 7ca661bb010e4106e4fac910612810b99f741805 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 21 Sep 2015 16:09:51 -0400 Subject: [PATCH 017/178] Fix for displaying tool form errors caused by http exceptions and when tool form doesn't exist. --- client/galaxy/scripts/mvc/tools/tools-form-base.js | 5 ++++- static/maps/mvc/tools/tools-form-base.js.map | 2 +- static/scripts/mvc/tools/tools-form-base.js | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/tools/tools-form-base.js b/client/galaxy/scripts/mvc/tools/tools-form-base.js index d3fa2cd8b0f..890276934bd 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -116,7 +116,10 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', console.debug(response); // show error - var error_message = response.error || 'Uncaught error.'; + var error_message = response.error || response.err_msg || 'Uncaught error.'; + if (self.form == undefined){ + self.form = new Form(); + } self.form.modal.show({ title : 'Tool cannot be executed', body : error_message, diff --git a/static/maps/mvc/tools/tools-form-base.js.map b/static/maps/mvc/tools/tools-form-base.js.map index a79eda9b999..c3a2df1b520 100644 --- a/static/maps/mvc/tools/tools-form-base.js.map +++ b/static/maps/mvc/tools/tools-form-base.js.map @@ -1 +1 @@ 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    "),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var d=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)e=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var e=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)e+="dataset_id="+b.dataset_id;else{e+="tool_version="+b.version+"&";var f=top.location.href,g=f.indexOf("?");-1!=f.indexOf("tool_id=")&&-1!==g&&(e+=f.slice(g+1))}}var h=this.deferred.register();a.request({type:"GET",url:e,success:function(a){d._buildForm(a.tool_model||a),!c&&d.form.message.update({status:"success",message:"Now you are using '"+d.options.name+"' version "+d.options.version+".",persistent:!1}),d.deferred.done(h)},error:function(a){d.deferred.done(h);var b=a.error||"Uncaught error.";d.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){d.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("
    "),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i)},error:function(a){e.deferred.done(i);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),e.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){e.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file From aed76f3744aba7b6c83659a9ad7dd079b9be1b70 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 21 Sep 2015 16:10:13 -0400 Subject: [PATCH 018/178] Do not attempt to rerun non-rerunable tools. --- lib/galaxy/webapps/galaxy/api/jobs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py index 655bf62b611..0bb5c690fa6 100644 --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -207,6 +207,8 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ): tool_id = job.tool_id tool_version = job.tool_version tool = self.app.toolbox.get_tool( tool_id, tool_version ) + if not tool.is_workflow_compatible: + raise exceptions.ConfigDoesNotAllowException( "Tool '%s' cannot be rerun." % ( tool_id ) ) return tool.to_json(trans, kwd={'__job_id__' : id}) def __dictify_associations( self, trans, *association_lists ): From aeda77c6005f58f4df2939098151d376bf6515a9 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Tue, 22 Sep 2015 10:07:12 -0400 Subject: [PATCH 019/178] Add "Galaxy" title to templates/webapps/galaxy/root/index.mako --- templates/webapps/galaxy/root/index.mako | 1 + 1 file changed, 1 insertion(+) diff --git a/templates/webapps/galaxy/root/index.mako b/templates/webapps/galaxy/root/index.mako index 64061e13b6e..ac4453a291a 100644 --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -3,6 +3,7 @@ ${h.js("libs/bibtex", "libs/jquery/jquery-ui")} ${h.css("jquery-ui/smoothness/jquery-ui")} ${h.css("base")} +<%def name="title()">Galaxy <%def name="javascripts()"> ${parent.javascripts()} ${h.templates("tool_link", "panel_section", "tool_search")} From 3d697937c7f9d3aff0178f013692d795c3b73eb6 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 22 Sep 2015 10:33:25 -0400 Subject: [PATCH 020/178] Rerun improvement -- instead of allowing someone to try to rerun the upload tool and showing an error message, just don't provide the option for it in the first place. --- client/galaxy/scripts/mvc/dataset/dataset-li-edit.js | 7 ++++++- lib/galaxy/managers/hdas.py | 9 +++++++++ static/maps/mvc/dataset/dataset-li-edit.js.map | 2 +- static/scripts/mvc/dataset/dataset-li-edit.js | 2 +- 4 files changed, 17 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js index 23a8181f3db..85769323fe2 100644 --- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js @@ -159,11 +159,16 @@ var DatasetListItemEdit = _super.extend( /** Render icon-button to re-run the job that created this dataset. */ _renderRerunButton : function(){ var creating_job = this.model.get('creating_job'); - return faIconButton({ + var rerunnable = this.model.get('rerunnable'); + if (!rerunnable){ + return; + } + else return faIconButton({ title : _l( 'Run this job again' ), href : this.model.urls.rerun, classes : 'rerun-btn', target : this.linkTarget, + disabled : !rerunnable, faIcon : 'fa-refresh', onclick : function(ev) { ev.preventDefault(); diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index db6e767d442..5165098bbfe 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -280,6 +280,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize 'peek', 'creating_job', + 'rerunnable', 'uuid', 'permissions', @@ -328,6 +329,7 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize 'resubmitted' : lambda i, k, **c: self.hda_manager.has_been_resubmitted( i ), 'creating_job' : self.serialize_creating_job, + 'rerunnable' : self.rerunnable, 'display_apps' : self.serialize_display_apps, 'display_types' : self.serialize_old_display_applications, @@ -439,6 +441,13 @@ class HDASerializer( # datasets._UnflattenedMetadataDatasetAssociationSerialize else: return None + def rerunnable( self, hda, key, **context ): + if hda.creating_job: + tool = self.app.toolbox.get_tool(hda.creating_job.tool_id, hda.creating_job.tool_version) + if tool and tool.is_workflow_compatible: + return True + return False + class HDADeserializer( datasets.DatasetAssociationDeserializer, taggable.TaggableDeserializerMixin, diff --git a/static/maps/mvc/dataset/dataset-li-edit.js.map b/static/maps/mvc/dataset/dataset-li-edit.js.map index 0436d840ee3..26c267ad438 100644 --- a/static/maps/mvc/dataset/dataset-li-edit.js.map +++ b/static/maps/mvc/dataset/dataset-li-edit.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/dataset/dataset-li-edit.js b/static/scripts/mvc/dataset/dataset-li-edit.js index f44b3f96cb1..8bc096ac20f 100644 --- a/static/scripts/mvc/dataset/dataset-li-edit.js +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -1,2 +1,2 @@ -define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this 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b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',h("An error occurred setting the metadata for this dataset"),'
    ',h("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
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    ',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',h("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); +define(["mvc/dataset/states","mvc/dataset/dataset-li","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/base-mvc","mvc/tools/tools-form","utils/localization"],function(a,b,c,d,e,f,g,h){var i=b.DatasetListItemView,j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.hasUser=a.hasUser,this.purgeAllowed=a.purgeAllowed||!1,this.tagsEditorShown=a.tagsEditorShown||!1,this.annotationEditorShown=a.annotationEditorShown||!1},_renderPrimaryActions:function(){var b=i.prototype._renderPrimaryActions.call(this);return this.model.get("state")===a.NOT_VIEWABLE?b:i.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===a.DISCARDED||!this.model.get("accessible"))return null;var b=this.model.get("purged"),c=this.model.get("deleted"),d={title:h("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return c||b?(d.disabled=!0,b?d.title=h("Cannot edit attributes of datasets removed from disk"):c&&(d.title=h("Undelete dataset to edit attributes"))):_.contains([a.UPLOAD,a.NEW],this.model.get("state"))&&(d.disabled=!0,d.title=h("This dataset is not yet editable")),e(d)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var a=this,b=this.model.isDeletedOrPurged();return e({title:h(b?"Dataset is already deleted":"Delete"),disabled:b,faIcon:"fa-times",classes:"delete-btn",onclick:function(){a.$el.find(".icon-btn.delete-btn").trigger("mouseout"),a.model.delete()}})},_renderDetails:function(){var b=i.prototype._renderDetails.call(this),c=this.model.get("state");return!this.model.isDeletedOrPurged()&&_.contains([a.OK,a.FAILED_METADATA],c)&&(this._renderTags(b),this._renderAnnotation(b),this._makeDbkeyEditLink(b)),this._setUpBehaviors(b),b},_renderSecondaryActions:function(){var b=i.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case a.UPLOAD:case a.NEW:case a.NOT_VIEWABLE:return b;case a.ERROR:return b.unshift(this._renderErrButton()),b.concat([this._renderRerunButton()]);case a.OK:case a.FAILED_METADATA:return b.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return b.concat([this._renderRerunButton()])},_renderErrButton:function(){return e({title:h("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var a=this.model.get("creating_job"),b=this.model.get("rerunnable");return b?e({title:h("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,disabled:!b,faIcon:"fa-refresh",onclick:function(b){b.preventDefault();var c=new g.View({job_id:a});c.deferred.execute(function(){Galaxy.app.display(c.$el)})}}):void 0},_renderVisualizationsButton:function(){var a=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||_.isEmpty(a))return null;if(!_.isObject(a[0]))return this.warn("Visualizations have been switched off"),null;var b=$(this.templates.visualizations(a,this));return b.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(b.find(".visualization-link").addBack(".visualization-link")),b},_addScratchBookFn:function(a){a.click(function(a){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",type:"url",content:$(this).attr("href")}),a.preventDefault(),a.stopPropagation())})},_renderTags:function(a){if(this.hasUser){var b=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:a.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.tagsEditorShown=!0},onhide:function(){b.tagsEditorShown=!1},$activator:e({title:h("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(a){if(this.hasUser){var b=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:a.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.annotationEditorShown=!0},onhide:function(){b.annotationEditorShown=!1},$activator:e({title:h("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(a){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var b=$('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);a.find(".dbkey .value").replaceWith(b)}},events:_.extend(_.clone(i.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(a){this.trigger("edit",this,a)},"click .delete-btn":function(a){this.trigger("delete",this,a)},"click .rerun-btn":function(a){this.trigger("rerun",this,a)},"click .report-err-btn":function(a){this.trigger("report-err",this,a)},"click .visualization-btn":function(a){this.trigger("visualize",this,a)},"click .dbkey a":function(a){this.trigger("edit",this,a)}}),_clickUndeleteLink:function(){return this.model.undelete(),!1},_clickPurgeLink:function(){return this.model.purge(),!1},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAEditView("+a+")"}});return j.prototype.templates=function(){var a=_.extend({},i.prototype.templates.warnings,{failed_metadata:f.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',h("An error occurred setting the metadata for this dataset"),'
    ',h("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:f.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
    ',h("This dataset has been deleted"),'
    ',h("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',h("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),b=f.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return _.extend({},i.prototype.templates,{warnings:a,visualizations:b})}(),{DatasetListItemEdit:j}}); //# sourceMappingURL=../../../maps/mvc/dataset/dataset-li-edit.js.map \ No newline at end of file From 7b7359b57ba213049d1c4f4a3cfa363f4a70a2b9 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 22 Sep 2015 16:22:53 +0100 Subject: [PATCH 021/178] flake8 lib/galaxy/webapps/tool_shed/model/migrate/versions/ . Fix 227 linting errors. --- .ci/flake8_blacklist.txt | 1 - .../migrate/versions/0001_initial_tables.py | 20 ++++----- .../versions/0002_add_tool_suite_column.py | 12 +++--- ...03_review_and_review_association_tables.py | 18 ++++---- .../versions/0004_repository_tables.py | 21 +++++----- .../versions/0005_drop_tool_related_tables.py | 23 +++++----- .../versions/0006_add_email_alerts_column.py | 12 +++--- ...ng_description_times_downloaded_columns.py | 13 +++--- .../0008_add_repository_metadata_table.py | 20 ++++----- .../versions/0009_add_malicious_column.py | 12 +++--- .../0010_add_new_repo_alert_column.py | 10 ++--- .../versions/0011_add_tool_versions_column.py | 20 ++++----- .../versions/0012_add_downloadable_column.py | 10 ++--- .../versions/0013_add_review_tables.py | 42 +++++++++++-------- .../versions/0014_add_deprecated_column.py | 13 +++--- .../versions/0015_add_api_keys_table.py | 16 ++++--- ...ols_functionally_correct_errors_columns.py | 12 +++--- ...ty_columns_to_repository_metadata_table.py | 13 +++--- ...18_add_repository_metadata_flag_columns.py | 13 +++--- ...est_table_and_test_install_error_column.py | 15 +++---- .../0020_add_repository_type_column.py | 12 +++--- .../0021_change_repository_type_value.py | 13 +++--- .../0022_add_repository_admin_roles.py | 42 ++++++++++--------- ...023_add_repository_url_and_hompeage_url.py | 12 +++--- .../migrate/versions/0024_password_reset.py | 14 ++----- .../migrate/versions/0025_session_timeout.py | 13 ++---- 26 files changed, 205 insertions(+), 217 deletions(-) diff --git a/.ci/flake8_blacklist.txt b/.ci/flake8_blacklist.txt index a938883ff77..362ac7c8ff3 100644 --- a/.ci/flake8_blacklist.txt +++ b/.ci/flake8_blacklist.txt @@ -6,7 +6,6 @@ doc/source/conf.py lib/galaxy/model/migrate/versions/ lib/galaxy/model/tool_shed_install/migrate/versions/ lib/galaxy/util/jstree.py -lib/galaxy/webapps/tool_shed/model/migrate/versions/ lib/pkg_resources.py scripts/api/ scripts/data_libraries/ diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py index 5520c2ae3ce..7c57d104694 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py @@ -1,17 +1,16 @@ """ Migration script to create initial tables. """ - -from sqlalchemy import * -from migrate import * - import datetime -now = datetime.datetime.utcnow +import logging +import sys + +from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Index, Integer, MetaData, String, Table, TEXT, UniqueConstraint # Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +from galaxy.model.custom_types import TrimmedString -import sys, logging +now = datetime.datetime.utcnow log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -78,10 +77,9 @@ GalaxySession_table = Table( "galaxy_session", metadata, Column( "remote_host", String( 255 ) ), Column( "remote_addr", String( 255 ) ), Column( "referer", TEXT ), - Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string + Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string Column( "is_valid", Boolean, default=False ), - Column( "prev_session_id", Integer ) # saves a reference to the previous session so we have a way to chain them together - ) + Column( "prev_session_id", Integer ) ) # saves a reference to the previous session so we have a way to chain them together Tool_table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), @@ -145,12 +143,14 @@ ToolAnnotationAssociation_table = Table( "tool_annotation_association", metadata Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "annotation", TEXT ) ) + def upgrade( migrate_engine ): print __doc__ metadata.bind = migrate_engine metadata.create_all() Index( 'ix_tool_annotation_association_annotation', ToolAnnotationAssociation_table.c.annotation, mysql_length=767 ).create() + def downgrade( migrate_engine ): # Operations to reverse the above upgrade go here. pass diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py index d4979e2ddd2..53e459241f6 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py @@ -1,13 +1,11 @@ """ Migration script to add the suite column to the tool table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, MetaData, Table -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -18,6 +16,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade( migrate_engine ): metadata.bind = migrate_engine print __doc__ @@ -27,7 +26,7 @@ def upgrade( migrate_engine ): c = Column( "suite", Boolean, default=False, index=True ) try: # Create - c.create( Tool_table, index_name = 'ix_tool_suite') + c.create( Tool_table, index_name='ix_tool_suite') assert c is Tool_table.c.suite # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': @@ -39,6 +38,7 @@ def upgrade( migrate_engine ): print "Adding suite column to the tool table failed: %s" % str( e ) log.debug( "Adding suite column to the tool table failed: %s" % str( e ) ) + def downgrade( migrate_engine ): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py index 72d5bb04dca..04089a6eb0d 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py @@ -1,16 +1,13 @@ """ Adds the tool_rating_association table, enabling tools to be rated along with review comments. """ -from sqlalchemy import * -from sqlalchemy.orm import * -from sqlalchemy.exc import * -from migrate import * -from migrate.changeset import * - import datetime -now = datetime.datetime.utcnow +import logging +import sys -import sys, logging +from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT + +now = datetime.datetime.utcnow log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -19,9 +16,6 @@ formatter = logging.Formatter( format ) handler.setFormatter( formatter ) log.addHandler( handler ) -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - metadata = MetaData() ToolRatingAssociation_table = Table( "tool_rating_association", metadata, @@ -33,6 +27,7 @@ ToolRatingAssociation_table = Table( "tool_rating_association", metadata, Column( "rating", Integer, index=True ), Column( "comment", TEXT ) ) + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -43,6 +38,7 @@ def upgrade(migrate_engine): except Exception, e: log.debug( "Creating tool_rating_association table failed: %s" % str( e ) ) + def downgrade(migrate_engine): # Load existing tables metadata.bind = migrate_engine diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py index 0cbebb38cdd..15b83e79343 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py @@ -1,16 +1,16 @@ """ Adds the repository, repository_rating_association and repository_category_association tables. """ -from sqlalchemy import * -from sqlalchemy.orm import * -from sqlalchemy.exc import * -from migrate import * -from migrate.changeset import * - import datetime -now = datetime.datetime.utcnow +import logging +import sys -import sys, logging +from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import TrimmedString + +now = datetime.datetime.utcnow log = logging.getLogger( __name__ ) log.setLevel( logging.DEBUG ) handler = logging.StreamHandler( sys.stdout ) @@ -19,9 +19,6 @@ formatter = logging.Formatter( format ) handler.setFormatter( formatter ) log.addHandler( handler ) -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - metadata = MetaData() Repository_table = Table( "repository", metadata, @@ -48,6 +45,7 @@ RepositoryCategoryAssociation_table = Table( "repository_category_association", Column( "repository_id", Integer, ForeignKey( "repository.id" ), index=True ), Column( "category_id", Integer, ForeignKey( "category.id" ), index=True ) ) + def upgrade(migrate_engine): print __doc__ # Load existing tables @@ -66,6 +64,7 @@ def upgrade(migrate_engine): except Exception, e: log.debug( "Creating repository_category_association table failed: %s" % str( e ) ) + def downgrade(migrate_engine): # Load existing tables metadata.bind = migrate_engine diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py index dd749c430d6..4795d197cc0 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py @@ -3,16 +3,17 @@ Drops the tool, tool_category_association, event, tool_event_association, tool_r tool_tag_association and tool_annotation_association tables since they are no longer used in the next-gen tool shed. """ -from sqlalchemy import * -from sqlalchemy.orm import * -from sqlalchemy.exc import * -from migrate import * -from migrate.changeset import * - import datetime -now = datetime.datetime.utcnow +import logging +import sys -import sys, logging +from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT +from sqlalchemy.exc import NoSuchTableError + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import TrimmedString + +now = datetime.datetime.utcnow log = logging.getLogger( __name__ ) log.setLevel( logging.DEBUG ) handler = logging.StreamHandler( sys.stdout ) @@ -21,11 +22,9 @@ formatter = logging.Formatter( format ) handler.setFormatter( formatter ) log.addHandler( handler ) -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - metadata = MetaData() + def upgrade(migrate_engine): print __doc__ # Load existing tables @@ -94,6 +93,8 @@ def upgrade(migrate_engine): Tool_table.drop() except Exception, e: log.debug( "Dropping tool table failed: %s" % str( e ) ) + + def downgrade(migrate_engine): # Load existing tables metadata.bind = migrate_engine diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py index 2f50fd33039..4cf344b76fa 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py @@ -1,16 +1,14 @@ """ Migration script to add the email_alerts column to the repository table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Column, MetaData, Table # Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +from galaxy.model.custom_types import JSONType -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -21,6 +19,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -36,6 +35,7 @@ def upgrade(migrate_engine): print "Adding email_alerts column to the repository table failed: %s" % str( e ) log.debug( "Adding email_alerts column to the repository table failed: %s" % str( e ) ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py index 51c841f2efd..4e742fb5924 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py @@ -1,16 +1,11 @@ """ Migration script to add the long_description and times_downloaded columns to the repository table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Column, Integer, MetaData, Table, TEXT -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -21,6 +16,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -50,6 +46,7 @@ def upgrade(migrate_engine): cmd = "UPDATE repository SET times_downloaded = 0" migrate_engine.execute( cmd ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py index ce48dfd8fb3..127a14b0c9c 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py @@ -1,18 +1,16 @@ """ Migration script to add the repository_metadata table. """ - -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * - import datetime -now = datetime.datetime.utcnow -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +import logging +import sys -import sys, logging +from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import JSONType, TrimmedString + +now = datetime.datetime.utcnow log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -31,6 +29,7 @@ RepositoryMetadata_table = Table( "repository_metadata", metadata, Column( "changeset_revision", TrimmedString( 255 ), index=True ), Column( "metadata", JSONType, nullable=True ) ) + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -42,6 +41,7 @@ def upgrade(migrate_engine): print str(e) log.debug( "Creating repository_metadata table failed: %s" % str( e ) ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py index 4cf4b2c0cbf..811b6a02900 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py @@ -1,13 +1,11 @@ """ Migration script to add the malicious column to the repository_metadata table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, MetaData, Table -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -18,6 +16,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade( migrate_engine ): print __doc__ metadata.bind = migrate_engine @@ -27,7 +26,7 @@ def upgrade( migrate_engine ): c = Column( "malicious", Boolean, default=False, index=True ) try: # Create - c.create( Repository_metadata_table, index_name = "ix_repository_metadata_malicious") + c.create( Repository_metadata_table, index_name="ix_repository_metadata_malicious") assert c is Repository_metadata_table.c.malicious # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': @@ -39,6 +38,7 @@ def upgrade( migrate_engine ): print "Adding malicious column to the repository_metadata table failed: %s" % str( e ) log.debug( "Adding malicious column to the repository_metadata table failed: %s" % str( e ) ) + def downgrade( migrate_engine ): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py index 9652e129c12..f30763eb859 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py @@ -1,13 +1,11 @@ """ Migration script to add the new_repo_alert column to the galaxy_user table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, MetaData, Table -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -18,6 +16,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -41,6 +40,7 @@ def upgrade(migrate_engine): print "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e ) log.debug( "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e ) ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py index c09b894ef8c..3d9bf261743 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py @@ -1,18 +1,16 @@ """ Migration script to add the tool_versions column to the repository_metadata table. """ - -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * - import datetime -now = datetime.datetime.utcnow -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +import logging +import sys -import sys, logging +from sqlalchemy import Column, MetaData, Table + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import JSONType + +now = datetime.datetime.utcnow log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -23,6 +21,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -36,6 +35,7 @@ def upgrade(migrate_engine): except Exception, e: print "Adding tool_versions column to the repository_metadata table failed: %s" % str( e ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py index 4746fe91a62..be9575f23a8 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py @@ -1,13 +1,11 @@ """ Migration script to add the downloadable column to the repository_metadata table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, MetaData, Table -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -18,6 +16,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -38,6 +37,7 @@ def upgrade(migrate_engine): except Exception, e: print "Adding downloadable column to the repository_metadata table failed: %s" % str( e ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py index a66a66f5027..ac80751c3bf 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py @@ -1,13 +1,14 @@ """ Migration script to add the repository_review, component_review and component tables and the Repository Reviewer group and role. """ -import datetime, logging, sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +import datetime +import logging +import sys + +from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT + # Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +from galaxy.model.custom_types import TrimmedString log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) @@ -24,6 +25,7 @@ NOW = datetime.datetime.utcnow REVIEWER = 'Repository Reviewer' ROLE_TYPE = 'system' + def nextval(migrate_engine, table, col='id' ): if migrate_engine.name in ['postgresql', 'postgres']: return "nextval('%s_%s_seq')" % ( table, col ) @@ -32,21 +34,23 @@ def nextval(migrate_engine, table, col='id' ): else: raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + def localtimestamp(migrate_engine): - if migrate_engine.name in ['postgresql', 'postgres'] or migrate_engine.name == 'mysql': - return "LOCALTIMESTAMP" - elif migrate_engine.name == 'sqlite': - return "current_date || ' ' || current_time" - else: - raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + if migrate_engine.name in ['postgresql', 'postgres'] or migrate_engine.name == 'mysql': + return "LOCALTIMESTAMP" + elif migrate_engine.name == 'sqlite': + return "current_date || ' ' || current_time" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + def boolean_false(migrate_engine): - if migrate_engine.name in ['postgresql', 'postgres'] or migrate_engine.name == 'mysql': - return False - elif migrate_engine.name == 'sqlite': - return 0 - else: - raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + if migrate_engine.name in ['postgresql', 'postgres'] or migrate_engine.name == 'mysql': + return False + elif migrate_engine.name == 'sqlite': + return 0 + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) RepositoryReview_table = Table( "repository_review", metadata, Column( "id", Integer, primary_key=True ), @@ -76,6 +80,7 @@ Component_table = Table( "component", metadata, Column( "name", TrimmedString( 255 ) ), Column( "description", TEXT ) ) + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -157,6 +162,7 @@ def upgrade(migrate_engine): cmd += ");" migrate_engine.execute( cmd ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py index 7742ba88fc1..2e4e50f1df7 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py @@ -1,16 +1,11 @@ """ Migration script to add the deprecated column to the repository table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, MetaData, Table -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -21,6 +16,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -42,6 +38,7 @@ def upgrade(migrate_engine): print "Adding deprecated column to the repository table failed: %s" % str( e ) log.debug( "Adding deprecated column to the repository table failed: %s" % str( e ) ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py index 3d05b1f9102..f8a783d35dd 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py @@ -1,12 +1,14 @@ """ Migration script to add the api_keys table. """ -import datetime, sys, logging -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * -from galaxy.model.custom_types import * +import datetime +import logging +import sys + +from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import TrimmedString log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) @@ -26,6 +28,7 @@ APIKeys_table = Table( "api_keys", metadata, Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "key", TrimmedString( 32 ), index=True, unique=True ) ) + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -35,6 +38,7 @@ def upgrade(migrate_engine): except Exception, e: log.debug( "Creating api_keys table failed: %s" % str( e ) ) + def downgrade(migrate_engine): # Load existing tables metadata.bind = migrate_engine diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py index b77a3363157..164514b4bc1 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py @@ -1,16 +1,14 @@ """ Migration script to add the tool_test_errors, do_not_test, tools_functionally_correct, and time_last_tested columns to the repository_metadata table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, DateTime, MetaData, Table # Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +from galaxy.model.custom_types import JSONType -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -21,6 +19,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -72,6 +71,7 @@ def upgrade(migrate_engine): print "Adding tool_test_errors column to the repository_metadata table failed: %s" % str( e ) log.debug( "Adding tool_test_errors column to the repository_metadata table failed: %s" % str( e ) ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py index e3ef412f354..9fa3836a975 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py @@ -2,16 +2,11 @@ Migration script to add the includes_datatypes, has_repository_dependencies, includes_tools, includes_tool_dependencies and includes_workflows columns to the repository_metadata table. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, MetaData, Table -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -22,6 +17,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -79,6 +75,7 @@ def upgrade(migrate_engine): except Exception, e: print "Adding includes_workflows column to the repository_metadata table failed: %s" % str( e ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py index 42ce9f2ddc0..c30065a4f5c 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py @@ -2,16 +2,15 @@ Migration script to alter the repository_metadata table by dropping the tool_test_errors column and adding columns tool_test_results, missing_test_components. """ +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Boolean, Column, MetaData, Table +from sqlalchemy.exc import NoSuchTableError # Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +from galaxy.model.custom_types import JSONType -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -22,6 +21,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade(migrate_engine): print __doc__ metadata.bind = migrate_engine @@ -64,6 +64,7 @@ def upgrade(migrate_engine): except Exception, e: print "Adding missing_test_components column to the repository_metadata table failed: %s" % str( e ) + def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py index 6803ca32618..5c4fc160eec 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py @@ -1,17 +1,16 @@ """ Migration script to add the skip_tool_test table and add the test_install_error column to the repository_metadata table. """ - -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * import datetime +import logging +import sys + +from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, MetaData, Table, TEXT +from sqlalchemy.exc import NoSuchTableError # Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +from galaxy.model.custom_types import TrimmedString -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -32,6 +31,7 @@ SkipToolTest_table = Table( "skip_tool_test", metadata, Column( "initial_changeset_revision", TrimmedString( 255 ), index=True ), Column( "comment" , TEXT ) ) + def upgrade( migrate_engine ): print __doc__ metadata.bind = migrate_engine @@ -64,6 +64,7 @@ def upgrade( migrate_engine ): except Exception, e: print "Creating the skip_tool_test table failed: %s" % str( e ) + def downgrade( migrate_engine ): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py index 3d247d9ded4..ec1622ea964 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py @@ -1,14 +1,12 @@ """Migration script to add the type column to the repository table.""" +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import Column, MetaData, Table # Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +from galaxy.model.custom_types import TrimmedString -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -19,6 +17,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade( migrate_engine ): print __doc__ metadata.bind = migrate_engine @@ -35,6 +34,7 @@ def upgrade( migrate_engine ): cmd = "UPDATE repository SET type = 'unrestricted'" migrate_engine.execute( cmd ) + def downgrade( migrate_engine ): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py index c88c38d7f84..ae7bfee05e0 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py @@ -1,14 +1,9 @@ """Migration script to change repository.type column value from generic to unrestricted.""" +import logging +import sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * +from sqlalchemy import MetaData -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -19,6 +14,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade( migrate_engine ): print __doc__ metadata.bind = migrate_engine @@ -27,6 +23,7 @@ def upgrade( migrate_engine ): cmd = "UPDATE repository SET type = 'unrestricted' WHERE type = 'generic'" migrate_engine.execute( cmd ) + def downgrade( migrate_engine ): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py index e30f985efc5..7dca5f49400 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py @@ -3,13 +3,12 @@ Migration script to create the repository_role_association table, insert name-sp repository administrative roles into the role table and associate each repository and owner with the appropriate name-spaced role. """ -import datetime, logging, sys -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * +import datetime +import logging +import sys + +from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, Table +from sqlalchemy.exc import NoSuchTableError log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) @@ -31,6 +30,7 @@ RepositoryRoleAssociation_table = Table( "repository_role_association", metadata Column( "create_time", DateTime, default=NOW ), Column( "update_time", DateTime, default=NOW, onupdate=NOW ) ) + def nextval( migrate_engine, table, col='id' ): if migrate_engine.name in [ 'postgresql', 'postgres' ]: return "nextval('%s_%s_seq')" % ( table, col ) @@ -39,21 +39,24 @@ def nextval( migrate_engine, table, col='id' ): else: raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + def localtimestamp( migrate_engine ): - if migrate_engine.name in [ 'postgresql', 'postgres', 'mysql' ]: - return "LOCALTIMESTAMP" - elif migrate_engine.name == 'sqlite': - return "current_date || ' ' || current_time" - else: - raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + if migrate_engine.name in [ 'postgresql', 'postgres', 'mysql' ]: + return "LOCALTIMESTAMP" + elif migrate_engine.name == 'sqlite': + return "current_date || ' ' || current_time" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + def boolean_false( migrate_engine ): - if migrate_engine.name in [ 'postgresql', 'postgres', 'mysql' ]: - return False - elif migrate_engine.name == 'sqlite': - return 0 - else: - raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + if migrate_engine.name in [ 'postgresql', 'postgres', 'mysql' ]: + return False + elif migrate_engine.name == 'sqlite': + return 0 + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + def upgrade( migrate_engine ): print __doc__ @@ -118,6 +121,7 @@ def upgrade( migrate_engine ): cmd += ");" migrate_engine.execute( cmd ) + def downgrade( migrate_engine ): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py index bc245b19b1b..aa8b624c6ac 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py @@ -2,15 +2,13 @@ Migration script to add the remote_repository_url and homepage_url columns to the repository table. """ +import logging +import sys + +from sqlalchemy import Column, MetaData, Table -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * from galaxy.model.custom_types import TrimmedString -import sys, logging - log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -21,6 +19,7 @@ log.addHandler( handler ) metadata = MetaData() + def upgrade( migrate_engine ): print __doc__ metadata.bind = migrate_engine @@ -37,6 +36,7 @@ def upgrade( migrate_engine ): except Exception, e: print "Adding remote_repository_url and homepage_url columns to the repository table failed: %s" % str( e ) + def downgrade( migrate_engine ): metadata.bind = migrate_engine metadata.reflect() diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py index 96be92b0258..63cacb803a3 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py @@ -1,19 +1,13 @@ """ Migration script for the password reset table """ - -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * -from galaxy.model.custom_types import * - import datetime -now = datetime.datetime.utcnow - import logging -log = logging.getLogger( __name__ ) +from sqlalchemy import Column, DateTime, ForeignKey, Integer, MetaData, String, Table + +now = datetime.datetime.utcnow +log = logging.getLogger( __name__ ) metadata = MetaData() PasswordResetToken_table = Table("password_reset_token", metadata, diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py index cf92c0f0e27..fc63674a88b 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py @@ -1,18 +1,13 @@ """ Migration script to add session update time (used for timeouts) """ -from sqlalchemy import * -from sqlalchemy.orm import * -from migrate import * -from migrate.changeset import * -from galaxy.model.custom_types import * - import datetime -now = datetime.datetime.utcnow - import logging -log = logging.getLogger( __name__ ) +from sqlalchemy import Column, DateTime, MetaData, Table + +now = datetime.datetime.utcnow +log = logging.getLogger( __name__ ) metadata = MetaData() From b2433f077d0de6925792e9e2c3d04cfa13308d8d Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Tue, 22 Sep 2015 14:26:13 -0400 Subject: [PATCH 022/178] Add encoded IDs to job error reports and also include a direct link to dataset's show_params. --- lib/galaxy/tools/errors.py | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/tools/errors.py b/lib/galaxy/tools/errors.py index 60313d72ed1..2813df5f647 100644 --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -11,9 +11,9 @@ GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server "${host}" ----------------------------------------------------------------------------- -This is in reference to dataset id ${dataset_id} from history id ${history_id} +This is in reference to dataset id ${dataset_id} (${dataset_id_encoded}) from history id ${history_id} (${history_id_encoded}) ----------------------------------------------------------------------------- -You should be able to view the history containing the related history item +You should be able to view the history containing the related history item (${hda_id_encoded}) ${hid}: ${history_item_name} @@ -26,7 +26,8 @@ The user ${email_str} provided the following information: ${message} ----------------------------------------------------------------------------- -job id: ${job_id} +info url: ${hda_show_params_link} +job id: ${job_id} (${job_id_encoded}) tool id: ${job_tool_id} tool version: ${tool_version} job pid or drm id: ${job_runner_external_id} @@ -81,7 +82,10 @@ class ErrorReporter( object ): hda = self.hda job = self.job host = web.url_for( '/', qualified=True ) - history_view_link = web.url_for( controller="history", action="view", id=self.app.security.encode_id( hda.history_id ), qualified=True ) + history_id_encoded = self.app.security.encode_id( hda.history_id ) + history_view_link = web.url_for( controller="history", action="view", id=history_id_encoded, qualified=True ) + hda_id_encoded = self.app.security.encode_id( hda.id ) + hda_show_params_link=web.url_for( controller="dataset", action="show_params", dataset_id=hda_id_encoded, qualified=True ) # Build the email message if user and user.email != email: email_str = "'%s' (providing preferred contact email '%s')" % (user.email, email) @@ -89,11 +93,16 @@ class ErrorReporter( object ): email_str = "'%s'" % (email or 'anonymously') self.report = string.Template( error_report_template ) \ .safe_substitute( host=host, + dataset_id_encoded=self.app.security.encode_id( hda.dataset_id ), dataset_id=hda.dataset_id, + history_id_encoded=history_id_encoded, history_id=hda.history_id, + hda_id_encoded=hda_id_encoded, hid=hda.hid, history_item_name=hda.get_display_name(), history_view_link=history_view_link, + hda_show_params_link=hda_show_params_link, + job_id_encoded=self.app.security.encode_id( job.id ), job_id=job.id, tool_version=job.tool_version, job_tool_id=job.tool_id, From eac449ed1e733cb0aa01b527a2518dc712efe443 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Tue, 22 Sep 2015 14:37:26 -0400 Subject: [PATCH 023/178] white space fix --- lib/galaxy/tools/errors.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/errors.py b/lib/galaxy/tools/errors.py index 2813df5f647..251e1e894db 100644 --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -85,7 +85,7 @@ class ErrorReporter( object ): history_id_encoded = self.app.security.encode_id( hda.history_id ) history_view_link = web.url_for( controller="history", action="view", id=history_id_encoded, qualified=True ) hda_id_encoded = self.app.security.encode_id( hda.id ) - hda_show_params_link=web.url_for( controller="dataset", action="show_params", dataset_id=hda_id_encoded, qualified=True ) + hda_show_params_link = web.url_for( controller="dataset", action="show_params", dataset_id=hda_id_encoded, qualified=True ) # Build the email message if user and user.email != email: email_str = "'%s' (providing preferred contact email '%s')" % (user.email, email) From 02e61226b5681186426809d3497fdb2f0d46e466 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Tue, 22 Sep 2015 16:05:48 -0400 Subject: [PATCH 024/178] In log of collecting job metrics, print id, if available, in addition to the string representation of the has_metrics object. --- lib/galaxy/jobs/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index e1d713f601a..17100fec4e3 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1402,7 +1402,7 @@ class JobWrapper( object ): job = has_metrics.get_job() per_plugin_properties = self.app.job_metrics.collect_properties( job.destination_id, self.job_id, self.working_directory ) if per_plugin_properties: - log.info( "Collecting job metrics for %s" % has_metrics ) + log.info( "Collecting job metrics for %s: %s" % ( has_metrics, getattr( has_metrics, 'id', None ) ) ) for plugin, properties in per_plugin_properties.iteritems(): for metric_name, metric_value in properties.iteritems(): if metric_value is not None: From 03062478a9c381514a61240f25f54681f3cc733c Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 22 Sep 2015 16:37:20 -0400 Subject: [PATCH 025/178] expose lib create time; show error message when deleting folders --- .../scripts/mvc/library/library-foldertoolbar-view.js | 7 ++++++- lib/galaxy/managers/libraries.py | 6 ++++-- lib/galaxy/model/__init__.py | 2 +- lib/galaxy/util/__init__.py | 5 ++++- static/maps/mvc/library/library-foldertoolbar-view.js.map | 2 +- static/scripts/mvc/library/library-foldertoolbar-view.js | 4 ++-- 6 files changed, 18 insertions(+), 8 deletions(-) diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index 876c65853ea..36134c078bb 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -933,7 +933,11 @@ var FolderToolbarView = Backbone.View.extend({ var dataset_ids = []; checkedValues.each(function(){ if (this.parentElement.parentElement.id !== '') { - dataset_ids.push(this.parentElement.parentElement.id); + if (this.parentElement.parentElement.id.substring(0,1) == 'F'){ + mod_toastr.error('Deleting folders is not implemented yet'); + } else { + dataset_ids.push(this.parentElement.parentElement.id); + } } }); // init the progress bar @@ -1099,6 +1103,7 @@ var FolderToolbarView = Backbone.View.extend({ tmpl_array.push('

    <%- library.get("description") %>

    '); tmpl_array.push('

    Library synopsis:

    '); tmpl_array.push('

    <%- library.get("synopsis") %>

    '); + tmpl_array.push('

    ">created <%- library.get("create_time_pretty") %>

    '); tmpl_array.push('
    '); diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py index 538f956f28f..3092ded845d 100644 --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -10,6 +10,7 @@ from sqlalchemy.orm.exc import MultipleResultsFound from sqlalchemy.orm.exc import NoResultFound from galaxy import exceptions +from galaxy.util import pretty_print_time_interval log = logging.getLogger( __name__ ) @@ -29,8 +30,8 @@ class LibraryManager( object ): :param decoded_library_id: decoded library id :type decoded_library_id: int - :param check_accessible: flag whether to check that user can access item - :type check_accessible: bool + :param check_accessible: flag whether to check that user can access item + :type check_accessible: bool :returns: the requested library :rtype: Library @@ -181,6 +182,7 @@ class LibraryManager( object ): library_dict = library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) if trans.app.security_agent.library_is_public( library, contents=False ): library_dict[ 'public' ] = True + library_dict[ 'create_time_pretty'] = pretty_print_time_interval( library_dict[ 'create_time' ], precise=True ) current_user_roles = trans.get_current_user_roles() if not trans.user_is_admin(): library_dict[ 'can_user_add' ] = trans.app.security_agent.can_add_library_item( current_user_roles, library ) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 4811890336f..60f783d64c7 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2375,7 +2375,7 @@ class HistoryDatasetAssociationSubset( object ): class Library( object, Dictifiable, HasName ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) dict_collection_visible_keys = ( 'id', 'name' ) - dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id' ) + dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id', 'create_time' ) def __init__( self, name=None, description=None, synopsis=None, root_folder=None ): self.name = name or "Unnamed library" diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py index 5ff0f6a6b78..09235bcfe82 100644 --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -351,7 +351,10 @@ def pretty_print_time_interval( time=False, precise=False ): diff = now - datetime.fromtimestamp( time ) elif isinstance( time, datetime ): diff = now - time - elif not time: + elif isinstance( time, basestring ): + time = datetime.strptime( time, "%Y-%m-%dT%H:%M:%S.%f" ) + diff = now - time + else: diff = now - now second_diff = diff.seconds day_diff = diff.days diff --git a/static/maps/mvc/library/library-foldertoolbar-view.js.map b/static/maps/mvc/library/library-foldertoolbar-view.js.map index 0bc0fa10c1e..57d7b220afa 100644 --- a/static/maps/mvc/library/library-foldertoolbar-view.js.map 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\ No newline at end of file diff --git a/static/scripts/mvc/library/library-foldertoolbar-view.js b/static/scripts/mvc/library/library-foldertoolbar-view.js index 918c7bd46eb..d7b50850b37 100644 --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -1,3 +1,3 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file_or_folder===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+"/"+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[],e=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&e.push(this.parentElement.parentElement.id)});for(var f=[],g=c.length-1;g>=0;g--){var h=c[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=h,i.source="library",f.push(i)}for(var g=e.length-1;g>=0;g--){var j=e[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=j,i.source="library_folder",f.push(i)}this.initChainCallControl({length:f.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(f,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[],d=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&d.push(this.parentElement.parentElement.id)});var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+b,f={ld_ids:c,folder_ids:d};this.processDownload(e,f,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+=''}),$('
    '+e+"
    ").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.idb.id?1:a.id=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}))}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url=(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;g--){var h=new d.Item({id:e[g]});f.push(h)}this.options.chain_call_control.total_number=e.length,this.chainCallDeletingHdas(f)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push('
    '),tmpl_array.push(" DATA LIBRARIES"),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push(' "),tmpl_array.push("<% } else { %>"),tmpl_array.push(' '),tmpl_array.push("<% } %>"),tmpl_array.push(' '),tmpl_array.push(' "),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(" "),tmpl_array.push("
    "),tmpl_array.push('
    '),tmpl_array.push("
    "),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push("

    Library name:

    "),tmpl_array.push('

    <%- library.get("name") %>

    '),tmpl_array.push("

    Library description:

    "),tmpl_array.push('

    <%- library.get("description") %>

    '),tmpl_array.push("

    Library synopsis:

    "),tmpl_array.push('

    <%- library.get("synopsis") %>

    '),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push("
    "),tmpl_array.push(''),tmpl_array.push(''),tmpl_array.push("
    "),tmpl_array.push("
    "),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push(''),a.push("Select history: "),a.push('"),a.push(""),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('
    '),a.push("Importing selected datasets to history <%= _.escape(history_name) %>"),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('
    '),a.push("Adding selected datasets to library folder <%= _.escape(folder_name) %>"),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('
    '),a.push("
    "),a.push('
    '),a.push('
    '),a.push(' 0% Complete'),a.push("
    "),a.push("
    "),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('
    '),a.push('
    All files you select will be imported into the current folder.
    '),a.push(''),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push('
    '),a.push("
    "),a.push("
    "),a.push("

    You can set extension type and genome for all imported datasets at once:

    "),a.push("
    "),a.push('Type: '),a.push(' Genome: '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('
    '),a.push('
    All files within the given folders and their subfolders will be imported into the current folder.
    '),a.push('
    '),a.push('"),a.push('"),a.push("
    "),a.push(''),a.push("
    "),a.push("

    You can set extension type and genome for all imported datasets at once:

    "),a.push("
    "),a.push('Type: '),a.push(' Genome: '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('
    '),a.push('
    '),a.push("Select history: "),a.push('"),a.push("
    "),a.push("
    "),a.push('
    '),a.push("
    "),a.push("
    "),_.template(a.join(""))},templateHistoryContents:function(){var a=[];return a.push("Choose the datasets to import:"),a.push("
      "),a.push(" <% _.each(history_contents, function(history_item) { %>"),a.push('
    • ">'),a.push(' <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'),a.push("
      • "),a.push(" <% }); %>"),a.push("
    "),_.template(a.join(""))},templatePaginator:function(){return tmpl_array=[],tmpl_array.push('
      '), -tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>"),tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
      • '),tmpl_array.push('
    • <% print( show_page - 1 ) %>
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push('
    • '),tmpl_array.push(' <% print( show_page ) %>'),tmpl_array.push("
      • "),tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>"),tmpl_array.push('
    • <% print( show_page + 1 ) %>
      • '),tmpl_array.push('
      • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
    • <% print( show_page + 1 ) %>
      • '),tmpl_array.push('
      • '),tmpl_array.push(" <% } %>"),tmpl_array.push("
    "),tmpl_array.push(" "),tmpl_array.push(' showing <%- items_shown %> of <%- total_items_count %> items'),tmpl_array.push(" "),_.template(tmpl_array.join(""))}});return{FolderToolbarView:f}}); +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file_or_folder===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+"/"+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[],e=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&e.push(this.parentElement.parentElement.id)});for(var f=[],g=c.length-1;g>=0;g--){var h=c[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=h,i.source="library",f.push(i)}for(var g=e.length-1;g>=0;g--){var j=e[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=j,i.source="library_folder",f.push(i)}this.initChainCallControl({length:f.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(f,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[],d=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&d.push(this.parentElement.parentElement.id)});var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+b,f={ld_ids:c,folder_ids:d};this.processDownload(e,f,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+=''}),$('
    '+e+"
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      • '),tmpl_array.push(" <% } %>"),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
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      • '),tmpl_array.push(" <% } %>"),tmpl_array.push('
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      • '),tmpl_array.push('
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This resolves #753 --- lib/galaxy/datatypes/binary.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 62a72373b29..4a6bdf0756e 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -41,11 +41,11 @@ class Binary( data.Data ): @staticmethod def register_sniffable_binary_format(data_type, ext, type_class): - Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext, "class": type_class}) + Binary.sniffable_binary_formats.append({"type": data_type, "ext": ext.lower(), "class": type_class}) @staticmethod def register_unsniffable_binary_ext(ext): - Binary.unsniffable_binary_formats.append(ext) + Binary.unsniffable_binary_formats.append(ext.lower()) @staticmethod def is_sniffable_binary( filename ): From fe642fe7fa66a53b4fbb1f89e200c10ead7854a6 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 22 Sep 2015 19:48:59 -0400 Subject: [PATCH 027/178] Tweak tool 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\ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-jobs.js b/static/scripts/mvc/tools/tools-jobs.js index f6926c6c383..89da5ea8c4b 100644 --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}}); +define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a));var d=[];a.outputs.forEach(function(a){d.push(a.id)}),f._refreshHdas(d)},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}}return!0},_refreshHdas:function(a){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a)}}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map \ No newline at end of file From c96f0e35859beecfc76df92dee4ed11bece438bb Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Tue, 22 Sep 2015 19:16:17 -0500 Subject: [PATCH 028/178] Quote value to fix configparser error --- lib/galaxy/web/base/interactive_environments.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index e3650992944..078820bc689 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -67,7 +67,7 @@ class InteractiveEnviornmentRequest(object): # their defaults dictionary instead. default_dict['command_inject'] = '--sig-proxy=true' default_dict['docker_hostname'] = 'localhost' - default_dict['wx_tempdir'] = False + default_dict['wx_tempdir'] = 'False' viz_config = ConfigParser.SafeConfigParser(default_dict) conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" ) if not os.path.exists( conf_path ): From 130b3f2d75f7f6af4087078f4f653c3ee645774b Mon Sep 17 00:00:00 2001 From: Jelle Scholtalbers Date: Wed, 23 Sep 2015 14:28:03 +0200 Subject: [PATCH 029/178] Add docker command wrapper. For example, to change the current group to docker, which is needed when user belongs to (too) many groups) --- .../ipython/config/ipython.ini.sample | 6 ++++++ lib/galaxy/web/base/interactive_environments.py | 8 ++++++-- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample index e7881deceee..c8624ca72ec 100644 --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -17,6 +17,12 @@ image = bgruening/docker-ipython-notebook:dev # Additional arguments that are passed to the `docker run` command. command_inject = --sig-proxy=true -e DEBUG=false +# Command to wrap around the full docker command. +# For example, `sg 'docker' '{cmd}'` where {cmd} will be replaced by the full +# docker command. Make sure to surround the {cmd} with single quotes('). +# Default: empty +#command_wrapper = + # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the # Docker host of the spawned container if that is also not set. diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index e3650992944..4edd71e1bda 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -68,6 +68,7 @@ class InteractiveEnviornmentRequest(object): default_dict['command_inject'] = '--sig-proxy=true' default_dict['docker_hostname'] = 'localhost' default_dict['wx_tempdir'] = False + default_dict['command_wrapper'] = '' viz_config = ConfigParser.SafeConfigParser(default_dict) conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" ) if not os.path.exists( conf_path ): @@ -181,7 +182,7 @@ class InteractiveEnviornmentRequest(object): conf.update(env_override) env_str = ' '.join(['-e "%s=%s"' % (key.upper(), item) for key, item in conf.items()]) volume_str = ' '.join(['-v "%s"' % volume for volume in volumes]) - return '%s run %s -d %s -p %s:%s -v "%s:/import/" %s %s' % \ + cmd = '%s run %s -d %s -p %s:%s -v "%s:/import/" %s %s' % \ (self.attr.viz_config.get("docker", "command"), env_str, self.attr.viz_config.get("docker", "command_inject"), @@ -189,7 +190,10 @@ class InteractiveEnviornmentRequest(object): temp_dir, volume_str, self.attr.viz_config.get("docker", "image")) - + cmd_wrapper = self.attr.viz_config.get("docker", "command_wrapper") + if cmd_wrapper != '' and '{cmd}' in cmd_wrapper: + cmd = cmd_wrapper.format( cmd=cmd ) + return cmd def launch(self, raw_cmd=None, env_override={}, volumes=[]): if raw_cmd is None: raw_cmd = self.docker_cmd(env_override=env_override, volumes=volumes) From 684be5f6a5c4ac91d6df2c5ec4f1e2866a538965 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 23 Sep 2015 12:02:06 +0100 Subject: [PATCH 030/178] Functional test to verify RData is not decompressed in upload process. --- test/api/helpers.py | 18 +++++++++++++++--- test/api/test_tools.py | 17 ++++++++++++++++- test/base/test_data.py | 2 +- test/base/twilltestcase.py | 2 +- 4 files changed, 33 insertions(+), 6 deletions(-) diff --git a/test/api/helpers.py b/test/api/helpers.py index dfb07f46776..ebe0d493046 100644 --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -100,10 +100,14 @@ class BaseDatasetPopulator( object ): file_type = kwds.get( "file_type", 'txt' ) upload_params = { 'files_0|NAME': name, - 'files_0|url_paste': content, 'dbkey': dbkey, 'file_type': file_type, } + if isinstance( content, file ): + upload_params[ "files_0|file_data"] = content + else: + upload_params[ 'files_0|url_paste' ] = content + if "to_posix_lines" in kwds: upload_params[ "files_0|to_posix_lines"] = kwds[ "to_posix_lines" ] if "space_to_tab" in kwds: @@ -116,6 +120,10 @@ class BaseDatasetPopulator( object ): ) def run_tool_payload( self, tool_id, inputs, history_id, **kwds ): + if "files_0|file_data" in inputs: + kwds[ "__files" ] = { "files_0|file_data": inputs[ "files_0|file_data" ] } + del inputs[ "files_0|file_data" ] + return dict( tool_id=tool_id, inputs=json.dumps(inputs), @@ -174,8 +182,12 @@ class DatasetPopulator( BaseDatasetPopulator ): def __init__( self, galaxy_interactor ): self.galaxy_interactor = galaxy_interactor - def _post( self, route, data={} ): - return self.galaxy_interactor.post( route, data ) + def _post( self, route, data={}, files=None ): + files = data.get( "__files", None ) + if files is not None: + del data[ "__files" ] + + return self.galaxy_interactor.post( route, data, files=files ) def _get( self, route ): return self.galaxy_interactor.get( route ) diff --git a/test/api/test_tools.py b/test/api/test_tools.py index 74fa95d743c..edf177e3737 100644 --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -5,6 +5,7 @@ from .helpers import DatasetPopulator from .helpers import DatasetCollectionPopulator from .helpers import LibraryPopulator from .helpers import skip_without_tool +from base.test_data import TestDataResolver class ToolsTestCase( api.ApiTestCase ): @@ -109,6 +110,12 @@ class ToolsTestCase( api.ApiTestCase ): result_content = self._upload_and_get_content( table ) self.assertEquals( result_content, table ) + def test_rdata_not_decompressed( self ): + # Prevent regression of https://github.com/galaxyproject/galaxy/issues/753 + rdata_path = TestDataResolver().get_filename("1.RData") + rdata_metadata = self._upload_and_get_details( open(rdata_path, "rb"), file_type="auto" ) + self.assertEquals( rdata_metadata[ "file_ext" ], "rdata" ) + @skip_without_tool( "multi_select" ) def test_multi_select_as_list( self ): history_id = self.dataset_populator.new_history() @@ -1042,12 +1049,20 @@ class ToolsTestCase( api.ApiTestCase ): else: return create_response - def _upload_and_get_content( self, content, **upload_kwds ): + def _upload( self, content, **upload_kwds ): history_id = self.dataset_populator.new_history() new_dataset = self.dataset_populator.new_dataset( history_id, content=content, **upload_kwds ) self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + return history_id, new_dataset + + def _upload_and_get_content( self, content, **upload_kwds ): + history_id, new_dataset = self._upload( content, **upload_kwds ) return self.dataset_populator.get_history_dataset_content( history_id, dataset=new_dataset ) + def _upload_and_get_details( self, content, **upload_kwds ): + history_id, new_dataset = self._upload( content, **upload_kwds ) + return self.dataset_populator.get_history_dataset_details( history_id, dataset=new_dataset ) + def __tool_ids( self ): index = self._get( "tools" ) tools_index = index.json() diff --git a/test/base/test_data.py b/test/base/test_data.py index fa14c8f93fd..6114e342a61 100644 --- a/test/base/test_data.py +++ b/test/base/test_data.py @@ -23,7 +23,7 @@ LIST_SEP = re.compile("\s*,\s*") class TestDataResolver(object): - def __init__(self, env_var, environ=os.environ): + def __init__(self, env_var='GALAXY_TEST_FILE_DIR', environ=os.environ): file_dirs = environ.get(env_var, None) if file_dirs: self.resolvers = map(lambda u: build_resolver(u, environ), LIST_SEP.split(file_dirs)) diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 88fdae40c6b..fa956559081 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -50,7 +50,7 @@ class TwillTestCase( unittest.TestCase ): self.host = os.environ.get( 'GALAXY_TEST_HOST' ) self.port = os.environ.get( 'GALAXY_TEST_PORT' ) self.url = "http://%s:%s" % ( self.host, self.port ) - self.test_data_resolver = TestDataResolver( 'GALAXY_TEST_FILE_DIR' ) + self.test_data_resolver = TestDataResolver( ) self.tool_shed_test_file = os.environ.get( 'GALAXY_TOOL_SHED_TEST_FILE', None ) if self.tool_shed_test_file: f = open( self.tool_shed_test_file, 'r' ) From 292642ed91de908bf4e1e3f8705147bc7fd2ca1b Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 23 Sep 2015 09:41:16 -0400 Subject: [PATCH 031/178] Fix upload event binding to be input and change instead of just relying on keyup. This fixes https://github.com/galaxyproject/galaxy/issues/762 --- client/galaxy/scripts/mvc/upload/default/default-row.js | 2 +- static/maps/mvc/upload/default/default-row.js.map | 2 +- static/scripts/mvc/upload/default/default-row.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/upload/default/default-row.js b/client/galaxy/scripts/mvc/upload/default/default-row.js index 642c7265fd0..467a0ef0928 100644 --- a/client/galaxy/scripts/mvc/upload/default/default-row.js +++ b/client/galaxy/scripts/mvc/upload/default/default-row.js @@ -110,7 +110,7 @@ return Backbone.View.extend({ .on('mousedown', function(e) { e.preventDefault(); }); // handle text editing event - this.$('#text-content').on('keyup', function(e) { + this.$('#text-content').on('change input', function(e) { self.model.set('url_paste', $(e.target).val()); self.model.set('file_size', $(e.target).val().length); }); diff --git a/static/maps/mvc/upload/default/default-row.js.map b/static/maps/mvc/upload/default/default-row.js.map index 148221cf9e9..9071a7c6c5a 100644 --- a/static/maps/mvc/upload/default/default-row.js.map +++ b/static/maps/mvc/upload/default/default-row.js.map @@ -1 +1 @@ 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    You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
      
    0%
    You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
      
    0%