From 7e0ccbe2146e51dc4cd44c56fec352c0e0b34857 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Tue, 16 Jun 2015 15:26:27 -0500 Subject: [PATCH 01/68] Apply patch --- .../galaxy/scripts/libs/jquery.sparklines.js | 3054 +++++++++++++++++ static/maps/libs/jquery.sparklines.js.map | 1 + templates/spark_base.mako | 27 + 3 files changed, 3082 insertions(+) create mode 100644 client/galaxy/scripts/libs/jquery.sparklines.js create mode 100644 static/maps/libs/jquery.sparklines.js.map create mode 100644 templates/spark_base.mako diff --git a/client/galaxy/scripts/libs/jquery.sparklines.js b/client/galaxy/scripts/libs/jquery.sparklines.js new file mode 100644 index 00000000000..43b24c080a6 --- /dev/null +++ b/client/galaxy/scripts/libs/jquery.sparklines.js @@ -0,0 +1,3054 @@ +/** +* +* jquery.sparkline.js +* +* v2.1.2 +* (c) Splunk, Inc +* Contact: Gareth Watts (gareth@splunk.com) +* http://omnipotent.net/jquery.sparkline/ +* +* Generates inline sparkline charts from data supplied either to the method +* or inline in HTML +* +* Compatible with Internet Explorer 6.0+ and modern browsers equipped with the canvas tag +* (Firefox 2.0+, Safari, Opera, etc) +* +* License: New BSD License +* +* Copyright (c) 2012, Splunk Inc. +* All rights reserved. +* +* Redistribution and use in source and binary forms, with or without modification, +* are permitted provided that the following conditions are met: +* +* * Redistributions of source code must retain the above copyright notice, +* this list of conditions and the following disclaimer. +* * Redistributions in binary form must reproduce the above copyright notice, +* this list of conditions and the following disclaimer in the documentation +* and/or other materials provided with the distribution. +* * Neither the name of Splunk Inc nor the names of its contributors may +* be used to endorse or promote products derived from this software without +* specific prior written permission. +* +* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY +* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES +* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT +* SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT +* OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) +* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +* +* +* Usage: +* $(selector).sparkline(values, options) +* +* If values is undefined or set to 'html' then the data values are read from the specified tag: +*

Sparkline: 1,4,6,6,8,5,3,5

+* $('.sparkline').sparkline(); +* There must be no spaces in the enclosed data set +* +* Otherwise values must be an array of numbers or null values +*

Sparkline: This text replaced if the browser is compatible

+* $('#sparkline1').sparkline([1,4,6,6,8,5,3,5]) +* $('#sparkline2').sparkline([1,4,6,null,null,5,3,5]) +* +* Values can also be specified in an HTML comment, or as a values attribute: +*

Sparkline:

+*

Sparkline:

+* $('.sparkline').sparkline(); +* +* For line charts, x values can also be specified: +*

Sparkline: 1:1,2.7:4,3.4:6,5:6,6:8,8.7:5,9:3,10:5

+* $('#sparkline1').sparkline([ [1,1], [2.7,4], [3.4,6], [5,6], [6,8], [8.7,5], [9,3], [10,5] ]) +* +* By default, options should be passed in as teh second argument to the sparkline function: +* $('.sparkline').sparkline([1,2,3,4], {type: 'bar'}) +* +* Options can also be set by passing them on the tag itself. This feature is disabled by default though +* as there's a slight performance overhead: +* $('.sparkline').sparkline([1,2,3,4], {enableTagOptions: true}) +*

Sparkline: loading

+* Prefix all options supplied as tag attribute with "spark" (configurable by setting tagOptionPrefix) +* +* Supported options: +* lineColor - Color of the line used for the chart +* fillColor - Color used to fill in the chart - Set to '' or false for a transparent chart +* width - Width of the chart - Defaults to 3 times the number of values in pixels +* height - Height of the chart - Defaults to the height of the containing element +* chartRangeMin - Specify the minimum value to use for the Y range of the chart - Defaults to the minimum value supplied +* chartRangeMax - Specify the maximum value to use for the Y range of the chart - Defaults to the maximum value supplied +* chartRangeClip - Clip out of range values to the max/min specified by chartRangeMin and chartRangeMax +* chartRangeMinX - Specify the minimum value to use for the X range of the chart - Defaults to the minimum value supplied +* chartRangeMaxX - Specify the maximum value to use for the X range of the chart - Defaults to the maximum value supplied +* composite - If true then don't erase any existing chart attached to the tag, but draw +* another chart over the top - Note that width and height are ignored if an +* existing chart is detected. +* tagValuesAttribute - Name of tag attribute to check for data values - Defaults to 'values' +* enableTagOptions - Whether to check tags for sparkline options +* tagOptionPrefix - Prefix used for options supplied as tag attributes - Defaults to 'spark' +* disableHiddenCheck - If set to true, then the plugin will assume that charts will never be drawn into a +* hidden dom element, avoding a browser reflow +* disableInteraction - If set to true then all mouseover/click interaction behaviour will be disabled, +* making the plugin perform much like it did in 1.x +* disableTooltips - If set to true then tooltips will be disabled - Defaults to false (tooltips enabled) +* disableHighlight - If set to true then highlighting of selected chart elements on mouseover will be disabled +* defaults to false (highlights enabled) +* highlightLighten - Factor to lighten/darken highlighted chart values by - Defaults to 1.4 for a 40% increase +* tooltipContainer - Specify which DOM element the tooltip should be rendered into - defaults to document.body +* tooltipClassname - Optional CSS classname to apply to tooltips - If not specified then a default style will be applied +* tooltipOffsetX - How many pixels away from the mouse pointer to render the tooltip on the X axis +* tooltipOffsetY - How many pixels away from the mouse pointer to render the tooltip on the r axis +* tooltipFormatter - Optional callback that allows you to override the HTML displayed in the tooltip +* callback is given arguments of (sparkline, options, fields) +* tooltipChartTitle - If specified then the tooltip uses the string specified by this setting as a title +* tooltipFormat - A format string or SPFormat object (or an array thereof for multiple entries) +* to control the format of the tooltip +* tooltipPrefix - A string to prepend to each field displayed in a tooltip +* tooltipSuffix - A string to append to each field displayed in a tooltip +* tooltipSkipNull - If true then null values will not have a tooltip displayed (defaults to true) +* tooltipValueLookups - An object or range map to map field values to tooltip strings +* (eg. to map -1 to "Lost", 0 to "Draw", and 1 to "Win") +* numberFormatter - Optional callback for formatting numbers in tooltips +* numberDigitGroupSep - Character to use for group separator in numbers "1,234" - Defaults to "," +* numberDecimalMark - Character to use for the decimal point when formatting numbers - Defaults to "." +* numberDigitGroupCount - Number of digits between group separator - Defaults to 3 +* +* There are 7 types of sparkline, selected by supplying a "type" option of 'line' (default), +* 'bar', 'tristate', 'bullet', 'discrete', 'pie' or 'box' +* line - Line chart. Options: +* spotColor - Set to '' to not end each line in a circular spot +* minSpotColor - If set, color of spot at minimum value +* maxSpotColor - If set, color of spot at maximum value +* spotRadius - Radius in pixels +* lineWidth - Width of line in pixels +* normalRangeMin +* normalRangeMax - If set draws a filled horizontal bar between these two values marking the "normal" +* or expected range of values +* normalRangeColor - Color to use for the above bar +* drawNormalOnTop - Draw the normal range above the chart fill color if true +* defaultPixelsPerValue - Defaults to 3 pixels of width for each value in the chart +* highlightSpotColor - The color to use for drawing a highlight spot on mouseover - Set to null to disable +* highlightLineColor - The color to use for drawing a highlight line on mouseover - Set to null to disable +* valueSpots - Specify which points to draw spots on, and in which color. Accepts a range map +* +* bar - Bar chart. Options: +* barColor - Color of bars for postive values +* negBarColor - Color of bars for negative values +* zeroColor - Color of bars with zero values +* nullColor - Color of bars with null values - Defaults to omitting the bar entirely +* barWidth - Width of bars in pixels +* colorMap - Optional mappnig of values to colors to override the *BarColor values above +* can be an Array of values to control the color of individual bars or a range map +* to specify colors for individual ranges of values +* barSpacing - Gap between bars in pixels +* zeroAxis - Centers the y-axis around zero if true +* +* tristate - Charts values of win (>0), lose (<0) or draw (=0) +* posBarColor - Color of win values +* negBarColor - Color of lose values +* zeroBarColor - Color of draw values +* barWidth - Width of bars in pixels +* barSpacing - Gap between bars in pixels +* colorMap - Optional mappnig of values to colors to override the *BarColor values above +* can be an Array of values to control the color of individual bars or a range map +* to specify colors for individual ranges of values +* +* discrete - Options: +* lineHeight - Height of each line in pixels - Defaults to 30% of the graph height +* thesholdValue - Values less than this value will be drawn using thresholdColor instead of lineColor +* thresholdColor +* +* bullet - Values for bullet graphs msut be in the order: target, performance, range1, range2, range3, ... +* options: +* targetColor - The color of the vertical target marker +* targetWidth - The width of the target marker in pixels +* performanceColor - The color of the performance measure horizontal bar +* rangeColors - Colors to use for each qualitative range background color +* +* pie - Pie chart. Options: +* sliceColors - An array of colors to use for pie slices +* offset - Angle in degrees to offset the first slice - Try -90 or +90 +* borderWidth - Width of border to draw around the pie chart, in pixels - Defaults to 0 (no border) +* borderColor - Color to use for the pie chart border - Defaults to #000 +* +* box - Box plot. Options: +* raw - Set to true to supply pre-computed plot points as values +* values should be: low_outlier, low_whisker, q1, median, q3, high_whisker, high_outlier +* When set to false you can supply any number of values and the box plot will +* be computed for you. Default is false. +* showOutliers - Set to true (default) to display outliers as circles +* outlierIQR - Interquartile range used to determine outliers. Default 1.5 +* boxLineColor - Outline color of the box +* boxFillColor - Fill color for the box +* whiskerColor - Line color used for whiskers +* outlierLineColor - Outline color of outlier circles +* outlierFillColor - Fill color of the outlier circles +* spotRadius - Radius of outlier circles +* medianColor - Line color of the median line +* target - Draw a target cross hair at the supplied value (default undefined) +* +* +* +* Examples: +* $('#sparkline1').sparkline(myvalues, { lineColor: '#f00', fillColor: false }); +* $('.barsparks').sparkline('html', { type:'bar', height:'40px', barWidth:5 }); +* $('#tristate').sparkline([1,1,-1,1,0,0,-1], { type:'tristate' }): +* $('#discrete').sparkline([1,3,4,5,5,3,4,5], { type:'discrete' }); +* $('#bullet').sparkline([10,12,12,9,7], { type:'bullet' }); +* $('#pie').sparkline([1,1,2], { type:'pie' }); +*/ + +/*jslint regexp: true, browser: true, jquery: true, white: true, nomen: false, plusplus: false, maxerr: 500, indent: 4 */ + +(function(document, Math, undefined) { // performance/minified-size optimization +(function(factory) { + if(typeof define === 'function' && define.amd) { + define(['jquery'], factory); + } else if (jQuery && !jQuery.fn.sparkline) { + factory(jQuery); + } +} +(function($) { + 'use strict'; + + var UNSET_OPTION = {}, + getDefaults, createClass, SPFormat, clipval, quartile, normalizeValue, normalizeValues, + remove, isNumber, all, sum, addCSS, ensureArray, formatNumber, RangeMap, + MouseHandler, Tooltip, barHighlightMixin, + line, bar, tristate, discrete, bullet, pie, box, defaultStyles, initStyles, + VShape, VCanvas_base, VCanvas_canvas, VCanvas_vml, pending, shapeCount = 0; + + /** + * Default configuration settings + */ + getDefaults = function () { + return { + // Settings common to most/all chart types + common: { + type: 'line', + lineColor: '#00f', + fillColor: '#cdf', + defaultPixelsPerValue: 3, + width: 'auto', + height: 'auto', + composite: false, + tagValuesAttribute: 'values', + tagOptionsPrefix: 'spark', + enableTagOptions: false, + enableHighlight: true, + highlightLighten: 1.4, + tooltipSkipNull: true, + tooltipPrefix: '', + tooltipSuffix: '', + disableHiddenCheck: false, + numberFormatter: false, + numberDigitGroupCount: 3, + numberDigitGroupSep: ',', + numberDecimalMark: '.', + disableTooltips: false, + disableInteraction: false + }, + // Defaults for line charts + line: { + spotColor: '#f80', + highlightSpotColor: '#5f5', + highlightLineColor: '#f22', + spotRadius: 1.5, + minSpotColor: '#f80', + maxSpotColor: '#f80', + lineWidth: 1, + normalRangeMin: undefined, + normalRangeMax: undefined, + normalRangeColor: '#ccc', + drawNormalOnTop: false, + chartRangeMin: undefined, + chartRangeMax: undefined, + chartRangeMinX: undefined, + chartRangeMaxX: undefined, + tooltipFormat: new SPFormat('● {{prefix}}{{y}}{{suffix}}') + }, + // Defaults for bar charts + bar: { + barColor: '#3366cc', + negBarColor: '#f44', + stackedBarColor: ['#3366cc', '#dc3912', '#ff9900', '#109618', '#66aa00', + '#dd4477', '#0099c6', '#990099'], + zeroColor: undefined, + nullColor: undefined, + zeroAxis: true, + barWidth: 4, + barSpacing: 1, + chartRangeMax: undefined, + chartRangeMin: undefined, + chartRangeClip: false, + colorMap: undefined, + tooltipFormat: new SPFormat('● {{prefix}}{{value}}{{suffix}}') + }, + // Defaults for tristate charts + tristate: { + barWidth: 4, + barSpacing: 1, + posBarColor: '#6f6', + negBarColor: '#f44', + zeroBarColor: '#999', + colorMap: {}, + tooltipFormat: new SPFormat('● {{value:map}}'), + tooltipValueLookups: { map: { '-1': 'Loss', '0': 'Draw', '1': 'Win' } } + }, + // Defaults for discrete charts + discrete: { + lineHeight: 'auto', + thresholdColor: undefined, + thresholdValue: 0, + chartRangeMax: undefined, + chartRangeMin: undefined, + chartRangeClip: false, + tooltipFormat: new SPFormat('{{prefix}}{{value}}{{suffix}}') + }, + // Defaults for bullet charts + bullet: { + targetColor: '#f33', + targetWidth: 3, // width of the target bar in pixels + performanceColor: '#33f', + rangeColors: ['#d3dafe', '#a8b6ff', '#7f94ff'], + base: undefined, // set this to a number to change the base start number + tooltipFormat: new SPFormat('{{fieldkey:fields}} - {{value}}'), + tooltipValueLookups: { fields: {r: 'Range', p: 'Performance', t: 'Target'} } + }, + // Defaults for pie charts + pie: { + offset: 0, + sliceColors: ['#3366cc', '#dc3912', '#ff9900', '#109618', '#66aa00', + '#dd4477', '#0099c6', '#990099'], + borderWidth: 0, + borderColor: '#000', + tooltipFormat: new SPFormat('● {{value}} ({{percent.1}}%)') + }, + // Defaults for box plots + box: { + raw: false, + boxLineColor: '#000', + boxFillColor: '#cdf', + whiskerColor: '#000', + outlierLineColor: '#333', + outlierFillColor: '#fff', + medianColor: '#f00', + showOutliers: true, + outlierIQR: 1.5, + spotRadius: 1.5, + target: undefined, + targetColor: '#4a2', + chartRangeMax: undefined, + chartRangeMin: undefined, + tooltipFormat: new SPFormat('{{field:fields}}: {{value}}'), + tooltipFormatFieldlistKey: 'field', + tooltipValueLookups: { fields: { lq: 'Lower Quartile', med: 'Median', + uq: 'Upper Quartile', lo: 'Left Outlier', ro: 'Right Outlier', + lw: 'Left Whisker', rw: 'Right Whisker'} } + } + }; + }; + + // You can have tooltips use a css class other than jqstooltip by specifying tooltipClassname + defaultStyles = '.jqstooltip { ' + + 'position: absolute;' + + 'left: 0px;' + + 'top: 0px;' + + 'visibility: hidden;' + + 'background: rgb(0, 0, 0) transparent;' + + 'background-color: rgba(0,0,0,0.6);' + + 'filter:progid:DXImageTransform.Microsoft.gradient(startColorstr=#99000000, endColorstr=#99000000);' + + '-ms-filter: "progid:DXImageTransform.Microsoft.gradient(startColorstr=#99000000, endColorstr=#99000000)";' + + 'color: white;' + + 'font: 10px arial, san serif;' + + 'text-align: left;' + + 'white-space: nowrap;' + + 'padding: 5px;' + + 'border: 1px solid white;' + + 'z-index: 10000;' + + '}' + + '.jqsfield { ' + + 'color: white;' + + 'font: 10px arial, san serif;' + + 'text-align: left;' + + '}'; + + /** + * Utilities + */ + + createClass = function (/* [baseclass, [mixin, ...]], definition */) { + var Class, args; + Class = function () { + this.init.apply(this, arguments); + }; + if (arguments.length > 1) { + if (arguments[0]) { + Class.prototype = $.extend(new arguments[0](), arguments[arguments.length - 1]); + Class._super = arguments[0].prototype; + } else { + Class.prototype = arguments[arguments.length - 1]; + } + if (arguments.length > 2) { + args = Array.prototype.slice.call(arguments, 1, -1); + args.unshift(Class.prototype); + $.extend.apply($, args); + } + } else { + Class.prototype = arguments[0]; + } + Class.prototype.cls = Class; + return Class; + }; + + /** + * Wraps a format string for tooltips + * {{x}} + * {{x.2} + * {{x:months}} + */ + $.SPFormatClass = SPFormat = createClass({ + fre: /\{\{([\w.]+?)(:(.+?))?\}\}/g, + precre: /(\w+)\.(\d+)/, + + init: function (format, fclass) { + this.format = format; + this.fclass = fclass; + }, + + render: function (fieldset, lookups, options) { + var self = this, + fields = fieldset, + match, token, lookupkey, fieldvalue, prec; + return this.format.replace(this.fre, function () { + var lookup; + token = arguments[1]; + lookupkey = arguments[3]; + match = self.precre.exec(token); + if (match) { + prec = match[2]; + token = match[1]; + } else { + prec = false; + } + fieldvalue = fields[token]; + if (fieldvalue === undefined) { + return ''; + } + if (lookupkey && lookups && lookups[lookupkey]) { + lookup = lookups[lookupkey]; + if (lookup.get) { // RangeMap + return lookups[lookupkey].get(fieldvalue) || fieldvalue; + } else { + return lookups[lookupkey][fieldvalue] || fieldvalue; + } + } + if (isNumber(fieldvalue)) { + if (options.get('numberFormatter')) { + fieldvalue = options.get('numberFormatter')(fieldvalue); + } else { + fieldvalue = formatNumber(fieldvalue, prec, + options.get('numberDigitGroupCount'), + options.get('numberDigitGroupSep'), + options.get('numberDecimalMark')); + } + } + return fieldvalue; + }); + } + }); + + // convience method to avoid needing the new operator + $.spformat = function(format, fclass) { + return new SPFormat(format, fclass); + }; + + clipval = function (val, min, max) { + if (val < min) { + return min; + } + if (val > max) { + return max; + } + return val; + }; + + quartile = function (values, q) { + var vl; + if (q === 2) { + vl = Math.floor(values.length / 2); + return values.length % 2 ? values[vl] : (values[vl-1] + values[vl]) / 2; + } else { + if (values.length % 2 ) { // odd + vl = (values.length * q + q) / 4; + return vl % 1 ? (values[Math.floor(vl)] + values[Math.floor(vl) - 1]) / 2 : values[vl-1]; + } else { //even + vl = (values.length * q + 2) / 4; + return vl % 1 ? (values[Math.floor(vl)] + values[Math.floor(vl) - 1]) / 2 : values[vl-1]; + + } + } + }; + + normalizeValue = function (val) { + var nf; + switch (val) { + case 'undefined': + val = undefined; + break; + case 'null': + val = null; + break; + case 'true': + val = true; + break; + case 'false': + val = false; + break; + default: + nf = parseFloat(val); + if (val == nf) { + val = nf; + } + } + return val; + }; + + normalizeValues = function (vals) { + var i, result = []; + for (i = vals.length; i--;) { + result[i] = normalizeValue(vals[i]); + } + return result; + }; + + remove = function (vals, filter) { + var i, vl, result = []; + for (i = 0, vl = vals.length; i < vl; i++) { + if (vals[i] !== filter) { + result.push(vals[i]); + } + } + return result; + }; + + isNumber = function (num) { + return !isNaN(parseFloat(num)) && isFinite(num); + }; + + formatNumber = function (num, prec, groupsize, groupsep, decsep) { + var p, i; + num = (prec === false ? parseFloat(num).toString() : num.toFixed(prec)).split(''); + p = (p = $.inArray('.', num)) < 0 ? num.length : p; + if (p < num.length) { + num[p] = decsep; + } + for (i = p - groupsize; i > 0; i -= groupsize) { + num.splice(i, 0, groupsep); + } + return num.join(''); + }; + + // determine if all values of an array match a value + // returns true if the array is empty + all = function (val, arr, ignoreNull) { + var i; + for (i = arr.length; i--; ) { + if (ignoreNull && arr[i] === null) continue; + if (arr[i] !== val) { + return false; + } + } + return true; + }; + + // sums the numeric values in an array, ignoring other values + sum = function (vals) { + var total = 0, i; + for (i = vals.length; i--;) { + total += typeof vals[i] === 'number' ? vals[i] : 0; + } + return total; + }; + + ensureArray = function (val) { + return $.isArray(val) ? val : [val]; + }; + + // http://paulirish.com/2008/bookmarklet-inject-new-css-rules/ + addCSS = function(css) { + var tag; + //if ('\v' == 'v') /* ie only */ { + if (document.createStyleSheet) { + document.createStyleSheet().cssText = css; + } else { + tag = document.createElement('style'); + tag.type = 'text/css'; + document.getElementsByTagName('head')[0].appendChild(tag); + tag[(typeof document.body.style.WebkitAppearance == 'string') /* webkit only */ ? 'innerText' : 'innerHTML'] = css; + } + }; + + // Provide a cross-browser interface to a few simple drawing primitives + $.fn.simpledraw = function (width, height, useExisting, interact) { + var target, mhandler; + if (useExisting && (target = this.data('_jqs_vcanvas'))) { + return target; + } + + if ($.fn.sparkline.canvas === false) { + // We've already determined that neither Canvas nor VML are available + return false; + + } else if ($.fn.sparkline.canvas === undefined) { + // No function defined yet -- need to see if we support Canvas or VML + var el = document.createElement('canvas'); + if (!!(el.getContext && el.getContext('2d'))) { + // Canvas is available + $.fn.sparkline.canvas = function(width, height, target, interact) { + return new VCanvas_canvas(width, height, target, interact); + }; + } else if (document.namespaces && !document.namespaces.v) { + // VML is available + document.namespaces.add('v', 'urn:schemas-microsoft-com:vml', '#default#VML'); + $.fn.sparkline.canvas = function(width, height, target, interact) { + return new VCanvas_vml(width, height, target); + }; + } else { + // Neither Canvas nor VML are available + $.fn.sparkline.canvas = false; + return false; + } + } + + if (width === undefined) { + width = $(this).innerWidth(); + } + if (height === undefined) { + height = $(this).innerHeight(); + } + + target = $.fn.sparkline.canvas(width, height, this, interact); + + mhandler = $(this).data('_jqs_mhandler'); + if (mhandler) { + mhandler.registerCanvas(target); + } + return target; + }; + + $.fn.cleardraw = function () { + var target = this.data('_jqs_vcanvas'); + if (target) { + target.reset(); + } + }; + + $.RangeMapClass = RangeMap = createClass({ + init: function (map) { + var key, range, rangelist = []; + for (key in map) { + if (map.hasOwnProperty(key) && typeof key === 'string' && key.indexOf(':') > -1) { + range = key.split(':'); + range[0] = range[0].length === 0 ? -Infinity : parseFloat(range[0]); + range[1] = range[1].length === 0 ? Infinity : parseFloat(range[1]); + range[2] = map[key]; + rangelist.push(range); + } + } + this.map = map; + this.rangelist = rangelist || false; + }, + + get: function (value) { + var rangelist = this.rangelist, + i, range, result; + if ((result = this.map[value]) !== undefined) { + return result; + } + if (rangelist) { + for (i = rangelist.length; i--;) { + range = rangelist[i]; + if (range[0] <= value && range[1] >= value) { + return range[2]; + } + } + } + return undefined; + } + }); + + // Convenience function + $.range_map = function(map) { + return new RangeMap(map); + }; + + MouseHandler = createClass({ + init: function (el, options) { + var $el = $(el); + this.$el = $el; + this.options = options; + this.currentPageX = 0; + this.currentPageY = 0; + this.el = el; + this.splist = []; + this.tooltip = null; + this.over = false; + this.displayTooltips = !options.get('disableTooltips'); + this.highlightEnabled = !options.get('disableHighlight'); + }, + + registerSparkline: function (sp) { + this.splist.push(sp); + if (this.over) { + this.updateDisplay(); + } + }, + + registerCanvas: function (canvas) { + var $canvas = $(canvas.canvas); + this.canvas = canvas; + this.$canvas = $canvas; + $canvas.mouseenter($.proxy(this.mouseenter, this)); + $canvas.mouseleave($.proxy(this.mouseleave, this)); + $canvas.click($.proxy(this.mouseclick, this)); + }, + + reset: function (removeTooltip) { + this.splist = []; + if (this.tooltip && removeTooltip) { + this.tooltip.remove(); + this.tooltip = undefined; + } + }, + + mouseclick: function (e) { + var clickEvent = $.Event('sparklineClick'); + clickEvent.originalEvent = e; + clickEvent.sparklines = this.splist; + this.$el.trigger(clickEvent); + }, + + mouseenter: function (e) { + $(document.body).unbind('mousemove.jqs'); + $(document.body).bind('mousemove.jqs', $.proxy(this.mousemove, this)); + this.over = true; + this.currentPageX = e.pageX; + this.currentPageY = e.pageY; + this.currentEl = e.target; + if (!this.tooltip && this.displayTooltips) { + this.tooltip = new Tooltip(this.options); + this.tooltip.updatePosition(e.pageX, e.pageY); + } + this.updateDisplay(); + }, + + mouseleave: function () { + $(document.body).unbind('mousemove.jqs'); + var splist = this.splist, + spcount = splist.length, + needsRefresh = false, + sp, i; + this.over = false; + this.currentEl = null; + + if (this.tooltip) { + this.tooltip.remove(); + this.tooltip = null; + } + + for (i = 0; i < spcount; i++) { + sp = splist[i]; + if (sp.clearRegionHighlight()) { + needsRefresh = true; + } + } + + if (needsRefresh) { + this.canvas.render(); + } + }, + + mousemove: function (e) { + this.currentPageX = e.pageX; + this.currentPageY = e.pageY; + this.currentEl = e.target; + if (this.tooltip) { + this.tooltip.updatePosition(e.pageX, e.pageY); + } + this.updateDisplay(); + }, + + updateDisplay: function () { + var splist = this.splist, + spcount = splist.length, + needsRefresh = false, + offset = this.$canvas.offset(), + localX = this.currentPageX - offset.left, + localY = this.currentPageY - offset.top, + tooltiphtml, sp, i, result, changeEvent; + if (!this.over) { + return; + } + for (i = 0; i < spcount; i++) { + sp = splist[i]; + result = sp.setRegionHighlight(this.currentEl, localX, localY); + if (result) { + needsRefresh = true; + } + } + if (needsRefresh) { + changeEvent = $.Event('sparklineRegionChange'); + changeEvent.sparklines = this.splist; + this.$el.trigger(changeEvent); + if (this.tooltip) { + tooltiphtml = ''; + for (i = 0; i < spcount; i++) { + sp = splist[i]; + tooltiphtml += sp.getCurrentRegionTooltip(); + } + this.tooltip.setContent(tooltiphtml); + } + if (!this.disableHighlight) { + this.canvas.render(); + } + } + if (result === null) { + this.mouseleave(); + } + } + }); + + + Tooltip = createClass({ + sizeStyle: 'position: static !important;' + + 'display: block !important;' + + 'visibility: hidden !important;' + + 'float: left !important;', + + init: function (options) { + var tooltipClassname = options.get('tooltipClassname', 'jqstooltip'), + sizetipStyle = this.sizeStyle, + offset; + this.container = options.get('tooltipContainer') || document.body; + this.tooltipOffsetX = options.get('tooltipOffsetX', 10); + this.tooltipOffsetY = options.get('tooltipOffsetY', 12); + // remove any previous lingering tooltip + $('#jqssizetip').remove(); + $('#jqstooltip').remove(); + this.sizetip = $('
', { + id: 'jqssizetip', + style: sizetipStyle, + 'class': tooltipClassname + }); + this.tooltip = $('
', { + id: 'jqstooltip', + 'class': tooltipClassname + }).appendTo(this.container); + // account for the container's location + offset = this.tooltip.offset(); + this.offsetLeft = offset.left; + this.offsetTop = offset.top; + this.hidden = true; + $(window).unbind('resize.jqs scroll.jqs'); + $(window).bind('resize.jqs scroll.jqs', $.proxy(this.updateWindowDims, this)); + this.updateWindowDims(); + }, + + updateWindowDims: function () { + this.scrollTop = $(window).scrollTop(); + this.scrollLeft = $(window).scrollLeft(); + this.scrollRight = this.scrollLeft + $(window).width(); + this.updatePosition(); + }, + + getSize: function (content) { + this.sizetip.html(content).appendTo(this.container); + this.width = this.sizetip.width() + 1; + this.height = this.sizetip.height(); + this.sizetip.remove(); + }, + + setContent: function (content) { + if (!content) { + this.tooltip.css('visibility', 'hidden'); + this.hidden = true; + return; + } + this.getSize(content); + this.tooltip.html(content) + .css({ + 'width': this.width, + 'height': this.height, + 'visibility': 'visible' + }); + if (this.hidden) { + this.hidden = false; + this.updatePosition(); + } + }, + + updatePosition: function (x, y) { + if (x === undefined) { + if (this.mousex === undefined) { + return; + } + x = this.mousex - this.offsetLeft; + y = this.mousey - this.offsetTop; + + } else { + this.mousex = x = x - this.offsetLeft; + this.mousey = y = y - this.offsetTop; + } + if (!this.height || !this.width || this.hidden) { + return; + } + + y -= this.height + this.tooltipOffsetY; + x += this.tooltipOffsetX; + + if (y < this.scrollTop) { + y = this.scrollTop; + } + if (x < this.scrollLeft) { + x = this.scrollLeft; + } else if (x + this.width > this.scrollRight) { + x = this.scrollRight - this.width; + } + + this.tooltip.css({ + 'left': x, + 'top': y + }); + }, + + remove: function () { + this.tooltip.remove(); + this.sizetip.remove(); + this.sizetip = this.tooltip = undefined; + $(window).unbind('resize.jqs scroll.jqs'); + } + }); + + initStyles = function() { + addCSS(defaultStyles); + }; + + $(initStyles); + + pending = []; + $.fn.sparkline = function (userValues, userOptions) { + return this.each(function () { + var options = new $.fn.sparkline.options(this, userOptions), + $this = $(this), + render, i; + render = function () { + var values, width, height, tmp, mhandler, sp, vals; + if (userValues === 'html' || userValues === undefined) { + vals = this.getAttribute(options.get('tagValuesAttribute')); + if (vals === undefined || vals === null) { + vals = $this.html(); + } + values = vals.replace(/(^\s*\s*$)|\s+/g, '').split(','); + } else { + values = userValues; + } + + width = options.get('width') === 'auto' ? values.length * options.get('defaultPixelsPerValue') : options.get('width'); + if (options.get('height') === 'auto') { + if (!options.get('composite') || !$.data(this, '_jqs_vcanvas')) { + // must be a better way to get the line height + tmp = document.createElement('span'); + tmp.innerHTML = 'a'; + $this.html(tmp); + height = $(tmp).innerHeight() || $(tmp).height(); + $(tmp).remove(); + tmp = null; + } + } else { + height = options.get('height'); + } + + if (!options.get('disableInteraction')) { + mhandler = $.data(this, '_jqs_mhandler'); + if (!mhandler) { + mhandler = new MouseHandler(this, options); + $.data(this, '_jqs_mhandler', mhandler); + } else if (!options.get('composite')) { + mhandler.reset(); + } + } else { + mhandler = false; + } + + if (options.get('composite') && !$.data(this, '_jqs_vcanvas')) { + if (!$.data(this, '_jqs_errnotify')) { + alert('Attempted to attach a composite sparkline to an element with no existing sparkline'); + $.data(this, '_jqs_errnotify', true); + } + return; + } + + sp = new $.fn.sparkline[options.get('type')](this, values, options, width, height); + + sp.render(); + + if (mhandler) { + mhandler.registerSparkline(sp); + } + }; + if (($(this).html() && !options.get('disableHiddenCheck') && $(this).is(':hidden')) || !$(this).parents('body').length) { + if (!options.get('composite') && $.data(this, '_jqs_pending')) { + // remove any existing references to the element + for (i = pending.length; i; i--) { + if (pending[i - 1][0] == this) { + pending.splice(i - 1, 1); + } + } + } + pending.push([this, render]); + $.data(this, '_jqs_pending', true); + } else { + render.call(this); + } + }); + }; + + $.fn.sparkline.defaults = getDefaults(); + + + $.sparkline_display_visible = function () { + var el, i, pl; + var done = []; + for (i = 0, pl = pending.length; i < pl; i++) { + el = pending[i][0]; + if ($(el).is(':visible') && !$(el).parents().is(':hidden')) { + pending[i][1].call(el); + $.data(pending[i][0], '_jqs_pending', false); + done.push(i); + } else if (!$(el).closest('html').length && !$.data(el, '_jqs_pending')) { + // element has been inserted and removed from the DOM + // If it was not yet inserted into the dom then the .data request + // will return true. + // removing from the dom causes the data to be removed. + $.data(pending[i][0], '_jqs_pending', false); + done.push(i); + } + } + for (i = done.length; i; i--) { + pending.splice(done[i - 1], 1); + } + }; + + + /** + * User option handler + */ + $.fn.sparkline.options = createClass({ + init: function (tag, userOptions) { + var extendedOptions, defaults, base, tagOptionType; + this.userOptions = userOptions = userOptions || {}; + this.tag = tag; + this.tagValCache = {}; + defaults = $.fn.sparkline.defaults; + base = defaults.common; + this.tagOptionsPrefix = userOptions.enableTagOptions && (userOptions.tagOptionsPrefix || base.tagOptionsPrefix); + + tagOptionType = this.getTagSetting('type'); + if (tagOptionType === UNSET_OPTION) { + extendedOptions = defaults[userOptions.type || base.type]; + } else { + extendedOptions = defaults[tagOptionType]; + } + this.mergedOptions = $.extend({}, base, extendedOptions, userOptions); + }, + + + getTagSetting: function (key) { + var prefix = this.tagOptionsPrefix, + val, i, pairs, keyval; + if (prefix === false || prefix === undefined) { + return UNSET_OPTION; + } + if (this.tagValCache.hasOwnProperty(key)) { + val = this.tagValCache.key; + } else { + val = this.tag.getAttribute(prefix + key); + if (val === undefined || val === null) { + val = UNSET_OPTION; + } else if (val.substr(0, 1) === '[') { + val = val.substr(1, val.length - 2).split(','); + for (i = val.length; i--;) { + val[i] = normalizeValue(val[i].replace(/(^\s*)|(\s*$)/g, '')); + } + } else if (val.substr(0, 1) === '{') { + pairs = val.substr(1, val.length - 2).split(','); + val = {}; + for (i = pairs.length; i--;) { + keyval = pairs[i].split(':', 2); + val[keyval[0].replace(/(^\s*)|(\s*$)/g, '')] = normalizeValue(keyval[1].replace(/(^\s*)|(\s*$)/g, '')); + } + } else { + val = normalizeValue(val); + } + this.tagValCache.key = val; + } + return val; + }, + + get: function (key, defaultval) { + var tagOption = this.getTagSetting(key), + result; + if (tagOption !== UNSET_OPTION) { + return tagOption; + } + return (result = this.mergedOptions[key]) === undefined ? defaultval : result; + } + }); + + + $.fn.sparkline._base = createClass({ + disabled: false, + + init: function (el, values, options, width, height) { + this.el = el; + this.$el = $(el); + this.values = values; + this.options = options; + this.width = width; + this.height = height; + this.currentRegion = undefined; + }, + + /** + * Setup the canvas + */ + initTarget: function () { + var interactive = !this.options.get('disableInteraction'); + if (!(this.target = this.$el.simpledraw(this.width, this.height, this.options.get('composite'), interactive))) { + this.disabled = true; + } else { + this.canvasWidth = this.target.pixelWidth; + this.canvasHeight = this.target.pixelHeight; + } + }, + + /** + * Actually render the chart to the canvas + */ + render: function () { + if (this.disabled) { + this.el.innerHTML = ''; + return false; + } + return true; + }, + + /** + * Return a region id for a given x/y co-ordinate + */ + getRegion: function (x, y) { + }, + + /** + * Highlight an item based on the moused-over x,y co-ordinate + */ + setRegionHighlight: function (el, x, y) { + var currentRegion = this.currentRegion, + highlightEnabled = !this.options.get('disableHighlight'), + newRegion; + if (x > this.canvasWidth || y > this.canvasHeight || x < 0 || y < 0) { + return null; + } + newRegion = this.getRegion(el, x, y); + if (currentRegion !== newRegion) { + if (currentRegion !== undefined && highlightEnabled) { + this.removeHighlight(); + } + this.currentRegion = newRegion; + if (newRegion !== undefined && highlightEnabled) { + this.renderHighlight(); + } + return true; + } + return false; + }, + + /** + * Reset any currently highlighted item + */ + clearRegionHighlight: function () { + if (this.currentRegion !== undefined) { + this.removeHighlight(); + this.currentRegion = undefined; + return true; + } + return false; + }, + + renderHighlight: function () { + this.changeHighlight(true); + }, + + removeHighlight: function () { + this.changeHighlight(false); + }, + + changeHighlight: function (highlight) {}, + + /** + * Fetch the HTML to display as a tooltip + */ + getCurrentRegionTooltip: function () { + var options = this.options, + header = '', + entries = [], + fields, formats, formatlen, fclass, text, i, + showFields, showFieldsKey, newFields, fv, + formatter, format, fieldlen, j; + if (this.currentRegion === undefined) { + return ''; + } + fields = this.getCurrentRegionFields(); + formatter = options.get('tooltipFormatter'); + if (formatter) { + return formatter(this, options, fields); + } + if (options.get('tooltipChartTitle')) { + header += '
' + options.get('tooltipChartTitle') + '
\n'; + } + formats = this.options.get('tooltipFormat'); + if (!formats) { + return ''; + } + if (!$.isArray(formats)) { + formats = [formats]; + } + if (!$.isArray(fields)) { + fields = [fields]; + } + showFields = this.options.get('tooltipFormatFieldlist'); + showFieldsKey = this.options.get('tooltipFormatFieldlistKey'); + if (showFields && showFieldsKey) { + // user-selected ordering of fields + newFields = []; + for (i = fields.length; i--;) { + fv = fields[i][showFieldsKey]; + if ((j = $.inArray(fv, showFields)) != -1) { + newFields[j] = fields[i]; + } + } + fields = newFields; + } + formatlen = formats.length; + fieldlen = fields.length; + for (i = 0; i < formatlen; i++) { + format = formats[i]; + if (typeof format === 'string') { + format = new SPFormat(format); + } + fclass = format.fclass || 'jqsfield'; + for (j = 0; j < fieldlen; j++) { + if (!fields[j].isNull || !options.get('tooltipSkipNull')) { + $.extend(fields[j], { + prefix: options.get('tooltipPrefix'), + suffix: options.get('tooltipSuffix') + }); + text = format.render(fields[j], options.get('tooltipValueLookups'), options); + entries.push('
' + text + '
'); + } + } + } + if (entries.length) { + return header + entries.join('\n'); + } + return ''; + }, + + getCurrentRegionFields: function () {}, + + calcHighlightColor: function (color, options) { + var highlightColor = options.get('highlightColor'), + lighten = options.get('highlightLighten'), + parse, mult, rgbnew, i; + if (highlightColor) { + return highlightColor; + } + if (lighten) { + // extract RGB values + parse = /^#([0-9a-f])([0-9a-f])([0-9a-f])$/i.exec(color) || /^#([0-9a-f]{2})([0-9a-f]{2})([0-9a-f]{2})$/i.exec(color); + if (parse) { + rgbnew = []; + mult = color.length === 4 ? 16 : 1; + for (i = 0; i < 3; i++) { + rgbnew[i] = clipval(Math.round(parseInt(parse[i + 1], 16) * mult * lighten), 0, 255); + } + return 'rgb(' + rgbnew.join(',') + ')'; + } + + } + return color; + } + + }); + + barHighlightMixin = { + changeHighlight: function (highlight) { + var currentRegion = this.currentRegion, + target = this.target, + shapeids = this.regionShapes[currentRegion], + newShapes; + // will be null if the region value was null + if (shapeids) { + newShapes = this.renderRegion(currentRegion, highlight); + if ($.isArray(newShapes) || $.isArray(shapeids)) { + target.replaceWithShapes(shapeids, newShapes); + this.regionShapes[currentRegion] = $.map(newShapes, function (newShape) { + return newShape.id; + }); + } else { + target.replaceWithShape(shapeids, newShapes); + this.regionShapes[currentRegion] = newShapes.id; + } + } + }, + + render: function () { + var values = this.values, + target = this.target, + regionShapes = this.regionShapes, + shapes, ids, i, j; + + if (!this.cls._super.render.call(this)) { + return; + } + for (i = values.length; i--;) { + shapes = this.renderRegion(i); + if (shapes) { + if ($.isArray(shapes)) { + ids = []; + for (j = shapes.length; j--;) { + shapes[j].append(); + ids.push(shapes[j].id); + } + regionShapes[i] = ids; + } else { + shapes.append(); + regionShapes[i] = shapes.id; // store just the shapeid + } + } else { + // null value + regionShapes[i] = null; + } + } + target.render(); + } + }; + + /** + * Line charts + */ + $.fn.sparkline.line = line = createClass($.fn.sparkline._base, { + type: 'line', + + init: function (el, values, options, width, height) { + line._super.init.call(this, el, values, options, width, height); + this.vertices = []; + this.regionMap = []; + this.xvalues = []; + this.yvalues = []; + this.yminmax = []; + this.hightlightSpotId = null; + this.lastShapeId = null; + this.initTarget(); + }, + + getRegion: function (el, x, y) { + var i, + regionMap = this.regionMap; // maps regions to value positions + for (i = regionMap.length; i--;) { + if (regionMap[i] !== null && x >= regionMap[i][0] && x <= regionMap[i][1]) { + return regionMap[i][2]; + } + } + return undefined; + }, + + getCurrentRegionFields: function () { + var currentRegion = this.currentRegion; + return { + isNull: this.yvalues[currentRegion] === null, + x: this.xvalues[currentRegion], + y: this.yvalues[currentRegion], + color: this.options.get('lineColor'), + fillColor: this.options.get('fillColor'), + offset: currentRegion + }; + }, + + renderHighlight: function () { + var currentRegion = this.currentRegion, + target = this.target, + vertex = this.vertices[currentRegion], + options = this.options, + spotRadius = options.get('spotRadius'), + highlightSpotColor = options.get('highlightSpotColor'), + highlightLineColor = options.get('highlightLineColor'), + highlightSpot, highlightLine; + + if (!vertex) { + return; + } + if (spotRadius && highlightSpotColor) { + highlightSpot = target.drawCircle(vertex[0], vertex[1], + spotRadius, undefined, highlightSpotColor); + this.highlightSpotId = highlightSpot.id; + target.insertAfterShape(this.lastShapeId, highlightSpot); + } + if (highlightLineColor) { + highlightLine = target.drawLine(vertex[0], this.canvasTop, vertex[0], + this.canvasTop + this.canvasHeight, highlightLineColor); + this.highlightLineId = highlightLine.id; + target.insertAfterShape(this.lastShapeId, highlightLine); + } + }, + + removeHighlight: function () { + var target = this.target; + if (this.highlightSpotId) { + target.removeShapeId(this.highlightSpotId); + this.highlightSpotId = null; + } + if (this.highlightLineId) { + target.removeShapeId(this.highlightLineId); + this.highlightLineId = null; + } + }, + + scanValues: function () { + var values = this.values, + valcount = values.length, + xvalues = this.xvalues, + yvalues = this.yvalues, + yminmax = this.yminmax, + i, val, isStr, isArray, sp; + for (i = 0; i < valcount; i++) { + val = values[i]; + isStr = typeof(values[i]) === 'string'; + isArray = typeof(values[i]) === 'object' && values[i] instanceof Array; + sp = isStr && values[i].split(':'); + if (isStr && sp.length === 2) { // x:y + xvalues.push(Number(sp[0])); + yvalues.push(Number(sp[1])); + yminmax.push(Number(sp[1])); + } else if (isArray) { + xvalues.push(val[0]); + yvalues.push(val[1]); + yminmax.push(val[1]); + } else { + xvalues.push(i); + if (values[i] === null || values[i] === 'null') { + yvalues.push(null); + } else { + yvalues.push(Number(val)); + yminmax.push(Number(val)); + } + } + } + if (this.options.get('xvalues')) { + xvalues = this.options.get('xvalues'); + } + + this.maxy = this.maxyorg = Math.max.apply(Math, yminmax); + this.miny = this.minyorg = Math.min.apply(Math, yminmax); + + this.maxx = Math.max.apply(Math, xvalues); + this.minx = Math.min.apply(Math, xvalues); + + this.xvalues = xvalues; + this.yvalues = yvalues; + this.yminmax = yminmax; + + }, + + processRangeOptions: function () { + var options = this.options, + normalRangeMin = options.get('normalRangeMin'), + normalRangeMax = options.get('normalRangeMax'); + + if (normalRangeMin !== undefined) { + if (normalRangeMin < this.miny) { + this.miny = normalRangeMin; + } + if (normalRangeMax > this.maxy) { + this.maxy = normalRangeMax; + } + } + if (options.get('chartRangeMin') !== undefined && (options.get('chartRangeClip') || options.get('chartRangeMin') < this.miny)) { + this.miny = options.get('chartRangeMin'); + } + if (options.get('chartRangeMax') !== undefined && (options.get('chartRangeClip') || options.get('chartRangeMax') > this.maxy)) { + this.maxy = options.get('chartRangeMax'); + } + if (options.get('chartRangeMinX') !== undefined && (options.get('chartRangeClipX') || options.get('chartRangeMinX') < this.minx)) { + this.minx = options.get('chartRangeMinX'); + } + if (options.get('chartRangeMaxX') !== undefined && (options.get('chartRangeClipX') || options.get('chartRangeMaxX') > this.maxx)) { + this.maxx = options.get('chartRangeMaxX'); + } + + }, + + drawNormalRange: function (canvasLeft, canvasTop, canvasHeight, canvasWidth, rangey) { + var normalRangeMin = this.options.get('normalRangeMin'), + normalRangeMax = this.options.get('normalRangeMax'), + ytop = canvasTop + Math.round(canvasHeight - (canvasHeight * ((normalRangeMax - this.miny) / rangey))), + height = Math.round((canvasHeight * (normalRangeMax - normalRangeMin)) / rangey); + this.target.drawRect(canvasLeft, ytop, canvasWidth, height, undefined, this.options.get('normalRangeColor')).append(); + }, + + render: function () { + var options = this.options, + target = this.target, + canvasWidth = this.canvasWidth, + canvasHeight = this.canvasHeight, + vertices = this.vertices, + spotRadius = options.get('spotRadius'), + regionMap = this.regionMap, + rangex, rangey, yvallast, + canvasTop, canvasLeft, + vertex, path, paths, x, y, xnext, xpos, xposnext, + last, next, yvalcount, lineShapes, fillShapes, plen, + valueSpots, hlSpotsEnabled, color, xvalues, yvalues, i; + + if (!line._super.render.call(this)) { + return; + } + + this.scanValues(); + this.processRangeOptions(); + + xvalues = this.xvalues; + yvalues = this.yvalues; + + if (!this.yminmax.length || this.yvalues.length < 2) { + // empty or all null valuess + return; + } + + canvasTop = canvasLeft = 0; + + rangex = this.maxx - this.minx === 0 ? 1 : this.maxx - this.minx; + rangey = this.maxy - this.miny === 0 ? 1 : this.maxy - this.miny; + yvallast = this.yvalues.length - 1; + + if (spotRadius && (canvasWidth < (spotRadius * 4) || canvasHeight < (spotRadius * 4))) { + spotRadius = 0; + } + if (spotRadius) { + // adjust the canvas size as required so that spots will fit + hlSpotsEnabled = options.get('highlightSpotColor') && !options.get('disableInteraction'); + if (hlSpotsEnabled || options.get('minSpotColor') || (options.get('spotColor') && yvalues[yvallast] === this.miny)) { + canvasHeight -= Math.ceil(spotRadius); + } + if (hlSpotsEnabled || options.get('maxSpotColor') || (options.get('spotColor') && yvalues[yvallast] === this.maxy)) { + canvasHeight -= Math.ceil(spotRadius); + canvasTop += Math.ceil(spotRadius); + } + if (hlSpotsEnabled || + ((options.get('minSpotColor') || options.get('maxSpotColor')) && (yvalues[0] === this.miny || yvalues[0] === this.maxy))) { + canvasLeft += Math.ceil(spotRadius); + canvasWidth -= Math.ceil(spotRadius); + } + if (hlSpotsEnabled || options.get('spotColor') || + (options.get('minSpotColor') || options.get('maxSpotColor') && + (yvalues[yvallast] === this.miny || yvalues[yvallast] === this.maxy))) { + canvasWidth -= Math.ceil(spotRadius); + } + } + + + canvasHeight--; + + if (options.get('normalRangeMin') !== undefined && !options.get('drawNormalOnTop')) { + this.drawNormalRange(canvasLeft, canvasTop, canvasHeight, canvasWidth, rangey); + } + + path = []; + paths = [path]; + last = next = null; + yvalcount = yvalues.length; + for (i = 0; i < yvalcount; i++) { + x = xvalues[i]; + xnext = xvalues[i + 1]; + y = yvalues[i]; + xpos = canvasLeft + Math.round((x - this.minx) * (canvasWidth / rangex)); + xposnext = i < yvalcount - 1 ? canvasLeft + Math.round((xnext - this.minx) * (canvasWidth / rangex)) : canvasWidth; + next = xpos + ((xposnext - xpos) / 2); + regionMap[i] = [last || 0, next, i]; + last = next; + if (y === null) { + if (i) { + if (yvalues[i - 1] !== null) { + path = []; + paths.push(path); + } + vertices.push(null); + } + } else { + if (y < this.miny) { + y = this.miny; + } + if (y > this.maxy) { + y = this.maxy; + } + if (!path.length) { + // previous value was null + path.push([xpos, canvasTop + canvasHeight]); + } + vertex = [xpos, canvasTop + Math.round(canvasHeight - (canvasHeight * ((y - this.miny) / rangey)))]; + path.push(vertex); + vertices.push(vertex); + } + } + + lineShapes = []; + fillShapes = []; + plen = paths.length; + for (i = 0; i < plen; i++) { + path = paths[i]; + if (path.length) { + if (options.get('fillColor')) { + path.push([path[path.length - 1][0], (canvasTop + canvasHeight)]); + fillShapes.push(path.slice(0)); + path.pop(); + } + // if there's only a single point in this path, then we want to display it + // as a vertical line which means we keep path[0] as is + if (path.length > 2) { + // else we want the first value + path[0] = [path[0][0], path[1][1]]; + } + lineShapes.push(path); + } + } + + // draw the fill first, then optionally the normal range, then the line on top of that + plen = fillShapes.length; + for (i = 0; i < plen; i++) { + target.drawShape(fillShapes[i], + options.get('fillColor'), options.get('fillColor')).append(); + } + + if (options.get('normalRangeMin') !== undefined && options.get('drawNormalOnTop')) { + this.drawNormalRange(canvasLeft, canvasTop, canvasHeight, canvasWidth, rangey); + } + + plen = lineShapes.length; + for (i = 0; i < plen; i++) { + target.drawShape(lineShapes[i], options.get('lineColor'), undefined, + options.get('lineWidth')).append(); + } + + if (spotRadius && options.get('valueSpots')) { + valueSpots = options.get('valueSpots'); + if (valueSpots.get === undefined) { + valueSpots = new RangeMap(valueSpots); + } + for (i = 0; i < yvalcount; i++) { + color = valueSpots.get(yvalues[i]); + if (color) { + target.drawCircle(canvasLeft + Math.round((xvalues[i] - this.minx) * (canvasWidth / rangex)), + canvasTop + Math.round(canvasHeight - (canvasHeight * ((yvalues[i] - this.miny) / rangey))), + spotRadius, undefined, + color).append(); + } + } + + } + if (spotRadius && options.get('spotColor') && yvalues[yvallast] !== null) { + target.drawCircle(canvasLeft + Math.round((xvalues[xvalues.length - 1] - this.minx) * (canvasWidth / rangex)), + canvasTop + Math.round(canvasHeight - (canvasHeight * ((yvalues[yvallast] - this.miny) / rangey))), + spotRadius, undefined, + options.get('spotColor')).append(); + } + if (this.maxy !== this.minyorg) { + if (spotRadius && options.get('minSpotColor')) { + x = xvalues[$.inArray(this.minyorg, yvalues)]; + target.drawCircle(canvasLeft + Math.round((x - this.minx) * (canvasWidth / rangex)), + canvasTop + Math.round(canvasHeight - (canvasHeight * ((this.minyorg - this.miny) / rangey))), + spotRadius, undefined, + options.get('minSpotColor')).append(); + } + if (spotRadius && options.get('maxSpotColor')) { + x = xvalues[$.inArray(this.maxyorg, yvalues)]; + target.drawCircle(canvasLeft + Math.round((x - this.minx) * (canvasWidth / rangex)), + canvasTop + Math.round(canvasHeight - (canvasHeight * ((this.maxyorg - this.miny) / rangey))), + spotRadius, undefined, + options.get('maxSpotColor')).append(); + } + } + + this.lastShapeId = target.getLastShapeId(); + this.canvasTop = canvasTop; + target.render(); + } + }); + + /** + * Bar charts + */ + $.fn.sparkline.bar = bar = createClass($.fn.sparkline._base, barHighlightMixin, { + type: 'bar', + + init: function (el, values, options, width, height) { + var barWidth = parseInt(options.get('barWidth'), 10), + barSpacing = parseInt(options.get('barSpacing'), 10), + chartRangeMin = options.get('chartRangeMin'), + chartRangeMax = options.get('chartRangeMax'), + chartRangeClip = options.get('chartRangeClip'), + stackMin = Infinity, + stackMax = -Infinity, + isStackString, groupMin, groupMax, stackRanges, + numValues, i, vlen, range, zeroAxis, xaxisOffset, min, max, clipMin, clipMax, + stacked, vlist, j, slen, svals, val, yoffset, yMaxCalc, canvasHeightEf; + bar._super.init.call(this, el, values, options, width, height); + + // scan values to determine whether to stack bars + for (i = 0, vlen = values.length; i < vlen; i++) { + val = values[i]; + isStackString = typeof(val) === 'string' && val.indexOf(':') > -1; + if (isStackString || $.isArray(val)) { + stacked = true; + if (isStackString) { + val = values[i] = normalizeValues(val.split(':')); + } + val = remove(val, null); // min/max will treat null as zero + groupMin = Math.min.apply(Math, val); + groupMax = Math.max.apply(Math, val); + if (groupMin < stackMin) { + stackMin = groupMin; + } + if (groupMax > stackMax) { + stackMax = groupMax; + } + } + } + + this.stacked = stacked; + this.regionShapes = {}; + this.barWidth = barWidth; + this.barSpacing = barSpacing; + this.totalBarWidth = barWidth + barSpacing; + this.width = width = (values.length * barWidth) + ((values.length - 1) * barSpacing); + + this.initTarget(); + + if (chartRangeClip) { + clipMin = chartRangeMin === undefined ? -Infinity : chartRangeMin; + clipMax = chartRangeMax === undefined ? Infinity : chartRangeMax; + } + + numValues = []; + stackRanges = stacked ? [] : numValues; + var stackTotals = []; + var stackRangesNeg = []; + for (i = 0, vlen = values.length; i < vlen; i++) { + if (stacked) { + vlist = values[i]; + values[i] = svals = []; + stackTotals[i] = 0; + stackRanges[i] = stackRangesNeg[i] = 0; + for (j = 0, slen = vlist.length; j < slen; j++) { + val = svals[j] = chartRangeClip ? clipval(vlist[j], clipMin, clipMax) : vlist[j]; + if (val !== null) { + if (val > 0) { + stackTotals[i] += val; + } + if (stackMin < 0 && stackMax > 0) { + if (val < 0) { + stackRangesNeg[i] += Math.abs(val); + } else { + stackRanges[i] += val; + } + } else { + stackRanges[i] += Math.abs(val - (val < 0 ? stackMax : stackMin)); + } + numValues.push(val); + } + } + } else { + val = chartRangeClip ? clipval(values[i], clipMin, clipMax) : values[i]; + val = values[i] = normalizeValue(val); + if (val !== null) { + numValues.push(val); + } + } + } + this.max = max = Math.max.apply(Math, numValues); + this.min = min = Math.min.apply(Math, numValues); + this.stackMax = stackMax = stacked ? Math.max.apply(Math, stackTotals) : max; + this.stackMin = stackMin = stacked ? Math.min.apply(Math, numValues) : min; + + if (options.get('chartRangeMin') !== undefined && (options.get('chartRangeClip') || options.get('chartRangeMin') < min)) { + min = options.get('chartRangeMin'); + } + if (options.get('chartRangeMax') !== undefined && (options.get('chartRangeClip') || options.get('chartRangeMax') > max)) { + max = options.get('chartRangeMax'); + } + + this.zeroAxis = zeroAxis = options.get('zeroAxis', true); + if (min <= 0 && max >= 0 && zeroAxis) { + xaxisOffset = 0; + } else if (zeroAxis == false) { + xaxisOffset = min; + } else if (min > 0) { + xaxisOffset = min; + } else { + xaxisOffset = max; + } + this.xaxisOffset = xaxisOffset; + + range = stacked ? (Math.max.apply(Math, stackRanges) + Math.max.apply(Math, stackRangesNeg)) : max - min; + + // as we plot zero/min values a single pixel line, we add a pixel to all other + // values - Reduce the effective canvas size to suit + this.canvasHeightEf = (zeroAxis && min < 0) ? this.canvasHeight - 2 : this.canvasHeight - 1; + + if (min < xaxisOffset) { + yMaxCalc = (stacked && max >= 0) ? stackMax : max; + yoffset = (yMaxCalc - xaxisOffset) / range * this.canvasHeight; + if (yoffset !== Math.ceil(yoffset)) { + this.canvasHeightEf -= 2; + yoffset = Math.ceil(yoffset); + } + } else { + yoffset = this.canvasHeight; + } + this.yoffset = yoffset; + + if ($.isArray(options.get('colorMap'))) { + this.colorMapByIndex = options.get('colorMap'); + this.colorMapByValue = null; + } else { + this.colorMapByIndex = null; + this.colorMapByValue = options.get('colorMap'); + if (this.colorMapByValue && this.colorMapByValue.get === undefined) { + this.colorMapByValue = new RangeMap(this.colorMapByValue); + } + } + + this.range = range; + }, + + getRegion: function (el, x, y) { + var result = Math.floor(x / this.totalBarWidth); + return (result < 0 || result >= this.values.length) ? undefined : result; + }, + + getCurrentRegionFields: function () { + var currentRegion = this.currentRegion, + values = ensureArray(this.values[currentRegion]), + result = [], + value, i; + for (i = values.length; i--;) { + value = values[i]; + result.push({ + isNull: value === null, + value: value, + color: this.calcColor(i, value, currentRegion), + offset: currentRegion + }); + } + return result; + }, + + calcColor: function (stacknum, value, valuenum) { + var colorMapByIndex = this.colorMapByIndex, + colorMapByValue = this.colorMapByValue, + options = this.options, + color, newColor; + if (this.stacked) { + color = options.get('stackedBarColor'); + } else { + color = (value < 0) ? options.get('negBarColor') : options.get('barColor'); + } + if (value === 0 && options.get('zeroColor') !== undefined) { + color = options.get('zeroColor'); + } + if (colorMapByValue && (newColor = colorMapByValue.get(value))) { + color = newColor; + } else if (colorMapByIndex && colorMapByIndex.length > valuenum) { + color = colorMapByIndex[valuenum]; + } + return $.isArray(color) ? color[stacknum % color.length] : color; + }, + + /** + * Render bar(s) for a region + */ + renderRegion: function (valuenum, highlight) { + var vals = this.values[valuenum], + options = this.options, + xaxisOffset = this.xaxisOffset, + result = [], + range = this.range, + stacked = this.stacked, + target = this.target, + x = valuenum * this.totalBarWidth, + canvasHeightEf = this.canvasHeightEf, + yoffset = this.yoffset, + y, height, color, isNull, yoffsetNeg, i, valcount, val, minPlotted, allMin; + + vals = $.isArray(vals) ? vals : [vals]; + valcount = vals.length; + val = vals[0]; + isNull = all(null, vals); + allMin = all(xaxisOffset, vals, true); + + if (isNull) { + if (options.get('nullColor')) { + color = highlight ? options.get('nullColor') : this.calcHighlightColor(options.get('nullColor'), options); + y = (yoffset > 0) ? yoffset - 1 : yoffset; + return target.drawRect(x, y, this.barWidth - 1, 0, color, color); + } else { + return undefined; + } + } + yoffsetNeg = yoffset; + for (i = 0; i < valcount; i++) { + val = vals[i]; + + if (stacked && val === xaxisOffset) { + if (!allMin || minPlotted) { + continue; + } + minPlotted = true; + } + + if (range > 0) { + height = Math.floor(canvasHeightEf * ((Math.abs(val - xaxisOffset) / range))) + 1; + } else { + height = 1; + } + if (val < xaxisOffset || (val === xaxisOffset && yoffset === 0)) { + y = yoffsetNeg; + yoffsetNeg += height; + } else { + y = yoffset - height; + yoffset -= height; + } + color = this.calcColor(i, val, valuenum); + if (highlight) { + color = this.calcHighlightColor(color, options); + } + result.push(target.drawRect(x, y, this.barWidth - 1, height - 1, color, color)); + } + if (result.length === 1) { + return result[0]; + } + return result; + } + }); + + /** + * Tristate charts + */ + $.fn.sparkline.tristate = tristate = createClass($.fn.sparkline._base, barHighlightMixin, { + type: 'tristate', + + init: function (el, values, options, width, height) { + var barWidth = parseInt(options.get('barWidth'), 10), + barSpacing = parseInt(options.get('barSpacing'), 10); + tristate._super.init.call(this, el, values, options, width, height); + + this.regionShapes = {}; + this.barWidth = barWidth; + this.barSpacing = barSpacing; + this.totalBarWidth = barWidth + barSpacing; + this.values = $.map(values, Number); + this.width = width = (values.length * barWidth) + ((values.length - 1) * barSpacing); + + if ($.isArray(options.get('colorMap'))) { + this.colorMapByIndex = options.get('colorMap'); + this.colorMapByValue = null; + } else { + this.colorMapByIndex = null; + this.colorMapByValue = options.get('colorMap'); + if (this.colorMapByValue && this.colorMapByValue.get === undefined) { + this.colorMapByValue = new RangeMap(this.colorMapByValue); + } + } + this.initTarget(); + }, + + getRegion: function (el, x, y) { + return Math.floor(x / this.totalBarWidth); + }, + + getCurrentRegionFields: function () { + var currentRegion = this.currentRegion; + return { + isNull: this.values[currentRegion] === undefined, + value: this.values[currentRegion], + color: this.calcColor(this.values[currentRegion], currentRegion), + offset: currentRegion + }; + }, + + calcColor: function (value, valuenum) { + var values = this.values, + options = this.options, + colorMapByIndex = this.colorMapByIndex, + colorMapByValue = this.colorMapByValue, + color, newColor; + + if (colorMapByValue && (newColor = colorMapByValue.get(value))) { + color = newColor; + } else if (colorMapByIndex && colorMapByIndex.length > valuenum) { + color = colorMapByIndex[valuenum]; + } else if (values[valuenum] < 0) { + color = options.get('negBarColor'); + } else if (values[valuenum] > 0) { + color = options.get('posBarColor'); + } else { + color = options.get('zeroBarColor'); + } + return color; + }, + + renderRegion: function (valuenum, highlight) { + var values = this.values, + options = this.options, + target = this.target, + canvasHeight, height, halfHeight, + x, y, color; + + canvasHeight = target.pixelHeight; + halfHeight = Math.round(canvasHeight / 2); + + x = valuenum * this.totalBarWidth; + if (values[valuenum] < 0) { + y = halfHeight; + height = halfHeight - 1; + } else if (values[valuenum] > 0) { + y = 0; + height = halfHeight - 1; + } else { + y = halfHeight - 1; + height = 2; + } + color = this.calcColor(values[valuenum], valuenum); + if (color === null) { + return; + } + if (highlight) { + color = this.calcHighlightColor(color, options); + } + return target.drawRect(x, y, this.barWidth - 1, height - 1, color, color); + } + }); + + /** + * Discrete charts + */ + $.fn.sparkline.discrete = discrete = createClass($.fn.sparkline._base, barHighlightMixin, { + type: 'discrete', + + init: function (el, values, options, width, height) { + discrete._super.init.call(this, el, values, options, width, height); + + this.regionShapes = {}; + this.values = values = $.map(values, Number); + this.min = Math.min.apply(Math, values); + this.max = Math.max.apply(Math, values); + this.range = this.max - this.min; + this.width = width = options.get('width') === 'auto' ? values.length * 2 : this.width; + this.interval = Math.floor(width / values.length); + this.itemWidth = width / values.length; + if (options.get('chartRangeMin') !== undefined && (options.get('chartRangeClip') || options.get('chartRangeMin') < this.min)) { + this.min = options.get('chartRangeMin'); + } + if (options.get('chartRangeMax') !== undefined && (options.get('chartRangeClip') || options.get('chartRangeMax') > this.max)) { + this.max = options.get('chartRangeMax'); + } + this.initTarget(); + if (this.target) { + this.lineHeight = options.get('lineHeight') === 'auto' ? Math.round(this.canvasHeight * 0.3) : options.get('lineHeight'); + } + }, + + getRegion: function (el, x, y) { + return Math.floor(x / this.itemWidth); + }, + + getCurrentRegionFields: function () { + var currentRegion = this.currentRegion; + return { + isNull: this.values[currentRegion] === undefined, + value: this.values[currentRegion], + offset: currentRegion + }; + }, + + renderRegion: function (valuenum, highlight) { + var values = this.values, + options = this.options, + min = this.min, + max = this.max, + range = this.range, + interval = this.interval, + target = this.target, + canvasHeight = this.canvasHeight, + lineHeight = this.lineHeight, + pheight = canvasHeight - lineHeight, + ytop, val, color, x; + + val = clipval(values[valuenum], min, max); + x = valuenum * interval; + ytop = Math.round(pheight - pheight * ((val - min) / range)); + color = (options.get('thresholdColor') && val < options.get('thresholdValue')) ? options.get('thresholdColor') : options.get('lineColor'); + if (highlight) { + color = this.calcHighlightColor(color, options); + } + return target.drawLine(x, ytop, x, ytop + lineHeight, color); + } + }); + + /** + * Bullet charts + */ + $.fn.sparkline.bullet = bullet = createClass($.fn.sparkline._base, { + type: 'bullet', + + init: function (el, values, options, width, height) { + var min, max, vals; + bullet._super.init.call(this, el, values, options, width, height); + + // values: target, performance, range1, range2, range3 + this.values = values = normalizeValues(values); + // target or performance could be null + vals = values.slice(); + vals[0] = vals[0] === null ? vals[2] : vals[0]; + vals[1] = values[1] === null ? vals[2] : vals[1]; + min = Math.min.apply(Math, values); + max = Math.max.apply(Math, values); + if (options.get('base') === undefined) { + min = min < 0 ? min : 0; + } else { + min = options.get('base'); + } + this.min = min; + this.max = max; + this.range = max - min; + this.shapes = {}; + this.valueShapes = {}; + this.regiondata = {}; + this.width = width = options.get('width') === 'auto' ? '4.0em' : width; + this.target = this.$el.simpledraw(width, height, options.get('composite')); + if (!values.length) { + this.disabled = true; + } + this.initTarget(); + }, + + getRegion: function (el, x, y) { + var shapeid = this.target.getShapeAt(el, x, y); + return (shapeid !== undefined && this.shapes[shapeid] !== undefined) ? this.shapes[shapeid] : undefined; + }, + + getCurrentRegionFields: function () { + var currentRegion = this.currentRegion; + return { + fieldkey: currentRegion.substr(0, 1), + value: this.values[currentRegion.substr(1)], + region: currentRegion + }; + }, + + changeHighlight: function (highlight) { + var currentRegion = this.currentRegion, + shapeid = this.valueShapes[currentRegion], + shape; + delete this.shapes[shapeid]; + switch (currentRegion.substr(0, 1)) { + case 'r': + shape = this.renderRange(currentRegion.substr(1), highlight); + break; + case 'p': + shape = this.renderPerformance(highlight); + break; + case 't': + shape = this.renderTarget(highlight); + break; + } + this.valueShapes[currentRegion] = shape.id; + this.shapes[shape.id] = currentRegion; + this.target.replaceWithShape(shapeid, shape); + }, + + renderRange: function (rn, highlight) { + var rangeval = this.values[rn], + rangewidth = Math.round(this.canvasWidth * ((rangeval - this.min) / this.range)), + color = this.options.get('rangeColors')[rn - 2]; + if (highlight) { + color = this.calcHighlightColor(color, this.options); + } + return this.target.drawRect(0, 0, rangewidth - 1, this.canvasHeight - 1, color, color); + }, + + renderPerformance: function (highlight) { + var perfval = this.values[1], + perfwidth = Math.round(this.canvasWidth * ((perfval - this.min) / this.range)), + color = this.options.get('performanceColor'); + if (highlight) { + color = this.calcHighlightColor(color, this.options); + } + return this.target.drawRect(0, Math.round(this.canvasHeight * 0.3), perfwidth - 1, + Math.round(this.canvasHeight * 0.4) - 1, color, color); + }, + + renderTarget: function (highlight) { + var targetval = this.values[0], + x = Math.round(this.canvasWidth * ((targetval - this.min) / this.range) - (this.options.get('targetWidth') / 2)), + targettop = Math.round(this.canvasHeight * 0.10), + targetheight = this.canvasHeight - (targettop * 2), + color = this.options.get('targetColor'); + if (highlight) { + color = this.calcHighlightColor(color, this.options); + } + return this.target.drawRect(x, targettop, this.options.get('targetWidth') - 1, targetheight - 1, color, color); + }, + + render: function () { + var vlen = this.values.length, + target = this.target, + i, shape; + if (!bullet._super.render.call(this)) { + return; + } + for (i = 2; i < vlen; i++) { + shape = this.renderRange(i).append(); + this.shapes[shape.id] = 'r' + i; + this.valueShapes['r' + i] = shape.id; + } + if (this.values[1] !== null) { + shape = this.renderPerformance().append(); + this.shapes[shape.id] = 'p1'; + this.valueShapes.p1 = shape.id; + } + if (this.values[0] !== null) { + shape = this.renderTarget().append(); + this.shapes[shape.id] = 't0'; + this.valueShapes.t0 = shape.id; + } + target.render(); + } + }); + + /** + * Pie charts + */ + $.fn.sparkline.pie = pie = createClass($.fn.sparkline._base, { + type: 'pie', + + init: function (el, values, options, width, height) { + var total = 0, i; + + pie._super.init.call(this, el, values, options, width, height); + + this.shapes = {}; // map shape ids to value offsets + this.valueShapes = {}; // maps value offsets to shape ids + this.values = values = $.map(values, Number); + + if (options.get('width') === 'auto') { + this.width = this.height; + } + + if (values.length > 0) { + for (i = values.length; i--;) { + total += values[i]; + } + } + this.total = total; + this.initTarget(); + this.radius = Math.floor(Math.min(this.canvasWidth, this.canvasHeight) / 2); + }, + + getRegion: function (el, x, y) { + var shapeid = this.target.getShapeAt(el, x, y); + return (shapeid !== undefined && this.shapes[shapeid] !== undefined) ? this.shapes[shapeid] : undefined; + }, + + getCurrentRegionFields: function () { + var currentRegion = this.currentRegion; + return { + isNull: this.values[currentRegion] === undefined, + value: this.values[currentRegion], + percent: this.values[currentRegion] / this.total * 100, + color: this.options.get('sliceColors')[currentRegion % this.options.get('sliceColors').length], + offset: currentRegion + }; + }, + + changeHighlight: function (highlight) { + var currentRegion = this.currentRegion, + newslice = this.renderSlice(currentRegion, highlight), + shapeid = this.valueShapes[currentRegion]; + delete this.shapes[shapeid]; + this.target.replaceWithShape(shapeid, newslice); + this.valueShapes[currentRegion] = newslice.id; + this.shapes[newslice.id] = currentRegion; + }, + + renderSlice: function (valuenum, highlight) { + var target = this.target, + options = this.options, + radius = this.radius, + borderWidth = options.get('borderWidth'), + offset = options.get('offset'), + circle = 2 * Math.PI, + values = this.values, + total = this.total, + next = offset ? (2*Math.PI)*(offset/360) : 0, + start, end, i, vlen, color; + + vlen = values.length; + for (i = 0; i < vlen; i++) { + start = next; + end = next; + if (total > 0) { // avoid divide by zero + end = next + (circle * (values[i] / total)); + } + if (valuenum === i) { + color = options.get('sliceColors')[i % options.get('sliceColors').length]; + if (highlight) { + color = this.calcHighlightColor(color, options); + } + + return target.drawPieSlice(radius, radius, radius - borderWidth, start, end, undefined, color); + } + next = end; + } + }, + + render: function () { + var target = this.target, + values = this.values, + options = this.options, + radius = this.radius, + borderWidth = options.get('borderWidth'), + shape, i; + + if (!pie._super.render.call(this)) { + return; + } + if (borderWidth) { + target.drawCircle(radius, radius, Math.floor(radius - (borderWidth / 2)), + options.get('borderColor'), undefined, borderWidth).append(); + } + for (i = values.length; i--;) { + if (values[i]) { // don't render zero values + shape = this.renderSlice(i).append(); + this.valueShapes[i] = shape.id; // store just the shapeid + this.shapes[shape.id] = i; + } + } + target.render(); + } + }); + + /** + * Box plots + */ + $.fn.sparkline.box = box = createClass($.fn.sparkline._base, { + type: 'box', + + init: function (el, values, options, width, height) { + box._super.init.call(this, el, values, options, width, height); + this.values = $.map(values, Number); + this.width = options.get('width') === 'auto' ? '4.0em' : width; + this.initTarget(); + if (!this.values.length) { + this.disabled = 1; + } + }, + + /** + * Simulate a single region + */ + getRegion: function () { + return 1; + }, + + getCurrentRegionFields: function () { + var result = [ + { field: 'lq', value: this.quartiles[0] }, + { field: 'med', value: this.quartiles[1] }, + { field: 'uq', value: this.quartiles[2] } + ]; + if (this.loutlier !== undefined) { + result.push({ field: 'lo', value: this.loutlier}); + } + if (this.routlier !== undefined) { + result.push({ field: 'ro', value: this.routlier}); + } + if (this.lwhisker !== undefined) { + result.push({ field: 'lw', value: this.lwhisker}); + } + if (this.rwhisker !== undefined) { + result.push({ field: 'rw', value: this.rwhisker}); + } + return result; + }, + + render: function () { + var target = this.target, + values = this.values, + vlen = values.length, + options = this.options, + canvasWidth = this.canvasWidth, + canvasHeight = this.canvasHeight, + minValue = options.get('chartRangeMin') === undefined ? Math.min.apply(Math, values) : options.get('chartRangeMin'), + maxValue = options.get('chartRangeMax') === undefined ? Math.max.apply(Math, values) : options.get('chartRangeMax'), + canvasLeft = 0, + lwhisker, loutlier, iqr, q1, q2, q3, rwhisker, routlier, i, + size, unitSize; + + if (!box._super.render.call(this)) { + return; + } + + if (options.get('raw')) { + if (options.get('showOutliers') && values.length > 5) { + loutlier = values[0]; + lwhisker = values[1]; + q1 = values[2]; + q2 = values[3]; + q3 = values[4]; + rwhisker = values[5]; + routlier = values[6]; + } else { + lwhisker = values[0]; + q1 = values[1]; + q2 = values[2]; + q3 = values[3]; + rwhisker = values[4]; + } + } else { + values.sort(function (a, b) { return a - b; }); + q1 = quartile(values, 1); + q2 = quartile(values, 2); + q3 = quartile(values, 3); + iqr = q3 - q1; + if (options.get('showOutliers')) { + lwhisker = rwhisker = undefined; + for (i = 0; i < vlen; i++) { + if (lwhisker === undefined && values[i] > q1 - (iqr * options.get('outlierIQR'))) { + lwhisker = values[i]; + } + if (values[i] < q3 + (iqr * options.get('outlierIQR'))) { + rwhisker = values[i]; + } + } + loutlier = values[0]; + routlier = values[vlen - 1]; + } else { + lwhisker = values[0]; + rwhisker = values[vlen - 1]; + } + } + this.quartiles = [q1, q2, q3]; + this.lwhisker = lwhisker; + this.rwhisker = rwhisker; + this.loutlier = loutlier; + this.routlier = routlier; + + unitSize = canvasWidth / (maxValue - minValue + 1); + if (options.get('showOutliers')) { + canvasLeft = Math.ceil(options.get('spotRadius')); + canvasWidth -= 2 * Math.ceil(options.get('spotRadius')); + unitSize = canvasWidth / (maxValue - minValue + 1); + if (loutlier < lwhisker) { + target.drawCircle((loutlier - minValue) * unitSize + canvasLeft, + canvasHeight / 2, + options.get('spotRadius'), + options.get('outlierLineColor'), + options.get('outlierFillColor')).append(); + } + if (routlier > rwhisker) { + target.drawCircle((routlier - minValue) * unitSize + canvasLeft, + canvasHeight / 2, + options.get('spotRadius'), + options.get('outlierLineColor'), + options.get('outlierFillColor')).append(); + } + } + + // box + target.drawRect( + Math.round((q1 - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight * 0.1), + Math.round((q3 - q1) * unitSize), + Math.round(canvasHeight * 0.8), + options.get('boxLineColor'), + options.get('boxFillColor')).append(); + // left whisker + target.drawLine( + Math.round((lwhisker - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight / 2), + Math.round((q1 - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight / 2), + options.get('lineColor')).append(); + target.drawLine( + Math.round((lwhisker - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight / 4), + Math.round((lwhisker - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight - canvasHeight / 4), + options.get('whiskerColor')).append(); + // right whisker + target.drawLine(Math.round((rwhisker - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight / 2), + Math.round((q3 - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight / 2), + options.get('lineColor')).append(); + target.drawLine( + Math.round((rwhisker - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight / 4), + Math.round((rwhisker - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight - canvasHeight / 4), + options.get('whiskerColor')).append(); + // median line + target.drawLine( + Math.round((q2 - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight * 0.1), + Math.round((q2 - minValue) * unitSize + canvasLeft), + Math.round(canvasHeight * 0.9), + options.get('medianColor')).append(); + if (options.get('target')) { + size = Math.ceil(options.get('spotRadius')); + target.drawLine( + Math.round((options.get('target') - minValue) * unitSize + canvasLeft), + Math.round((canvasHeight / 2) - size), + Math.round((options.get('target') - minValue) * unitSize + canvasLeft), + Math.round((canvasHeight / 2) + size), + options.get('targetColor')).append(); + target.drawLine( + Math.round((options.get('target') - minValue) * unitSize + canvasLeft - size), + Math.round(canvasHeight / 2), + Math.round((options.get('target') - minValue) * unitSize + canvasLeft + size), + Math.round(canvasHeight / 2), + options.get('targetColor')).append(); + } + target.render(); + } + }); + + // Setup a very simple "virtual canvas" to make drawing the few shapes we need easier + // This is accessible as $(foo).simpledraw() + + VShape = createClass({ + init: function (target, id, type, args) { + this.target = target; + this.id = id; + this.type = type; + this.args = args; + }, + append: function () { + this.target.appendShape(this); + return this; + } + }); + + VCanvas_base = createClass({ + _pxregex: /(\d+)(px)?\s*$/i, + + init: function (width, height, target) { + if (!width) { + return; + } + this.width = width; + this.height = height; + this.target = target; + this.lastShapeId = null; + if (target[0]) { + target = target[0]; + } + $.data(target, '_jqs_vcanvas', this); + }, + + drawLine: function (x1, y1, x2, y2, lineColor, lineWidth) { + return this.drawShape([[x1, y1], [x2, y2]], lineColor, lineWidth); + }, + + drawShape: function (path, lineColor, fillColor, lineWidth) { + return this._genShape('Shape', [path, lineColor, fillColor, lineWidth]); + }, + + drawCircle: function (x, y, radius, lineColor, fillColor, lineWidth) { + return this._genShape('Circle', [x, y, radius, lineColor, fillColor, lineWidth]); + }, + + drawPieSlice: function (x, y, radius, startAngle, endAngle, lineColor, fillColor) { + return this._genShape('PieSlice', [x, y, radius, startAngle, endAngle, lineColor, fillColor]); + }, + + drawRect: function (x, y, width, height, lineColor, fillColor) { + return this._genShape('Rect', [x, y, width, height, lineColor, fillColor]); + }, + + getElement: function () { + return this.canvas; + }, + + /** + * Return the most recently inserted shape id + */ + getLastShapeId: function () { + return this.lastShapeId; + }, + + /** + * Clear and reset the canvas + */ + reset: function () { + alert('reset not implemented'); + }, + + _insert: function (el, target) { + $(target).html(el); + }, + + /** + * Calculate the pixel dimensions of the canvas + */ + _calculatePixelDims: function (width, height, canvas) { + // XXX This should probably be a configurable option + var match; + match = this._pxregex.exec(height); + if (match) { + this.pixelHeight = match[1]; + } else { + this.pixelHeight = $(canvas).height(); + } + match = this._pxregex.exec(width); + if (match) { + this.pixelWidth = match[1]; + } else { + this.pixelWidth = $(canvas).width(); + } + }, + + /** + * Generate a shape object and id for later rendering + */ + _genShape: function (shapetype, shapeargs) { + var id = shapeCount++; + shapeargs.unshift(id); + return new VShape(this, id, shapetype, shapeargs); + }, + + /** + * Add a shape to the end of the render queue + */ + appendShape: function (shape) { + alert('appendShape not implemented'); + }, + + /** + * Replace one shape with another + */ + replaceWithShape: function (shapeid, shape) { + alert('replaceWithShape not implemented'); + }, + + /** + * Insert one shape after another in the render queue + */ + insertAfterShape: function (shapeid, shape) { + alert('insertAfterShape not implemented'); + }, + + /** + * Remove a shape from the queue + */ + removeShapeId: function (shapeid) { + alert('removeShapeId not implemented'); + }, + + /** + * Find a shape at the specified x/y co-ordinates + */ + getShapeAt: function (el, x, y) { + alert('getShapeAt not implemented'); + }, + + /** + * Render all queued shapes onto the canvas + */ + render: function () { + alert('render not implemented'); + } + }); + + VCanvas_canvas = createClass(VCanvas_base, { + init: function (width, height, target, interact) { + VCanvas_canvas._super.init.call(this, width, height, target); + this.canvas = document.createElement('canvas'); + if (target[0]) { + target = target[0]; + } + $.data(target, '_jqs_vcanvas', this); + $(this.canvas).css({ display: 'inline-block', width: width, height: height, verticalAlign: 'top' }); + this._insert(this.canvas, target); + this._calculatePixelDims(width, height, this.canvas); + this.canvas.width = this.pixelWidth; + this.canvas.height = this.pixelHeight; + this.interact = interact; + this.shapes = {}; + this.shapeseq = []; + this.currentTargetShapeId = undefined; + $(this.canvas).css({width: this.pixelWidth, height: this.pixelHeight}); + }, + + _getContext: function (lineColor, fillColor, lineWidth) { + var context = this.canvas.getContext('2d'); + if (lineColor !== undefined) { + context.strokeStyle = lineColor; + } + context.lineWidth = lineWidth === undefined ? 1 : lineWidth; + if (fillColor !== undefined) { + context.fillStyle = fillColor; + } + return context; + }, + + reset: function () { + var context = this._getContext(); + context.clearRect(0, 0, this.pixelWidth, this.pixelHeight); + this.shapes = {}; + this.shapeseq = []; + this.currentTargetShapeId = undefined; + }, + + _drawShape: function (shapeid, path, lineColor, fillColor, lineWidth) { + var context = this._getContext(lineColor, fillColor, lineWidth), + i, plen; + context.beginPath(); + context.moveTo(path[0][0] + 0.5, path[0][1] + 0.5); + for (i = 1, plen = path.length; i < plen; i++) { + context.lineTo(path[i][0] + 0.5, path[i][1] + 0.5); // the 0.5 offset gives us crisp pixel-width lines + } + if (lineColor !== undefined) { + context.stroke(); + } + if (fillColor !== undefined) { + context.fill(); + } + if (this.targetX !== undefined && this.targetY !== undefined && + context.isPointInPath(this.targetX, this.targetY)) { + this.currentTargetShapeId = shapeid; + } + }, + + _drawCircle: function (shapeid, x, y, radius, lineColor, fillColor, lineWidth) { + var context = this._getContext(lineColor, fillColor, lineWidth); + context.beginPath(); + context.arc(x, y, radius, 0, 2 * Math.PI, false); + if (this.targetX !== undefined && this.targetY !== undefined && + context.isPointInPath(this.targetX, this.targetY)) { + this.currentTargetShapeId = shapeid; + } + if (lineColor !== undefined) { + context.stroke(); + } + if (fillColor !== undefined) { + context.fill(); + } + }, + + _drawPieSlice: function (shapeid, x, y, radius, startAngle, endAngle, lineColor, fillColor) { + var context = this._getContext(lineColor, fillColor); + context.beginPath(); + context.moveTo(x, y); + context.arc(x, y, radius, startAngle, endAngle, false); + context.lineTo(x, y); + context.closePath(); + if (lineColor !== undefined) { + context.stroke(); + } + if (fillColor) { + context.fill(); + } + if (this.targetX !== undefined && this.targetY !== undefined && + context.isPointInPath(this.targetX, this.targetY)) { + this.currentTargetShapeId = shapeid; + } + }, + + _drawRect: function (shapeid, x, y, width, height, lineColor, fillColor) { + return this._drawShape(shapeid, [[x, y], [x + width, y], [x + width, y + height], [x, y + height], [x, y]], lineColor, fillColor); + }, + + appendShape: function (shape) { + this.shapes[shape.id] = shape; + this.shapeseq.push(shape.id); + this.lastShapeId = shape.id; + return shape.id; + }, + + replaceWithShape: function (shapeid, shape) { + var shapeseq = this.shapeseq, + i; + this.shapes[shape.id] = shape; + for (i = shapeseq.length; i--;) { + if (shapeseq[i] == shapeid) { + shapeseq[i] = shape.id; + } + } + delete this.shapes[shapeid]; + }, + + replaceWithShapes: function (shapeids, shapes) { + var shapeseq = this.shapeseq, + shapemap = {}, + sid, i, first; + + for (i = shapeids.length; i--;) { + shapemap[shapeids[i]] = true; + } + for (i = shapeseq.length; i--;) { + sid = shapeseq[i]; + if (shapemap[sid]) { + shapeseq.splice(i, 1); + delete this.shapes[sid]; + first = i; + } + } + for (i = shapes.length; i--;) { + shapeseq.splice(first, 0, shapes[i].id); + this.shapes[shapes[i].id] = shapes[i]; + } + + }, + + insertAfterShape: function (shapeid, shape) { + var shapeseq = this.shapeseq, + i; + for (i = shapeseq.length; i--;) { + if (shapeseq[i] === shapeid) { + shapeseq.splice(i + 1, 0, shape.id); + this.shapes[shape.id] = shape; + return; + } + } + }, + + removeShapeId: function (shapeid) { + var shapeseq = this.shapeseq, + i; + for (i = shapeseq.length; i--;) { + if (shapeseq[i] === shapeid) { + shapeseq.splice(i, 1); + break; + } + } + delete this.shapes[shapeid]; + }, + + getShapeAt: function (el, x, y) { + this.targetX = x; + this.targetY = y; + this.render(); + return this.currentTargetShapeId; + }, + + render: function () { + var shapeseq = this.shapeseq, + shapes = this.shapes, + shapeCount = shapeseq.length, + context = this._getContext(), + shapeid, shape, i; + context.clearRect(0, 0, this.pixelWidth, this.pixelHeight); + for (i = 0; i < shapeCount; i++) { + shapeid = shapeseq[i]; + shape = shapes[shapeid]; + this['_draw' + shape.type].apply(this, shape.args); + } + if (!this.interact) { + // not interactive so no need to keep the shapes array + this.shapes = {}; + this.shapeseq = []; + } + } + + }); + + VCanvas_vml = createClass(VCanvas_base, { + init: function (width, height, target) { + var groupel; + VCanvas_vml._super.init.call(this, width, height, target); + if (target[0]) { + target = target[0]; + } + $.data(target, '_jqs_vcanvas', this); + this.canvas = document.createElement('span'); + $(this.canvas).css({ display: 'inline-block', position: 'relative', overflow: 'hidden', width: width, height: height, margin: '0px', padding: '0px', verticalAlign: 'top'}); + this._insert(this.canvas, target); + this._calculatePixelDims(width, height, this.canvas); + this.canvas.width = this.pixelWidth; + this.canvas.height = this.pixelHeight; + groupel = ''; + this.canvas.insertAdjacentHTML('beforeEnd', groupel); + this.group = $(this.canvas).children()[0]; + this.rendered = false; + this.prerender = ''; + }, + + _drawShape: function (shapeid, path, lineColor, fillColor, lineWidth) { + var vpath = [], + initial, stroke, fill, closed, vel, plen, i; + for (i = 0, plen = path.length; i < plen; i++) { + vpath[i] = '' + (path[i][0]) + ',' + (path[i][1]); + } + initial = vpath.splice(0, 1); + lineWidth = lineWidth === undefined ? 1 : lineWidth; + stroke = lineColor === undefined ? ' stroked="false" ' : ' strokeWeight="' + lineWidth + 'px" strokeColor="' + lineColor + '" '; + fill = fillColor === undefined ? ' filled="false"' : ' fillColor="' + fillColor + '" filled="true" '; + closed = vpath[0] === vpath[vpath.length - 1] ? 'x ' : ''; + vel = '' + + ' '; + return vel; + }, + + _drawCircle: function (shapeid, x, y, radius, lineColor, fillColor, lineWidth) { + var stroke, fill, vel; + x -= radius; + y -= radius; + stroke = lineColor === undefined ? ' stroked="false" ' : ' strokeWeight="' + lineWidth + 'px" strokeColor="' + lineColor + '" '; + fill = fillColor === undefined ? ' filled="false"' : ' fillColor="' + fillColor + '" filled="true" '; + vel = ''; + return vel; + + }, + + _drawPieSlice: function (shapeid, x, y, radius, startAngle, endAngle, lineColor, fillColor) { + var vpath, startx, starty, endx, endy, stroke, fill, vel; + if (startAngle === endAngle) { + return ''; // VML seems to have problem when start angle equals end angle. + } + if ((endAngle - startAngle) === (2 * Math.PI)) { + startAngle = 0.0; // VML seems to have a problem when drawing a full circle that doesn't start 0 + endAngle = (2 * Math.PI); + } + + startx = x + Math.round(Math.cos(startAngle) * radius); + starty = y + Math.round(Math.sin(startAngle) * radius); + endx = x + Math.round(Math.cos(endAngle) * radius); + endy = y + Math.round(Math.sin(endAngle) * radius); + + if (startx === endx && starty === endy) { + if ((endAngle - startAngle) < Math.PI) { + // Prevent very small slices from being mistaken as a whole pie + return ''; + } + // essentially going to be the entire circle, so ignore startAngle + startx = endx = x + radius; + starty = endy = y; + } + + if (startx === endx && starty === endy && (endAngle - startAngle) < Math.PI) { + return ''; + } + + vpath = [x - radius, y - radius, x + radius, y + radius, startx, starty, endx, endy]; + stroke = lineColor === undefined ? ' stroked="false" ' : ' strokeWeight="1px" strokeColor="' + lineColor + '" '; + fill = fillColor === undefined ? ' filled="false"' : ' fillColor="' + fillColor + '" filled="true" '; + vel = '' + + ' '; + return vel; + }, + + _drawRect: function (shapeid, x, y, width, height, lineColor, fillColor) { + return this._drawShape(shapeid, [[x, y], [x, y + height], [x + width, y + height], [x + width, y], [x, y]], lineColor, fillColor); + }, + + reset: function () { + this.group.innerHTML = ''; + }, + + appendShape: function (shape) { + var vel = this['_draw' + shape.type].apply(this, shape.args); + if (this.rendered) { + this.group.insertAdjacentHTML('beforeEnd', vel); + } else { + this.prerender += vel; + } + this.lastShapeId = shape.id; + return shape.id; + }, + + replaceWithShape: function (shapeid, shape) { + var existing = $('#jqsshape' + shapeid), + vel = this['_draw' + shape.type].apply(this, shape.args); + existing[0].outerHTML = vel; + }, + + replaceWithShapes: function (shapeids, shapes) { + // replace the first shapeid with all the new shapes then toast the remaining old shapes + var existing = $('#jqsshape' + shapeids[0]), + replace = '', + slen = shapes.length, + i; + for (i = 0; i < slen; i++) { + replace += this['_draw' + shapes[i].type].apply(this, shapes[i].args); + } + existing[0].outerHTML = replace; + for (i = 1; i < shapeids.length; i++) { + $('#jqsshape' + shapeids[i]).remove(); + } + }, + + insertAfterShape: function (shapeid, shape) { + var existing = $('#jqsshape' + shapeid), + vel = this['_draw' + shape.type].apply(this, shape.args); + existing[0].insertAdjacentHTML('afterEnd', vel); + }, + + removeShapeId: function (shapeid) { + var existing = $('#jqsshape' + shapeid); + this.group.removeChild(existing[0]); + }, + + getShapeAt: function (el, x, y) { + var shapeid = el.id.substr(8); + return shapeid; + }, + + render: function () { + if (!this.rendered) { + // batch the intial render into a single repaint + this.group.innerHTML = this.prerender; + this.rendered = true; + } + } + }); + +}))}(document, Math)); \ No newline at end of file diff --git a/static/maps/libs/jquery.sparklines.js.map b/static/maps/libs/jquery.sparklines.js.map new file mode 100644 index 00000000000..54f300148cb --- /dev/null +++ b/static/maps/libs/jquery.sparklines.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/templates/spark_base.mako b/templates/spark_base.mako new file mode 100644 index 00000000000..da4410f1056 --- /dev/null +++ b/templates/spark_base.mako @@ -0,0 +1,27 @@ +<%def name="jqs_style()"> + + + +<%def name="make_sparkline(id, data, sparktype, length)"> + <% + color = '●' + if sparktype == "bar": + tooltip = color + '{{value}} ' + length + '' + else: + tooltip = color + '{{prefix}}{{y}} ' + length + '{{suffix}}' + %> + + \ No newline at end of file From 82456bb1347a054050789d02a4b5a03bad6f8bfe Mon Sep 17 00:00:00 2001 From: Airistotal Date: Tue, 16 Jun 2015 15:26:49 -0500 Subject: [PATCH 02/68] Apply Patch --- .../webapps/reports/controllers/jobs.py | 254 +++++++++++++++++- templates/base.mako | 1 + .../webapps/reports/jobs_errors_per_tool.mako | 13 +- .../webapps/reports/jobs_per_month_all.mako | 5 + .../reports/jobs_per_month_in_error.mako | 5 + templates/webapps/reports/jobs_per_tool.mako | 14 +- templates/webapps/reports/jobs_per_user.mako | 12 +- .../reports/jobs_specified_month_all.mako | 5 + .../jobs_specified_month_in_error.mako | 9 +- .../webapps/reports/jobs_tool_per_month.mako | 10 +- .../webapps/reports/jobs_user_per_month.mako | 12 +- 11 files changed, 318 insertions(+), 22 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index de3edcb1ead..848d38829f0 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -1,3 +1,4 @@ +from __future__ import print_function import calendar from collections import namedtuple from datetime import datetime, date, timedelta @@ -7,6 +8,7 @@ from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) +import re import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder @@ -271,6 +273,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): month_label = start_date.strftime( "%B" ) year_label = start_date.strftime( "%Y" ) + # Use to make the page table month_jobs = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id, @@ -280,13 +283,32 @@ class Jobs( BaseUIController, ReportQueryBuilder ): group_by=[ 'date' ], order_by=[ _order ] ) + # Use to make trendline + all_jobs = sa.select( ( model.Job.table.c.create_time.label('date'), model.Job.table.c.id.label('id') ), + whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id, + model.Job.table.c.create_time >= start_date, + model.Job.table.c.create_time < end_date ) ) + + trend = [0] * 24 jobs = [] for row in month_jobs.execute(): - jobs.append( ( row.date.strftime( "%A" ), - row.date.strftime( "%d" ), + trend = [0] * 24 + + row_dayname = row.date.strftime( "%A" ) + row_day = row.date.strftime( "%d" ) + + for job in all_jobs.execute(): + if row_day == job.date.strftime( "%d" ): + hour = int( job.date.strftime( "%-H" ) ) - 1 + trend[hour] += 1 + + jobs.append( ( row_dayname, + row_day, row.total_jobs, - row.date + row.date, + trend ) ) + return trans.fill_template( '/webapps/reports/jobs_specified_month_all.mako', order=order, arrow=arrow, @@ -334,12 +356,33 @@ class Jobs( BaseUIController, ReportQueryBuilder ): group_by=[ 'date' ], order_by=[ _order ] ) + # Use to make trendline + all_jobs_in_error = sa.select( ( model.Job.table.c.create_time.label('date'), model.Job.table.c.id.label('id') ), + whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id, + model.Job.table.c.state == 'error', + model.Job.table.c.create_time >= start_date, + model.Job.table.c.create_time < end_date ) ) + + trend = [0] * 24 jobs = [] for row in month_jobs_in_error.execute(): - jobs.append( ( row.date.strftime( "%A" ), - row.date, + trend = [0] * 24 + + row_dayname = row.date.strftime( "%A" ) + row_day = row.date.strftime( "%d" ) + + for job in all_jobs_in_error.execute(): + if row_day == job.date.strftime( "%d" ): + hour = int( job.date.strftime( "%-H" ) ) - 1 + trend[hour] += 1 + + jobs.append( ( row_dayname, + row_day, row.total_jobs, - row.date.strftime( "%d" ) ) ) + row.date, + trend + ) ) + return trans.fill_template( '/webapps/reports/jobs_specified_month_in_error.mako', order=order, arrow=arrow, @@ -369,26 +412,52 @@ class Jobs( BaseUIController, ReportQueryBuilder ): # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) + # Use to make the page table jobs_by_month = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), - sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), + sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=model.Job.table.c.user_id != monitor_user_id, from_obj=[ model.Job.table ], group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ _order ] ) + # Use to make sparkline + all_jobs = sa.select( ( self.select_month(model.Job.table.c.create_time).label('date'), model.Job.table.c.id.label('id') ) ) + + trends = dict() + for job in all_jobs.execute(): + job_day = int(job.date.strftime("%-d")) - 1 + job_month = int(job.date.strftime("%-m")) + job_month_name = job.date.strftime("%B") + job_year = job.date.strftime("%Y") + key = str( job_month_name + job_year) + + try: + trends[key][job_day] += 1 + except KeyError: + job_year = int(job_year) + wday, day_range = calendar.monthrange(job_year, job_month) + trends[key] = [0] * day_range + trends[key][job_day] += 1 + jobs = [] for row in jobs_by_month.execute(): + month = int(row.date.strftime("%-m")) + month_name = row.date.strftime("%B") + year = int(row.date.strftime("%Y")) + wday, day_range = calendar.monthrange(year, month) + jobs.append( ( row.date.strftime( "%Y-%m" ), row.total_jobs, - row.date.strftime( "%B" ), - row.date.strftime( "%y" ) + month_name, + year ) ) return trans.fill_template( '/webapps/reports/jobs_per_month_all.mako', order=order, arrow=arrow, sort_id=sort_id, + trends=trends, jobs=jobs, is_user_jobs_only=monitor_user_id, message=message ) @@ -411,6 +480,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) + # Use to make the page table jobs_in_error_by_month = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.state == 'error', @@ -419,12 +489,40 @@ class Jobs( BaseUIController, ReportQueryBuilder ): group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ _order ] ) + # Use to make trendline + all_jobs = sa.select( ( self.select_month(model.Job.table.c.create_time).label('date'), model.Job.table.c.id.label('id') ), + whereclause=sa.and_( model.Job.table.c.state == 'error', + model.Job.table.c.user_id != monitor_user_id )) + + trends = dict() + for job in all_jobs.execute(): + job_day = int(job.date.strftime("%-d")) - 1 + job_month = int(job.date.strftime("%-m")) + job_month_name = job.date.strftime("%B") + job_year = job.date.strftime("%Y") + key = str( job_month_name + job_year) + + try: + trends[key][job_day] += 1 + except KeyError: + job_year = int(job_year) + wday, day_range = calendar.monthrange(job_year, job_month) + trends[key] = [0] * day_range + trends[key][job_day] += 1 + jobs = [] for row in jobs_in_error_by_month.execute(): - jobs.append( ( row.date.strftime( "%Y-%m" ), - row.total_jobs, - row.date.strftime( "%B" ), - row.date.strftime( "%y" ) ) ) + month = int(row.date.strftime("%-m")) + month_name = row.date.strftime("%B") + year = int(row.date.strftime("%Y")) + wday, day_range = calendar.monthrange(year, month) + + jobs.append( ( + row.date.strftime( "%Y-%m" ), + row.total_jobs, + month_name, + year + ) ) return trans.fill_template( '/webapps/reports/jobs_per_month_in_error.mako', order=order, arrow=arrow, @@ -443,6 +541,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order + day_limit = 50 jobs = [] jobs_per_user = sa.select( ( model.User.table.c.email.label( 'user_email' ), @@ -450,6 +549,28 @@ class Jobs( BaseUIController, ReportQueryBuilder ): from_obj=[ sa.outerjoin( model.Job.table, model.User.table ) ], group_by=[ 'user_email' ], order_by=[ _order ] ) + + all_jobs_per_user = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), + model.Job.table.c.id.label( 'id' ), + model.User.table.c.email.label( 'user_email' ) ), + from_obj=[ sa.outerjoin( model.Job.table, model.User.table ) ] ) + + currday = datetime.today().date() + trends = dict() + for job in all_jobs_per_user.execute(): + curr_user = re.sub(r'\W+', '', job.user_email) + try: + day = currday - job.date + day = day.days + if day < day_limit: + trends[curr_user][day] += 1 + except KeyError: + trends[curr_user] = [0] * day_limit + day = currday - job.date + day = day.days + if day < day_limit: + trends[curr_user][day] += 1 + for row in jobs_per_user.execute(): if ( row.user_email is None ): jobs.append( ( 'Anonymous', @@ -459,10 +580,13 @@ class Jobs( BaseUIController, ReportQueryBuilder ): else: jobs.append( ( row.user_email, row.total_jobs ) ) + return trans.fill_template( '/webapps/reports/jobs_per_user.mako', order=order, arrow=arrow, sort_id=sort_id, + day_limit=day_limit, + trends=trends, jobs=jobs, message=message ) @@ -477,6 +601,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order + q = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, @@ -485,6 +610,30 @@ class Jobs( BaseUIController, ReportQueryBuilder ): from_obj=[ sa.join( model.Job.table, model.User.table ) ], group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ _order ] ) + + all_jobs_per_user = sa.select( ( model.Job.table.c.create_time.label( 'date' ), + model.Job.table.c.id.label( 'job_id' ) ), + whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, + model.GalaxySession.table.c.user_id == model.User.table.c.id, + model.User.table.c.email == email), + from_obj=[ sa.join( model.Job.table, model.User.table ) ] ) + + trends = dict() + for job in all_jobs_per_user.execute(): + job_day = int(job.date.strftime("%-d")) - 1 + job_month = int(job.date.strftime("%-m")) + job_month_name = job.date.strftime("%B") + job_year = job.date.strftime("%Y") + key = str( job_month_name + job_year) + + try: + trends[key][job_day] += 1 + except KeyError: + job_year = int(job_year) + wday, day_range = calendar.monthrange(job_year, job_month) + trends[key] = [0] * day_range + trends[key][job_day] += 1 + jobs = [] for row in q.execute(): jobs.append( ( row.date.strftime( "%Y-%m" ), @@ -496,6 +645,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): arrow=arrow, sort_id=sort_id, id=kwd.get('id'), + trends=trends, email=util.sanitize_text( email ), jobs=jobs, message=message ) @@ -510,6 +660,8 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order + day_limit = 50 + # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) @@ -520,13 +672,38 @@ class Jobs( BaseUIController, ReportQueryBuilder ): from_obj=[ model.Job.table ], group_by=[ 'tool_id' ], order_by=[ _order ] ) + + all_jobs_per_tool = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), + model.Job.table.c.id.label( 'id' ), + model.Job.table.c.tool_id.label( 'tool_id' ) ), + from_obj=[ model.Job.table ] ) + + currday = datetime.today().date() + trends = dict() + for job in all_jobs_per_tool.execute(): + curr_tool = re.sub(r'\W+', '', job.tool_id) + try: + day = currday - job.date + day = day.days + if day < day_limit: + trends[curr_tool][day] += 1 + except KeyError: + trends[curr_tool] = [0] * day_limit + day = currday - job.date + day = day.days + if day < day_limit: + trends[curr_tool][day] += 1 + for row in q.execute(): jobs.append( ( row.tool_id, row.total_jobs ) ) + return trans.fill_template( '/webapps/reports/jobs_per_tool.mako', order=order, arrow=arrow, sort_id=sort_id, + day_limit=day_limit, + trends=trends, jobs=jobs, message=message, is_user_jobs_only=monitor_user_id) @@ -545,6 +722,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order + day_limit = 50 # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) @@ -555,6 +733,31 @@ class Jobs( BaseUIController, ReportQueryBuilder ): from_obj=[ model.Job.table ], group_by=[ 'tool_id' ], order_by=[ _order ] ) + + all_jobs_per_tool_errors = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), + model.Job.table.c.id.label( 'id' ), + model.Job.table.c.tool_id.label( 'tool_id' ) ), + whereclause=sa.and_( model.Job.table.c.state == 'error', + model.Job.table.c.user_id != monitor_user_id ), + from_obj=[ model.Job.table ] + ) + + currday = datetime.today().date() + trends = dict() + for job in all_jobs_per_tool_errors.execute(): + curr_tool = re.sub(r'\W+', '', job.tool_id) + try: + day = currday - job.date + day = day.days + if day < day_limit: + trends[curr_tool][day] += 1 + except KeyError: + trends[curr_tool] = [0] * day_limit + day = currday - job.date + day = day.days + if day < day_limit: + trends[curr_tool][day] += 1 + jobs = [] for row in jobs_in_error_per_tool.execute(): jobs.append( ( row.total_jobs, row.tool_id ) ) @@ -562,6 +765,8 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order=order, arrow=arrow, sort_id=sort_id, + day_limit=day_limit, + trends=trends, jobs=jobs, message=message, is_user_jobs_only=monitor_user_id ) @@ -589,6 +794,28 @@ class Jobs( BaseUIController, ReportQueryBuilder ): from_obj=[ model.Job.table ], group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ _order ] ) + + # Use to make sparkline + all_jobs_for_tool = sa.select( ( self.select_month(model.Job.table.c.create_time).label('date'), model.Job.table.c.id.label('id') ), + whereclause=sa.and_( model.Job.table.c.tool_id == tool_id, + model.Job.table.c.user_id != monitor_user_id ), + from_obj=[ model.Job.table ] ) + trends = dict() + for job in all_jobs_for_tool.execute(): + job_day = int(job.date.strftime("%-d")) - 1 + job_month = int(job.date.strftime("%-m")) + job_month_name = job.date.strftime("%B") + job_year = job.date.strftime("%Y") + key = str( job_month_name + job_year) + + try: + trends[key][job_day] += 1 + except KeyError: + job_year = int(job_year) + wday, day_range = calendar.monthrange(job_year, job_month) + trends[key] = [0] * day_range + trends[key][job_day] += 1 + jobs = [] for row in q.execute(): jobs.append( ( row.date.strftime( "%Y-%m" ), @@ -601,6 +828,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): sort_id=sort_id, specified_date=specified_date, tool_id=tool_id, + trends=trends, jobs=jobs, message=message, is_user_jobs_only=monitor_user_id ) diff --git a/templates/base.mako b/templates/base.mako index dba96d2d483..0752855bd95 100644 --- a/templates/base.mako +++ b/templates/base.mako @@ -48,6 +48,7 @@ "libs/jquery/jquery", "libs/jquery/jquery.migrate", "libs/jquery/select2", + "libs/jquery.sparklines", "libs/bootstrap", "libs/underscore", "libs/backbone/backbone", diff --git a/templates/webapps/reports/jobs_errors_per_tool.mako b/templates/webapps/reports/jobs_errors_per_tool.mako index 6977be38960..6ce25222959 100644 --- a/templates/webapps/reports/jobs_errors_per_tool.mako +++ b/templates/webapps/reports/jobs_errors_per_tool.mako @@ -1,18 +1,26 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> +<%! + import re +%> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()}

Jobs In Error Per Tool

-
Click Tool ID to view details. Click error number to view job details.
+
+

Click Tool ID to view details. Click error number to view job details.

+

Graph goes from present to past(${day_limit} days).

+
%if len( jobs ) == 0: @@ -36,6 +44,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = re.sub(r'\W+', '', job[1]) %> %if ctr % 2 == 1: %else: @@ -43,6 +52,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "line", "/ day")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_per_month_all.mako b/templates/webapps/reports/jobs_per_month_all.mako index c8c044e96ae..0b8a08ccdca 100644 --- a/templates/webapps/reports/jobs_per_month_all.mako +++ b/templates/webapps/reports/jobs_per_month_all.mako @@ -1,11 +1,13 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()} @@ -36,6 +38,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = str(job[2]) + str(job[3]) %> %if ctr % 2 == 1: %else: @@ -43,6 +46,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "bar", "/ day")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_per_month_in_error.mako b/templates/webapps/reports/jobs_per_month_in_error.mako index b1eca3b99f1..742fd1e3d79 100644 --- a/templates/webapps/reports/jobs_per_month_in_error.mako +++ b/templates/webapps/reports/jobs_per_month_in_error.mako @@ -1,11 +1,13 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()} @@ -36,6 +38,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = str(job[2]) + str(job[3]) %> %if ctr % 2 == 1: %else: @@ -43,6 +46,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "bar", "/ day")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako index 90a866400d9..e6e31675f31 100644 --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -1,18 +1,25 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> +<%! + import re +%> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()} - +

Jobs Per Tool

-
Click Tool ID to view details
+
+ Click Tool ID to view details. Graph goes from present to past(${day_limit} days). +
There are no jobs in the error state.
${job[1]} ${job[0]}
${job[2]} ${job[3]} ${job[1]}
${job[2]} ${job[3]} ${job[1]}
%if len( jobs ) == 0: @@ -36,6 +43,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = re.sub(r'\W+', '', job[0]) %> %if ctr % 2 == 1: %else: @@ -43,6 +51,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "line", "/ day")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako index 4726ca9f7ab..5770d0063d3 100644 --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -1,18 +1,25 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> +<%! + import re +%> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()}

Jobs Per User

-
Click User to view details.
+
+ Click User to view details. Graph goes from present to past(${day_limit} days). +
There are no jobs.
${job[0]} ${job[1]}
%if len( jobs ) == 0: @@ -29,6 +36,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = re.sub(r'\W+', '', job[0]) %> %if ctr % 2 == 1: %else: @@ -36,6 +44,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "line", "/ day")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_specified_month_all.mako b/templates/webapps/reports/jobs_specified_month_all.mako index 7cfd0b1eaf8..15468ac9bb8 100644 --- a/templates/webapps/reports/jobs_specified_month_all.mako +++ b/templates/webapps/reports/jobs_specified_month_all.mako @@ -1,11 +1,13 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()} @@ -37,6 +39,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = job[1] %> %if ctr % 2 == 1: %else: @@ -45,6 +48,8 @@ ${get_css()} + ${make_sparkline(key, job[4], "bar", "/ hour")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_specified_month_in_error.mako b/templates/webapps/reports/jobs_specified_month_in_error.mako index 3ca44979401..4501ca1bc6e 100644 --- a/templates/webapps/reports/jobs_specified_month_in_error.mako +++ b/templates/webapps/reports/jobs_specified_month_in_error.mako @@ -1,11 +1,13 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()}
@@ -36,14 +38,17 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = job[1] %> %if ctr % 2 == 1:
%else: %endif - - + + + ${make_sparkline(key, job[4], "bar", "/ hour")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_tool_per_month.mako b/templates/webapps/reports/jobs_tool_per_month.mako index 916bfb661f3..8d5eea5ad78 100644 --- a/templates/webapps/reports/jobs_tool_per_month.mako +++ b/templates/webapps/reports/jobs_tool_per_month.mako @@ -1,11 +1,13 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> %if message: ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()} @@ -13,7 +15,10 @@ ${get_css()}

Jobs per month for tool "${tool_id}"

-
Click Jobs to view details
+
+

Click Jobs to view details.

+

Graph goes from first of the month to the last

+
There are no jobs.
${job[0]} ${job[1]}
${job[0]} ${month_label} ${job[1]}, ${year_label} ${job[2]}
${job[0]}${month_label} ${job[3]}, ${year_label}${job[2]}${month_label} ${job[1]}, ${year_label}${job[2]}
%if len( jobs ) == 0: @@ -37,6 +42,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = job[2] + job[3] %> %if ctr % 2 == 1: %else: @@ -44,6 +50,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "line", "/ day")} + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/jobs_user_per_month.mako b/templates/webapps/reports/jobs_user_per_month.mako index 7acbd73b0d5..d18d8c5235c 100644 --- a/templates/webapps/reports/jobs_user_per_month.mako +++ b/templates/webapps/reports/jobs_user_per_month.mako @@ -1,5 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <% from galaxy import util %> @@ -7,7 +8,8 @@ %if message: ${render_msg( message, 'done' )} %endif - + +${jqs_style()} ${get_css()} <% @@ -18,7 +20,10 @@ ${get_css()}

Jobs per month for user "${_email}"

-

Click Total Jobs to see the user's jobs for that month

+

+

Click Total Jobs to see the user's jobs for that month

+

Graph goes from first of the month to the last

+

There are no jobs for tool "${tool_id}"
${job[2]} ${job[3]} ${job[1]}
%if len( jobs ) == 0: @@ -35,6 +40,7 @@ ${get_css()} <% ctr = 0 %> %for job in jobs: + <% key = job[2] + job[3] %> %if ctr % 2 == 1: %else: @@ -42,6 +48,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "line", "/ day")} + <% ctr += 1 %> %endfor From 55eadd41f42fb8ddf9c46a21e5c1e3f8e2fe6d91 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Tue, 16 Jun 2015 15:38:38 -0500 Subject: [PATCH 03/68] Build with grunt --- static/scripts/libs/jquery.sparklines.js | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 static/scripts/libs/jquery.sparklines.js diff --git a/static/scripts/libs/jquery.sparklines.js b/static/scripts/libs/jquery.sparklines.js new file mode 100644 index 00000000000..7254f9a3725 --- /dev/null +++ b/static/scripts/libs/jquery.sparklines.js @@ -0,0 +1,3 @@ +!function(a,b,c){!function(a){"function"==typeof define&&define.amd?define(["jquery"],a):jQuery&&!jQuery.fn.sparkline&&a(jQuery)}(function(d){"use strict";var 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\n"),b=this.options.get("tooltipFormat"),!b)return"";if(d.isArray(b)||(b=[b]),d.isArray(a)||(a=[a]),j=this.options.get("tooltipFormatFieldlist"),k=this.options.get("tooltipFormatFieldlistKey"),j&&k){for(l=[],i=a.length;i--;)m=a[i][k],-1!=(q=d.inArray(m,j))&&(l[q]=a[i]);a=l}for(e=b.length,p=a.length,i=0;e>i;i++)for(o=b[i],"string"==typeof o&&(o=new g(o)),f=o.fclass||"jqsfield",q=0;p>q;q++)a[q].isNull&&r.get("tooltipSkipNull")||(d.extend(a[q],{prefix:r.get("tooltipPrefix"),suffix:r.get("tooltipSuffix")}),h=o.render(a[q],r.get("tooltipValueLookups"),r),t.push('
'+h+"
"));return t.length?s+t.join("\n"):""},getCurrentRegionFields:function(){},calcHighlightColor:function(a,c){var d,e,f,g,i=c.get("highlightColor"),j=c.get("highlightLighten");if(i)return i;if(j&&(d=/^#([0-9a-f])([0-9a-f])([0-9a-f])$/i.exec(a)||/^#([0-9a-f]{2})([0-9a-f]{2})([0-9a-f]{2})$/i.exec(a))){for(f=[],e=4===a.length?16:1,g=0;3>g;g++)f[g]=h(b.round(parseInt(d[g+1],16)*e*j),0,255);return"rgb("+f.join(",")+")"}return a}}),v={changeHighlight:function(a){var b,c=this.currentRegion,e=this.target,f=this.regionShapes[c];f&&(b=this.renderRegion(c,a),d.isArray(b)||d.isArray(f)?(e.replaceWithShapes(f,b),this.regionShapes[c]=d.map(b,function(a){return a.id})):(e.replaceWithShape(f,b),this.regionShapes[c]=b.id))},render:function(){var a,b,c,e,f=this.values,g=this.target,h=this.regionShapes;if(this.cls._super.render.call(this)){for(c=f.length;c--;)if(a=this.renderRegion(c))if(d.isArray(a)){for(b=[],e=a.length;e--;)a[e].append(),b.push(a[e].id);h[c]=b}else a.append(),h[c]=a.id;else h[c]=null;g.render()}}},d.fn.sparkline.line=w=f(d.fn.sparkline._base,{type:"line",init:function(a,b,c,d,e){w._super.init.call(this,a,b,c,d,e),this.vertices=[],this.regionMap=[],this.xvalues=[],this.yvalues=[],this.yminmax=[],this.hightlightSpotId=null,this.lastShapeId=null,this.initTarget()},getRegion:function(a,b){var d,e=this.regionMap;for(d=e.length;d--;)if(null!==e[d]&&b>=e[d][0]&&b<=e[d][1])return e[d][2];return c},getCurrentRegionFields:function(){var a=this.currentRegion;return{isNull:null===this.yvalues[a],x:this.xvalues[a],y:this.yvalues[a],color:this.options.get("lineColor"),fillColor:this.options.get("fillColor"),offset:a}},renderHighlight:function(){var a,b,d=this.currentRegion,e=this.target,f=this.vertices[d],g=this.options,h=g.get("spotRadius"),i=g.get("highlightSpotColor"),j=g.get("highlightLineColor");f&&(h&&i&&(a=e.drawCircle(f[0],f[1],h,c,i),this.highlightSpotId=a.id,e.insertAfterShape(this.lastShapeId,a)),j&&(b=e.drawLine(f[0],this.canvasTop,f[0],this.canvasTop+this.canvasHeight,j),this.highlightLineId=b.id,e.insertAfterShape(this.lastShapeId,b)))},removeHighlight:function(){var a=this.target;this.highlightSpotId&&(a.removeShapeId(this.highlightSpotId),this.highlightSpotId=null),this.highlightLineId&&(a.removeShapeId(this.highlightLineId),this.highlightLineId=null)},scanValues:function(){var a,c,d,e,f,g=this.values,h=g.length,i=this.xvalues,j=this.yvalues,k=this.yminmax;for(a=0;h>a;a++)c=g[a],d="string"==typeof g[a],e="object"==typeof g[a]&&g[a]instanceof Array,f=d&&g[a].split(":"),d&&2===f.length?(i.push(Number(f[0])),j.push(Number(f[1])),k.push(Number(f[1]))):e?(i.push(c[0]),j.push(c[1]),k.push(c[1])):(i.push(a),null===g[a]||"null"===g[a]?j.push(null):(j.push(Number(c)),k.push(Number(c))));this.options.get("xvalues")&&(i=this.options.get("xvalues")),this.maxy=this.maxyorg=b.max.apply(b,k),this.miny=this.minyorg=b.min.apply(b,k),this.maxx=b.max.apply(b,i),this.minx=b.min.apply(b,i),this.xvalues=i,this.yvalues=j,this.yminmax=k},processRangeOptions:function(){var a=this.options,b=a.get("normalRangeMin"),d=a.get("normalRangeMax");b!==c&&(bthis.maxy&&(this.maxy=d)),a.get("chartRangeMin")!==c&&(a.get("chartRangeClip")||a.get("chartRangeMin")this.maxy)&&(this.maxy=a.get("chartRangeMax")),a.get("chartRangeMinX")!==c&&(a.get("chartRangeClipX")||a.get("chartRangeMinX")this.maxx)&&(this.maxx=a.get("chartRangeMaxX"))},drawNormalRange:function(a,d,e,f,g){var h=this.options.get("normalRangeMin"),i=this.options.get("normalRangeMax"),j=d+b.round(e-e*((i-this.miny)/g)),k=b.round(e*(i-h)/g);this.target.drawRect(a,j,f,k,c,this.options.get("normalRangeColor")).append()},render:function(){var a,e,f,g,h,i,j,k,l,m,n,o,p,q,r,t,u,v,x,y,z,A,B,C,D,E=this.options,F=this.target,G=this.canvasWidth,H=this.canvasHeight,I=this.vertices,J=E.get("spotRadius"),K=this.regionMap;if(w._super.render.call(this)&&(this.scanValues(),this.processRangeOptions(),B=this.xvalues,C=this.yvalues,this.yminmax.length&&!(this.yvalues.length<2))){for(g=h=0,a=this.maxx-this.minx===0?1:this.maxx-this.minx,e=this.maxy-this.miny===0?1:this.maxy-this.miny,f=this.yvalues.length-1,J&&(4*J>G||4*J>H)&&(J=0),J&&(z=E.get("highlightSpotColor")&&!E.get("disableInteraction"),(z||E.get("minSpotColor")||E.get("spotColor")&&C[f]===this.miny)&&(H-=b.ceil(J)),(z||E.get("maxSpotColor")||E.get("spotColor")&&C[f]===this.maxy)&&(H-=b.ceil(J),g+=b.ceil(J)),(z||(E.get("minSpotColor")||E.get("maxSpotColor"))&&(C[0]===this.miny||C[0]===this.maxy))&&(h+=b.ceil(J),G-=b.ceil(J)),(z||E.get("spotColor")||E.get("minSpotColor")||E.get("maxSpotColor")&&(C[f]===this.miny||C[f]===this.maxy))&&(G-=b.ceil(J))),H--,E.get("normalRangeMin")===c||E.get("drawNormalOnTop")||this.drawNormalRange(h,g,H,G,e),j=[],k=[j],q=r=null,t=C.length,D=0;t>D;D++)l=B[D],n=B[D+1],m=C[D],o=h+b.round((l-this.minx)*(G/a)),p=t-1>D?h+b.round((n-this.minx)*(G/a)):G,r=o+(p-o)/2,K[D]=[q||0,r,D],q=r,null===m?D&&(null!==C[D-1]&&(j=[],k.push(j)),I.push(null)):(mthis.maxy&&(m=this.maxy),j.length||j.push([o,g+H]),i=[o,g+b.round(H-H*((m-this.miny)/e))],j.push(i),I.push(i));for(u=[],v=[],x=k.length,D=0;x>D;D++)j=k[D],j.length&&(E.get("fillColor")&&(j.push([j[j.length-1][0],g+H]),v.push(j.slice(0)),j.pop()),j.length>2&&(j[0]=[j[0][0],j[1][1]]),u.push(j));for(x=v.length,D=0;x>D;D++)F.drawShape(v[D],E.get("fillColor"),E.get("fillColor")).append();for(E.get("normalRangeMin")!==c&&E.get("drawNormalOnTop")&&this.drawNormalRange(h,g,H,G,e),x=u.length,D=0;x>D;D++)F.drawShape(u[D],E.get("lineColor"),c,E.get("lineWidth")).append();if(J&&E.get("valueSpots"))for(y=E.get("valueSpots"),y.get===c&&(y=new s(y)),D=0;t>D;D++)A=y.get(C[D]),A&&F.drawCircle(h+b.round((B[D]-this.minx)*(G/a)),g+b.round(H-H*((C[D]-this.miny)/e)),J,c,A).append();J&&E.get("spotColor")&&null!==C[f]&&F.drawCircle(h+b.round((B[B.length-1]-this.minx)*(G/a)),g+b.round(H-H*((C[f]-this.miny)/e)),J,c,E.get("spotColor")).append(),this.maxy!==this.minyorg&&(J&&E.get("minSpotColor")&&(l=B[d.inArray(this.minyorg,C)],F.drawCircle(h+b.round((l-this.minx)*(G/a)),g+b.round(H-H*((this.minyorg-this.miny)/e)),J,c,E.get("minSpotColor")).append()),J&&E.get("maxSpotColor")&&(l=B[d.inArray(this.maxyorg,C)],F.drawCircle(h+b.round((l-this.minx)*(G/a)),g+b.round(H-H*((this.maxyorg-this.miny)/e)),J,c,E.get("maxSpotColor")).append())),this.lastShapeId=F.getLastShapeId(),this.canvasTop=g,F.render()}}}),d.fn.sparkline.bar=x=f(d.fn.sparkline._base,v,{type:"bar",init:function(a,e,f,g,i){var m,n,o,p,q,r,t,u,v,w,y,z,A,B,C,D,E,F,G,H,I,J,K=parseInt(f.get("barWidth"),10),L=parseInt(f.get("barSpacing"),10),M=f.get("chartRangeMin"),N=f.get("chartRangeMax"),O=f.get("chartRangeClip"),P=1/0,Q=-(1/0);for(x._super.init.call(this,a,e,f,g,i),r=0,t=e.length;t>r;r++)H=e[r],m="string"==typeof H&&H.indexOf(":")>-1,(m||d.isArray(H))&&(C=!0,m&&(H=e[r]=k(H.split(":"))),H=l(H,null),n=b.min.apply(b,H),o=b.max.apply(b,H),P>n&&(P=n),o>Q&&(Q=o));this.stacked=C,this.regionShapes={},this.barWidth=K,this.barSpacing=L,this.totalBarWidth=K+L,this.width=g=e.length*K+(e.length-1)*L,this.initTarget(),O&&(A=M===c?-(1/0):M,B=N===c?1/0:N),q=[],p=C?[]:q;var R=[],S=[];for(r=0,t=e.length;t>r;r++)if(C)for(D=e[r],e[r]=G=[],R[r]=0,p[r]=S[r]=0,E=0,F=D.length;F>E;E++)H=G[E]=O?h(D[E],A,B):D[E],null!==H&&(H>0&&(R[r]+=H),0>P&&Q>0?0>H?S[r]+=b.abs(H):p[r]+=H:p[r]+=b.abs(H-(0>H?Q:P)),q.push(H));else H=O?h(e[r],A,B):e[r],H=e[r]=j(H),null!==H&&q.push(H);this.max=z=b.max.apply(b,q),this.min=y=b.min.apply(b,q),this.stackMax=Q=C?b.max.apply(b,R):z,this.stackMin=P=C?b.min.apply(b,q):y,f.get("chartRangeMin")!==c&&(f.get("chartRangeClip")||f.get("chartRangeMin")z)&&(z=f.get("chartRangeMax")),this.zeroAxis=v=f.get("zeroAxis",!0),w=0>=y&&z>=0&&v?0:0==v?y:y>0?y:z,this.xaxisOffset=w,u=C?b.max.apply(b,p)+b.max.apply(b,S):z-y,this.canvasHeightEf=v&&0>y?this.canvasHeight-2:this.canvasHeight-1,w>y?(J=C&&z>=0?Q:z,I=(J-w)/u*this.canvasHeight,I!==b.ceil(I)&&(this.canvasHeightEf-=2,I=b.ceil(I))):I=this.canvasHeight,this.yoffset=I,d.isArray(f.get("colorMap"))?(this.colorMapByIndex=f.get("colorMap"),this.colorMapByValue=null):(this.colorMapByIndex=null,this.colorMapByValue=f.get("colorMap"),this.colorMapByValue&&this.colorMapByValue.get===c&&(this.colorMapByValue=new s(this.colorMapByValue))),this.range=u},getRegion:function(a,d){var e=b.floor(d/this.totalBarWidth);return 0>e||e>=this.values.length?c:e},getCurrentRegionFields:function(){var a,b,c=this.currentRegion,d=q(this.values[c]),e=[];for(b=d.length;b--;)a=d[b],e.push({isNull:null===a,value:a,color:this.calcColor(b,a,c),offset:c});return e},calcColor:function(a,b,e){var f,g,h=this.colorMapByIndex,i=this.colorMapByValue,j=this.options;return f=j.get(this.stacked?"stackedBarColor":0>b?"negBarColor":"barColor"),0===b&&j.get("zeroColor")!==c&&(f=j.get("zeroColor")),i&&(g=i.get(b))?f=g:h&&h.length>e&&(f=h[e]),d.isArray(f)?f[a%f.length]:f},renderRegion:function(a,e){var f,g,h,i,j,k,l,m,o,p,q=this.values[a],r=this.options,s=this.xaxisOffset,t=[],u=this.range,v=this.stacked,w=this.target,x=a*this.totalBarWidth,y=this.canvasHeightEf,z=this.yoffset;if(q=d.isArray(q)?q:[q],l=q.length,m=q[0],i=n(null,q),p=n(s,q,!0),i)return r.get("nullColor")?(h=e?r.get("nullColor"):this.calcHighlightColor(r.get("nullColor"),r),f=z>0?z-1:z,w.drawRect(x,f,this.barWidth-1,0,h,h)):c;for(j=z,k=0;l>k;k++){if(m=q[k],v&&m===s){if(!p||o)continue;o=!0}g=u>0?b.floor(y*(b.abs(m-s)/u))+1:1,s>m||m===s&&0===z?(f=j,j+=g):(f=z-g,z-=g),h=this.calcColor(k,m,a),e&&(h=this.calcHighlightColor(h,r)),t.push(w.drawRect(x,f,this.barWidth-1,g-1,h,h))}return 1===t.length?t[0]:t}}),d.fn.sparkline.tristate=y=f(d.fn.sparkline._base,v,{type:"tristate",init:function(a,b,e,f,g){var h=parseInt(e.get("barWidth"),10),i=parseInt(e.get("barSpacing"),10);y._super.init.call(this,a,b,e,f,g),this.regionShapes={},this.barWidth=h,this.barSpacing=i,this.totalBarWidth=h+i,this.values=d.map(b,Number),this.width=f=b.length*h+(b.length-1)*i,d.isArray(e.get("colorMap"))?(this.colorMapByIndex=e.get("colorMap"),this.colorMapByValue=null):(this.colorMapByIndex=null,this.colorMapByValue=e.get("colorMap"),this.colorMapByValue&&this.colorMapByValue.get===c&&(this.colorMapByValue=new s(this.colorMapByValue))),this.initTarget()},getRegion:function(a,c){return b.floor(c/this.totalBarWidth)},getCurrentRegionFields:function(){var a=this.currentRegion;return{isNull:this.values[a]===c,value:this.values[a],color:this.calcColor(this.values[a],a),offset:a}},calcColor:function(a,b){var c,d,e=this.values,f=this.options,g=this.colorMapByIndex,h=this.colorMapByValue;return c=h&&(d=h.get(a))?d:g&&g.length>b?g[b]:f.get(e[b]<0?"negBarColor":e[b]>0?"posBarColor":"zeroBarColor")},renderRegion:function(a,c){var d,e,f,g,h,i,j=this.values,k=this.options,l=this.target;return d=l.pixelHeight,f=b.round(d/2),g=a*this.totalBarWidth,j[a]<0?(h=f,e=f-1):j[a]>0?(h=0,e=f-1):(h=f-1,e=2),i=this.calcColor(j[a],a),null!==i?(c&&(i=this.calcHighlightColor(i,k)),l.drawRect(g,h,this.barWidth-1,e-1,i,i)):void 0}}),d.fn.sparkline.discrete=z=f(d.fn.sparkline._base,v,{type:"discrete",init:function(a,e,f,g,h){z._super.init.call(this,a,e,f,g,h),this.regionShapes={},this.values=e=d.map(e,Number),this.min=b.min.apply(b,e),this.max=b.max.apply(b,e),this.range=this.max-this.min,this.width=g="auto"===f.get("width")?2*e.length:this.width,this.interval=b.floor(g/e.length),this.itemWidth=g/e.length,f.get("chartRangeMin")!==c&&(f.get("chartRangeClip")||f.get("chartRangeMin")this.max)&&(this.max=f.get("chartRangeMax")),this.initTarget(),this.target&&(this.lineHeight="auto"===f.get("lineHeight")?b.round(.3*this.canvasHeight):f.get("lineHeight"))},getRegion:function(a,c){return b.floor(c/this.itemWidth)},getCurrentRegionFields:function(){var a=this.currentRegion;return{isNull:this.values[a]===c,value:this.values[a],offset:a}},renderRegion:function(a,c){var d,e,f,g,i=this.values,j=this.options,k=this.min,l=this.max,m=this.range,n=this.interval,o=this.target,p=this.canvasHeight,q=this.lineHeight,r=p-q;return e=h(i[a],k,l),g=a*n,d=b.round(r-r*((e-k)/m)),f=j.get(j.get("thresholdColor")&&eh?h:0:e.get("base"),this.min=h,this.max=i,this.range=i-h,this.shapes={},this.valueShapes={},this.regiondata={},this.width=f="auto"===e.get("width")?"4.0em":f,this.target=this.$el.simpledraw(f,g,e.get("composite")),d.length||(this.disabled=!0),this.initTarget()},getRegion:function(a,b,d){var e=this.target.getShapeAt(a,b,d);return e!==c&&this.shapes[e]!==c?this.shapes[e]:c},getCurrentRegionFields:function(){var a=this.currentRegion;return{fieldkey:a.substr(0,1),value:this.values[a.substr(1)],region:a}},changeHighlight:function(a){var b,c=this.currentRegion,d=this.valueShapes[c];switch(delete this.shapes[d],c.substr(0,1)){case"r":b=this.renderRange(c.substr(1),a);break;case"p":b=this.renderPerformance(a);break;case"t":b=this.renderTarget(a)}this.valueShapes[c]=b.id,this.shapes[b.id]=c,this.target.replaceWithShape(d,b)},renderRange:function(a,c){var d=this.values[a],e=b.round(this.canvasWidth*((d-this.min)/this.range)),f=this.options.get("rangeColors")[a-2];return c&&(f=this.calcHighlightColor(f,this.options)),this.target.drawRect(0,0,e-1,this.canvasHeight-1,f,f)},renderPerformance:function(a){var c=this.values[1],d=b.round(this.canvasWidth*((c-this.min)/this.range)),e=this.options.get("performanceColor");return a&&(e=this.calcHighlightColor(e,this.options)),this.target.drawRect(0,b.round(.3*this.canvasHeight),d-1,b.round(.4*this.canvasHeight)-1,e,e)},renderTarget:function(a){var c=this.values[0],d=b.round(this.canvasWidth*((c-this.min)/this.range)-this.options.get("targetWidth")/2),e=b.round(.1*this.canvasHeight),f=this.canvasHeight-2*e,g=this.options.get("targetColor");return a&&(g=this.calcHighlightColor(g,this.options)),this.target.drawRect(d,e,this.options.get("targetWidth")-1,f-1,g,g)},render:function(){var a,b,c=this.values.length,d=this.target;if(A._super.render.call(this)){for(a=2;c>a;a++)b=this.renderRange(a).append(),this.shapes[b.id]="r"+a,this.valueShapes["r"+a]=b.id;null!==this.values[1]&&(b=this.renderPerformance().append(),this.shapes[b.id]="p1",this.valueShapes.p1=b.id),null!==this.values[0]&&(b=this.renderTarget().append(),this.shapes[b.id]="t0",this.valueShapes.t0=b.id),d.render()}}}),d.fn.sparkline.pie=B=f(d.fn.sparkline._base,{type:"pie",init:function(a,c,e,f,g){var h,i=0;if(B._super.init.call(this,a,c,e,f,g),this.shapes={},this.valueShapes={},this.values=c=d.map(c,Number),"auto"===e.get("width")&&(this.width=this.height),c.length>0)for(h=c.length;h--;)i+=c[h];this.total=i,this.initTarget(),this.radius=b.floor(b.min(this.canvasWidth,this.canvasHeight)/2)},getRegion:function(a,b,d){var e=this.target.getShapeAt(a,b,d);return e!==c&&this.shapes[e]!==c?this.shapes[e]:c},getCurrentRegionFields:function(){var a=this.currentRegion;return{isNull:this.values[a]===c,value:this.values[a],percent:this.values[a]/this.total*100,color:this.options.get("sliceColors")[a%this.options.get("sliceColors").length],offset:a}},changeHighlight:function(a){var b=this.currentRegion,c=this.renderSlice(b,a),d=this.valueShapes[b];delete this.shapes[d],this.target.replaceWithShape(d,c),this.valueShapes[b]=c.id,this.shapes[c.id]=b},renderSlice:function(a,d){var e,f,g,h,i,j=this.target,k=this.options,l=this.radius,m=k.get("borderWidth"),n=k.get("offset"),o=2*b.PI,p=this.values,q=this.total,r=n?2*b.PI*(n/360):0;for(h=p.length,g=0;h>g;g++){if(e=r,f=r,q>0&&(f=r+o*(p[g]/q)),a===g)return i=k.get("sliceColors")[g%k.get("sliceColors").length],d&&(i=this.calcHighlightColor(i,k)),j.drawPieSlice(l,l,l-m,e,f,c,i);r=f}},render:function(){var a,d,e=this.target,f=this.values,g=this.options,h=this.radius,i=g.get("borderWidth");if(B._super.render.call(this)){ +for(i&&e.drawCircle(h,h,b.floor(h-i/2),g.get("borderColor"),c,i).append(),d=f.length;d--;)f[d]&&(a=this.renderSlice(d).append(),this.valueShapes[d]=a.id,this.shapes[a.id]=d);e.render()}}}),d.fn.sparkline.box=C=f(d.fn.sparkline._base,{type:"box",init:function(a,b,c,e,f){C._super.init.call(this,a,b,c,e,f),this.values=d.map(b,Number),this.width="auto"===c.get("width")?"4.0em":e,this.initTarget(),this.values.length||(this.disabled=1)},getRegion:function(){return 1},getCurrentRegionFields:function(){var a=[{field:"lq",value:this.quartiles[0]},{field:"med",value:this.quartiles[1]},{field:"uq",value:this.quartiles[2]}];return this.loutlier!==c&&a.push({field:"lo",value:this.loutlier}),this.routlier!==c&&a.push({field:"ro",value:this.routlier}),this.lwhisker!==c&&a.push({field:"lw",value:this.lwhisker}),this.rwhisker!==c&&a.push({field:"rw",value:this.rwhisker}),a},render:function(){var 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filled="false"':' fillColor="'+g+'" filled="true" ',k=''},_drawPieSlice:function(a,d,e,f,g,h,i,j){var k,l,m,n,o,p,q,r;if(g===h)return"";if(h-g===2*b.PI&&(g=0,h=2*b.PI),l=d+b.round(b.cos(g)*f),m=e+b.round(b.sin(g)*f),n=d+b.round(b.cos(h)*f),o=e+b.round(b.sin(h)*f),l===n&&m===o){if(h-g ')},_drawRect:function(a,b,c,d,e,f,g){return this._drawShape(a,[[b,c],[b,c+e],[b+d,c+e],[b+d,c],[b,c]],f,g)},reset:function(){this.group.innerHTML=""},appendShape:function(a){var b=this["_draw"+a.type].apply(this,a.args);return this.rendered?this.group.insertAdjacentHTML("beforeEnd",b):this.prerender+=b,this.lastShapeId=a.id,a.id},replaceWithShape:function(a,b){var c=d("#jqsshape"+a),e=this["_draw"+b.type].apply(this,b.args);c[0].outerHTML=e},replaceWithShapes:function(a,b){var c,e=d("#jqsshape"+a[0]),f="",g=b.length;for(c=0;g>c;c++)f+=this["_draw"+b[c].type].apply(this,b[c].args);for(e[0].outerHTML=f,c=1;c Date: Tue, 16 Jun 2015 15:42:43 -0500 Subject: [PATCH 04/68] Bug fix for page crash --- lib/galaxy/webapps/reports/controllers/jobs.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 848d38829f0..1f2e32a43d3 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -527,6 +527,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order=order, arrow=arrow, sort_id=sort_id, + trends=trends, jobs=jobs, message=message, is_user_jobs_only=monitor_user_id ) From eca0329d26b607fa208bd9c07240d8511dfa7d3d Mon Sep 17 00:00:00 2001 From: Airistotal Date: Wed, 17 Jun 2015 13:01:19 -0500 Subject: [PATCH 05/68] Refactoring the creation of tool tips --- .../webapps/reports/controllers/jobs.py | 61 +++++++++++-------- .../reports/jobs_specified_month_all.mako | 2 +- .../jobs_specified_month_in_error.mako | 2 +- 3 files changed, 38 insertions(+), 27 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 1f2e32a43d3..65f4ee00d23 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -256,6 +256,8 @@ class Jobs( BaseUIController, ReportQueryBuilder ): params = util.Params( kwd ) monitor_email = params.get( 'monitor_email', 'monitor@bx.psu.edu' ) specs = sorter( 'date', kwd ) + offset = 0 + limit = 10 sort_id = specs.sort_id order = specs.order arrow = specs.arrow @@ -267,6 +269,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): # If specified_date is not received, we'll default to the current month specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) specified_month = specified_date[ :7 ] + year, month = map( int, specified_month.split( "-" ) ) start_date = date( year, month, 1 ) end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) @@ -281,7 +284,9 @@ class Jobs( BaseUIController, ReportQueryBuilder ): model.Job.table.c.create_time < end_date ), from_obj=[ model.Job.table ], group_by=[ 'date' ], - order_by=[ _order ] ) + order_by=[ _order ], + offset=offset, + limit=limit) # Use to make trendline all_jobs = sa.select( ( model.Job.table.c.create_time.label('date'), model.Job.table.c.id.label('id') ), @@ -289,24 +294,26 @@ class Jobs( BaseUIController, ReportQueryBuilder ): model.Job.table.c.create_time >= start_date, model.Job.table.c.create_time < end_date ) ) - trend = [0] * 24 + trends = dict() + for job in all_jobs.execute(): + job_hour = int(job.date.strftime("%-H")) + job_day = job.date.strftime("%d") + + try: + trends[job_day][job_hour] += 1 + except KeyError: + trends[job_day] = [0] * 24 + trends[job_day][job_hour] += 1 + jobs = [] for row in month_jobs.execute(): - trend = [0] * 24 - - row_dayname = row.date.strftime( "%A" ) - row_day = row.date.strftime( "%d" ) - - for job in all_jobs.execute(): - if row_day == job.date.strftime( "%d" ): - hour = int( job.date.strftime( "%-H" ) ) - 1 - trend[hour] += 1 + row_dayname = row.date.strftime("%A") + row_day = row.date.strftime("%d") jobs.append( ( row_dayname, row_day, row.total_jobs, - row.date, - trend + row.date ) ) return trans.fill_template( '/webapps/reports/jobs_specified_month_all.mako', @@ -317,6 +324,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): year_label=year_label, month=month, jobs=jobs, + trends=trends, is_user_jobs_only=monitor_user_id, message=message ) @@ -363,24 +371,26 @@ class Jobs( BaseUIController, ReportQueryBuilder ): model.Job.table.c.create_time >= start_date, model.Job.table.c.create_time < end_date ) ) - trend = [0] * 24 + trends = dict() + for job in all_jobs_in_error.execute(): + job_hour = int(job.date.strftime("%-H")) + job_day = job.date.strftime("%d") + + try: + trends[job_day][job_hour] += 1 + except KeyError: + trends[job_day] = [0] * 24 + trends[job_day][job_hour] += 1 + jobs = [] for row in month_jobs_in_error.execute(): - trend = [0] * 24 - - row_dayname = row.date.strftime( "%A" ) - row_day = row.date.strftime( "%d" ) - - for job in all_jobs_in_error.execute(): - if row_day == job.date.strftime( "%d" ): - hour = int( job.date.strftime( "%-H" ) ) - 1 - trend[hour] += 1 + row_dayname = row.date.strftime("%A") + row_day = row.date.strftime("%d") jobs.append( ( row_dayname, row_day, row.total_jobs, - row.date, - trend + row.date ) ) return trans.fill_template( '/webapps/reports/jobs_specified_month_in_error.mako', @@ -391,6 +401,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): year_label=year_label, month=month, jobs=jobs, + trends=trends, message=message, is_user_jobs_only=monitor_user_id ) diff --git a/templates/webapps/reports/jobs_specified_month_all.mako b/templates/webapps/reports/jobs_specified_month_all.mako index 15468ac9bb8..69b97d4492a 100644 --- a/templates/webapps/reports/jobs_specified_month_all.mako +++ b/templates/webapps/reports/jobs_specified_month_all.mako @@ -48,7 +48,7 @@ ${get_css()}
- ${make_sparkline(key, job[4], "bar", "/ hour")} + ${make_sparkline(key, trends[key], "bar", "/ hour")} <% ctr += 1 %> diff --git a/templates/webapps/reports/jobs_specified_month_in_error.mako b/templates/webapps/reports/jobs_specified_month_in_error.mako index 4501ca1bc6e..807205b0019 100644 --- a/templates/webapps/reports/jobs_specified_month_in_error.mako +++ b/templates/webapps/reports/jobs_specified_month_in_error.mako @@ -47,7 +47,7 @@ ${get_css()} - ${make_sparkline(key, job[4], "bar", "/ hour")} + ${make_sparkline(key, trends[key], "bar", "/ hour")} <% ctr += 1 %> From 6b021b1c989e3b62e24d11fff86d73c66ee019b2 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Mon, 22 Jun 2015 08:20:43 -0500 Subject: [PATCH 06/68] Added type checking and casting for certain errors --- lib/galaxy/webapps/reports/controllers/jobs.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 65f4ee00d23..edf02630098 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -570,7 +570,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): currday = datetime.today().date() trends = dict() for job in all_jobs_per_user.execute(): - curr_user = re.sub(r'\W+', '', job.user_email) + curr_user = re.sub(r'\W+', '', str(job.user_email)) try: day = currday - job.date day = day.days @@ -690,10 +690,10 @@ class Jobs( BaseUIController, ReportQueryBuilder ): model.Job.table.c.tool_id.label( 'tool_id' ) ), from_obj=[ model.Job.table ] ) - currday = datetime.today().date() + currday = date.today() trends = dict() for job in all_jobs_per_tool.execute(): - curr_tool = re.sub(r'\W+', '', job.tool_id) + curr_tool = re.sub(r'\W+', '', str(job.tool_id)) try: day = currday - job.date day = day.days @@ -754,10 +754,10 @@ class Jobs( BaseUIController, ReportQueryBuilder ): from_obj=[ model.Job.table ] ) - currday = datetime.today().date() + currday = date.today() trends = dict() for job in all_jobs_per_tool_errors.execute(): - curr_tool = re.sub(r'\W+', '', job.tool_id) + curr_tool = re.sub(r'\W+', '', str(job.tool_id)) try: day = currday - job.date day = day.days @@ -769,6 +769,12 @@ class Jobs( BaseUIController, ReportQueryBuilder ): day = day.days if day < day_limit: trends[curr_tool][day] += 1 + except TypeError: + day = currday - date(job.date) + day = day.days + if day < day_limit: + trends[curr_tool][day] += 1 + jobs = [] for row in jobs_in_error_per_tool.execute(): From bc69acb8a99ea93b0179d2c2495c9d37e85464e9 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Mon, 22 Jun 2015 08:26:42 -0500 Subject: [PATCH 07/68] Added whitespace to pass Travis CI. --- lib/galaxy/webapps/reports/controllers/jobs.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index edf02630098..ebe478ed6ef 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -774,7 +774,6 @@ class Jobs( BaseUIController, ReportQueryBuilder ): day = day.days if day < day_limit: trends[curr_tool][day] += 1 - jobs = [] for row in jobs_in_error_per_tool.execute(): From 3a9ff2a1dd8b6e9f997335742532a511ae7c04b8 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Mon, 22 Jun 2015 10:24:33 -0500 Subject: [PATCH 08/68] Added compatibility for postgres, bug fix where sparklines broke when no jobs were done in the past 50 days(arbitrary amount decided in code) --- .../webapps/reports/controllers/jobs.py | 48 +++++++++++-------- .../webapps/reports/jobs_errors_per_tool.mako | 5 +- templates/webapps/reports/jobs_per_tool.mako | 5 +- templates/webapps/reports/jobs_per_user.mako | 5 +- 4 files changed, 41 insertions(+), 22 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index ebe478ed6ef..8a57daf2937 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -11,6 +11,7 @@ pkg_resources.require( "SQLAlchemy >= 0.4" ) import re import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder +import sys import logging log = logging.getLogger( __name__ ) @@ -570,16 +571,18 @@ class Jobs( BaseUIController, ReportQueryBuilder ): currday = datetime.today().date() trends = dict() for job in all_jobs_per_user.execute(): - curr_user = re.sub(r'\W+', '', str(job.user_email)) + curr_user = re.sub(r'\W+', '', job.user_email) try: day = currday - job.date - day = day.days + except TypeError: + day = currday - datetime.date(job.date) + + day = day.days + try: if day < day_limit: trends[curr_user][day] += 1 except KeyError: trends[curr_user] = [0] * day_limit - day = currday - job.date - day = day.days if day < day_limit: trends[curr_user][day] += 1 @@ -685,9 +688,10 @@ class Jobs( BaseUIController, ReportQueryBuilder ): group_by=[ 'tool_id' ], order_by=[ _order ] ) - all_jobs_per_tool = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), - model.Job.table.c.id.label( 'id' ), - model.Job.table.c.tool_id.label( 'tool_id' ) ), + all_jobs_per_tool = sa.select( ( model.Job.table.c.tool_id.label( 'tool_id' ), + model.Job.table.c.id.label( 'id' ), + self.select_month( model.Job.table.c.create_time ).label( 'date' ) ), + whereclause=model.Job.table.c.user_id != monitor_user_id, from_obj=[ model.Job.table ] ) currday = date.today() @@ -696,13 +700,15 @@ class Jobs( BaseUIController, ReportQueryBuilder ): curr_tool = re.sub(r'\W+', '', str(job.tool_id)) try: day = currday - job.date - day = day.days + except TypeError: + day = currday - datetime.date(job.date) + + day = day.days + try: if day < day_limit: trends[curr_tool][day] += 1 except KeyError: trends[curr_tool] = [0] * day_limit - day = currday - job.date - day = day.days if day < day_limit: trends[curr_tool][day] += 1 @@ -710,6 +716,14 @@ class Jobs( BaseUIController, ReportQueryBuilder ): jobs.append( ( row.tool_id, row.total_jobs ) ) + print("==========jobs==================", file=sys.stderr) + for job in jobs: + print(re.sub(r'\W+', '', job[0]), file=sys.stderr) + + print("==========trends==================", file=sys.stderr) + for item in trends.keys(): + print(item, file=sys.stderr) + return trans.fill_template( '/webapps/reports/jobs_per_tool.mako', order=order, arrow=arrow, @@ -760,21 +774,17 @@ class Jobs( BaseUIController, ReportQueryBuilder ): curr_tool = re.sub(r'\W+', '', str(job.tool_id)) try: day = currday - job.date - day = day.days + except TypeError: + day = currday - datetime.date(job.date) + + day = day.days + try: if day < day_limit: trends[curr_tool][day] += 1 except KeyError: trends[curr_tool] = [0] * day_limit - day = currday - job.date - day = day.days if day < day_limit: trends[curr_tool][day] += 1 - except TypeError: - day = currday - date(job.date) - day = day.days - if day < day_limit: - trends[curr_tool][day] += 1 - jobs = [] for row in jobs_in_error_per_tool.execute(): jobs.append( ( row.total_jobs, row.tool_id ) ) diff --git a/templates/webapps/reports/jobs_errors_per_tool.mako b/templates/webapps/reports/jobs_errors_per_tool.mako index 6ce25222959..5de08d9b71e 100644 --- a/templates/webapps/reports/jobs_errors_per_tool.mako +++ b/templates/webapps/reports/jobs_errors_per_tool.mako @@ -52,7 +52,10 @@ ${get_css()} %endif - ${make_sparkline(key, trends[key], "line", "/ day")} + %try: + ${make_sparkline(key, trends[key], "line", "/ day")} + %except KeyError: + %endtry <% ctr += 1 %> diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako index e6e31675f31..7d5b621c905 100644 --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -51,7 +51,10 @@ ${get_css()} %endif - ${make_sparkline(key, trends[key], "line", "/ day")} + %try: + ${make_sparkline(key, trends[key], "line", "/ day")} + %except KeyError: + %endtry <% ctr += 1 %> diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako index 5770d0063d3..00021fac347 100644 --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -44,7 +44,10 @@ ${get_css()} %endif - ${make_sparkline(key, trends[key], "line", "/ day")} + %try: + ${make_sparkline(key, trends[key], "line", "/ day")} + %except KeyError: + %endtry <% ctr += 1 %> From d870a24071341a4e874d9367cc22088264a1e683 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Mon, 22 Jun 2015 12:45:39 -0500 Subject: [PATCH 09/68] Added option for how long sparklines jobs per user, jobs per tool and errors per tool are --- .../webapps/reports/controllers/jobs.py | 101 ++++++++++++------ templates/spark_base.mako | 51 +++++++++ templates/webapps/reports/index.mako | 2 +- .../webapps/reports/jobs_errors_per_tool.mako | 7 +- templates/webapps/reports/jobs_per_tool.mako | 7 +- templates/webapps/reports/jobs_per_user.mako | 7 +- 6 files changed, 135 insertions(+), 40 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 8a57daf2937..7aff6d4ef50 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -6,6 +6,7 @@ from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_, not_, or_ +from math import floor import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import re @@ -554,7 +555,19 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order - day_limit = 50 + time_period = kwd.get('spark_time') + if time_period == "days": + _time_period = 1.0 + elif time_period == "weeks": + _time_period = 7.0 + elif time_period == "months": + _time_period = 30.0 + elif time_period == "years": + _time_period = 365.0 + else: + time_period = "days" + _time_period = 1.0 + limit = 30 jobs = [] jobs_per_user = sa.select( ( model.User.table.c.email.label( 'user_email' ), @@ -568,7 +581,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): model.User.table.c.email.label( 'user_email' ) ), from_obj=[ sa.outerjoin( model.Job.table, model.User.table ) ] ) - currday = datetime.today().date() + currday = date.today() trends = dict() for job in all_jobs_per_user.execute(): curr_user = re.sub(r'\W+', '', job.user_email) @@ -578,13 +591,15 @@ class Jobs( BaseUIController, ReportQueryBuilder ): day = currday - datetime.date(job.date) day = day.days + container = floor(day / _time_period) + container = int(container) try: - if day < day_limit: - trends[curr_user][day] += 1 + if container < limit: + trends[curr_user][container] += 1 except KeyError: - trends[curr_user] = [0] * day_limit - if day < day_limit: - trends[curr_user][day] += 1 + trends[curr_user] = [0] * limit + if container < limit: + trends[curr_user][container] += 1 for row in jobs_per_user.execute(): if ( row.user_email is None ): @@ -600,7 +615,8 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order=order, arrow=arrow, sort_id=sort_id, - day_limit=day_limit, + limit=limit, + time_period=time_period, trends=trends, jobs=jobs, message=message ) @@ -675,7 +691,20 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order - day_limit = 50 + time_period = kwd.get('spark_time') + if time_period == "days": + _time_period = 1.0 + elif time_period == "weeks": + _time_period = 7.0 + elif time_period == "months": + _time_period = 30.0 + elif time_period == "years": + _time_period = 365.0 + else: + time_period = "days" + _time_period = 1.0 + + limit = 30 # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) @@ -704,31 +733,26 @@ class Jobs( BaseUIController, ReportQueryBuilder ): day = currday - datetime.date(job.date) day = day.days + container = floor(day / _time_period) + container = int(container) try: - if day < day_limit: - trends[curr_tool][day] += 1 + if container < limit: + trends[curr_tool][container] += 1 except KeyError: - trends[curr_tool] = [0] * day_limit - if day < day_limit: - trends[curr_tool][day] += 1 + trends[curr_tool] = [0] * limit + if container < limit: + trends[curr_tool][container] += 1 for row in q.execute(): jobs.append( ( row.tool_id, row.total_jobs ) ) - print("==========jobs==================", file=sys.stderr) - for job in jobs: - print(re.sub(r'\W+', '', job[0]), file=sys.stderr) - - print("==========trends==================", file=sys.stderr) - for item in trends.keys(): - print(item, file=sys.stderr) - return trans.fill_template( '/webapps/reports/jobs_per_tool.mako', order=order, arrow=arrow, sort_id=sort_id, - day_limit=day_limit, + limit=limit, + time_period=time_period, trends=trends, jobs=jobs, message=message, @@ -748,7 +772,20 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order - day_limit = 50 + time_period = kwd.get('spark_time') + if time_period == "days": + _time_period = 1.0 + elif time_period == "weeks": + _time_period = 7.0 + elif time_period == "months": + _time_period = 30.0 + elif time_period == "years": + _time_period = 365.0 + else: + time_period = "days" + _time_period = 1.0 + + limit = 30 # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) @@ -777,14 +814,17 @@ class Jobs( BaseUIController, ReportQueryBuilder ): except TypeError: day = currday - datetime.date(job.date) + #convert day into days/weeks/months/years day = day.days + container = floor(day / _time_period) + container = int(container) try: - if day < day_limit: - trends[curr_tool][day] += 1 + if container < limit: + trends[curr_tool][container] += 1 except KeyError: - trends[curr_tool] = [0] * day_limit - if day < day_limit: - trends[curr_tool][day] += 1 + trends[curr_tool] = [0] * limit + if day < limit: + trends[curr_tool][container] += 1 jobs = [] for row in jobs_in_error_per_tool.execute(): jobs.append( ( row.total_jobs, row.tool_id ) ) @@ -792,7 +832,8 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order=order, arrow=arrow, sort_id=sort_id, - day_limit=day_limit, + limit=limit, + time_period=time_period, trends=trends, jobs=jobs, message=message, diff --git a/templates/spark_base.mako b/templates/spark_base.mako index da4410f1056..ea19597f6b1 100644 --- a/templates/spark_base.mako +++ b/templates/spark_base.mako @@ -8,6 +8,57 @@ +<%def name="spark_css()"> + + + +<%def name="make_spark_settings( controller, action, limit, sort_id, order, time_period )"> +
+
+ + + ${limit} + + + +
+ + <%def name="make_sparkline(id, data, sparktype, length)"> <% color = '●' diff --git a/templates/webapps/reports/index.mako b/templates/webapps/reports/index.mako index 0ab41755770..8a259dad093 100644 --- a/templates/webapps/reports/index.mako +++ b/templates/webapps/reports/index.mako @@ -53,7 +53,7 @@
Jobs in error per month
Jobs per user
Jobs per tool
-
Errors per tool
+
Errors per tool
diff --git a/templates/webapps/reports/jobs_errors_per_tool.mako b/templates/webapps/reports/jobs_errors_per_tool.mako index 5de08d9b71e..d2c40a0d425 100644 --- a/templates/webapps/reports/jobs_errors_per_tool.mako +++ b/templates/webapps/reports/jobs_errors_per_tool.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <%! import re @@ -10,6 +10,7 @@ ${render_msg( message, 'done' )} %endif +${spark_css()} ${jqs_style()} ${get_css()} @@ -19,7 +20,7 @@ ${get_css()}

Jobs In Error Per Tool

Click Tool ID to view details. Click error number to view job details.

-

Graph goes from present to past(${day_limit} days).

+ Graph goes from present to past for ${make_spark_settings( "jobs", "errors_per_tool", limit, sort_id, order, time_period )}
There are no jobs for user "${ _email }"
${job[2]} ${job[3]} ${job[1]}
${job[0]} ${month_label} ${job[1]}, ${year_label} ${job[2]}
${job[0]} ${month_label} ${job[1]}, ${year_label} ${job[2]}
${job[1]} ${job[0]}
${job[0]} ${job[1]}
${job[0]} ${job[1]}
%if len( jobs ) == 0: @@ -53,7 +54,7 @@ ${get_css()} %try: - ${make_sparkline(key, trends[key], "line", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ day")} %except KeyError: %endtry diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako index 7d5b621c905..f43342e4e0f 100644 --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <%! import re @@ -10,6 +10,7 @@ ${render_msg( message, 'done' )} %endif +${spark_css()} ${jqs_style()} ${get_css()} @@ -18,7 +19,7 @@ ${get_css()}

Jobs Per Tool

- Click Tool ID to view details. Graph goes from present to past(${day_limit} days). + Click Tool ID to view details. Graph goes from present to past ${make_spark_settings( "jobs", "per_tool", limit, sort_id, order, time_period )}
${job[1]} ${job[0]}
%if len( jobs ) == 0: @@ -52,7 +53,7 @@ ${get_css()} %try: - ${make_sparkline(key, trends[key], "line", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ day")} %except KeyError: %endtry diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako index 00021fac347..8db19930fd8 100644 --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <%! import re @@ -10,6 +10,7 @@ ${render_msg( message, 'done' )} %endif +${spark_css()} ${jqs_style()} ${get_css()} @@ -18,7 +19,7 @@ ${get_css()}

Jobs Per User

- Click User to view details. Graph goes from present to past(${day_limit} days). + Click User to view details. Graph goes from present to past ${make_spark_settings( "jobs", "per_user", limit, sort_id, order, time_period )}
${job[0]} ${job[1]}
%if len( jobs ) == 0: @@ -45,7 +46,7 @@ ${get_css()} %try: - ${make_sparkline(key, trends[key], "line", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ day")} %except KeyError: %endtry From e286c14f6b718853124ae1ab5b83d7e2f07be5e9 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Mon, 22 Jun 2015 12:47:47 -0500 Subject: [PATCH 10/68] Added whitespace for CI --- lib/galaxy/webapps/reports/controllers/jobs.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 7aff6d4ef50..fd1f3abf1ad 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -12,7 +12,6 @@ pkg_resources.require( "SQLAlchemy >= 0.4" ) import re import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder -import sys import logging log = logging.getLogger( __name__ ) @@ -784,7 +783,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): else: time_period = "days" _time_period = 1.0 - + limit = 30 # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) @@ -814,7 +813,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): except TypeError: day = currday - datetime.date(job.date) - #convert day into days/weeks/months/years + # convert day into days/weeks/months/years day = day.days container = floor(day / _time_period) container = int(container) From 895d09cd9b3682e99e1f365fa87970f0a425ff47 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Mon, 22 Jun 2015 13:33:11 -0500 Subject: [PATCH 11/68] Fixed bug on Jobs per month page where postgres was showing all jobs on same day in sparkline --- lib/galaxy/webapps/reports/controllers/jobs.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index fd1f3abf1ad..108d0efba53 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -433,14 +433,16 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order_by=[ _order ] ) # Use to make sparkline - all_jobs = sa.select( ( self.select_month(model.Job.table.c.create_time).label('date'), model.Job.table.c.id.label('id') ) ) + all_jobs = sa.select( ( self.select_month(model.Job.table.c.create_time).label('month'), + self.select_day(model.Job.table.c.create_time).label('day'), + model.Job.table.c.id.label('id') ) ) trends = dict() for job in all_jobs.execute(): - job_day = int(job.date.strftime("%-d")) - 1 - job_month = int(job.date.strftime("%-m")) - job_month_name = job.date.strftime("%B") - job_year = job.date.strftime("%Y") + job_day = int(job.day.strftime("%-d")) - 1 + job_month = int(job.month.strftime("%-m")) + job_month_name = job.month.strftime("%B") + job_year = job.month.strftime("%Y") key = str( job_month_name + job_year) try: From 08049542aacf23acff2c53b13bc7775d342bba16 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Mon, 22 Jun 2015 13:47:07 -0500 Subject: [PATCH 12/68] Small bug fix in sparklines tool tip where it said day even though it was measured in weeks/months/years --- templates/webapps/reports/jobs_errors_per_tool.mako | 2 +- templates/webapps/reports/jobs_per_tool.mako | 2 +- templates/webapps/reports/jobs_per_user.mako | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/templates/webapps/reports/jobs_errors_per_tool.mako b/templates/webapps/reports/jobs_errors_per_tool.mako index d2c40a0d425..9b0bb819288 100644 --- a/templates/webapps/reports/jobs_errors_per_tool.mako +++ b/templates/webapps/reports/jobs_errors_per_tool.mako @@ -54,7 +54,7 @@ ${get_css()} %try: - ${make_sparkline(key, trends[key], "bar", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])} %except KeyError: %endtry diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako index f43342e4e0f..a6725de8b61 100644 --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -53,7 +53,7 @@ ${get_css()} %try: - ${make_sparkline(key, trends[key], "bar", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])} %except KeyError: %endtry diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako index 8db19930fd8..95a1eec659e 100644 --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -46,7 +46,7 @@ ${get_css()} %try: - ${make_sparkline(key, trends[key], "bar", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])} %except KeyError: %endtry From 1c7017cf4b44f55d94bdbb9d3e2dbbd8f757d032 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Thu, 25 Jun 2015 15:37:45 -0500 Subject: [PATCH 13/68] Fixed a bug where the queries truncated the days so the sparklines didn't display correctly --- .../webapps/reports/controllers/jobs.py | 52 +++++++++---------- .../webapps/reports/jobs_per_month_all.mako | 2 +- .../webapps/reports/jobs_tool_per_month.mako | 2 +- .../webapps/reports/jobs_user_per_month.mako | 2 +- 4 files changed, 28 insertions(+), 30 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 108d0efba53..409edf6c80f 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -433,16 +433,15 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order_by=[ _order ] ) # Use to make sparkline - all_jobs = sa.select( ( self.select_month(model.Job.table.c.create_time).label('month'), - self.select_day(model.Job.table.c.create_time).label('day'), + all_jobs = sa.select( ( self.select_day(model.Job.table.c.create_time).label('date'), model.Job.table.c.id.label('id') ) ) trends = dict() for job in all_jobs.execute(): - job_day = int(job.day.strftime("%-d")) - 1 - job_month = int(job.month.strftime("%-m")) - job_month_name = job.month.strftime("%B") - job_year = job.month.strftime("%Y") + job_day = int(job.date.strftime("%-d")) - 1 + job_month = int(job.date.strftime("%-m")) + job_month_name = job.date.strftime("%B") + job_year = job.date.strftime("%Y") key = str( job_month_name + job_year) try: @@ -504,9 +503,10 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order_by=[ _order ] ) # Use to make trendline - all_jobs = sa.select( ( self.select_month(model.Job.table.c.create_time).label('date'), model.Job.table.c.id.label('id') ), + all_jobs = sa.select( ( self.select_day(model.Job.table.c.create_time).label('date'), + model.Job.table.c.id.label('id') ), whereclause=sa.and_( model.Job.table.c.state == 'error', - model.Job.table.c.user_id != monitor_user_id )) + model.Job.table.c.user_id != monitor_user_id ) ) trends = dict() for job in all_jobs.execute(): @@ -577,12 +577,12 @@ class Jobs( BaseUIController, ReportQueryBuilder ): group_by=[ 'user_email' ], order_by=[ _order ] ) - all_jobs_per_user = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), - model.Job.table.c.id.label( 'id' ), - model.User.table.c.email.label( 'user_email' ) ), + all_jobs_per_user = sa.select( ( model.Job.table.c.id.label( 'id' ), + model.Job.table.c.create_time.label( 'date' ), + model.User.table.c.email.label( 'user_email' ) ), from_obj=[ sa.outerjoin( model.Job.table, model.User.table ) ] ) - currday = date.today() + currday = datetime.today() trends = dict() for job in all_jobs_per_user.execute(): curr_user = re.sub(r'\W+', '', job.user_email) @@ -636,18 +636,14 @@ class Jobs( BaseUIController, ReportQueryBuilder ): q = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), - whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, - model.GalaxySession.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == email ), + whereclause=model.User.table.c.email == email, from_obj=[ sa.join( model.Job.table, model.User.table ) ], group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ _order ] ) all_jobs_per_user = sa.select( ( model.Job.table.c.create_time.label( 'date' ), model.Job.table.c.id.label( 'job_id' ) ), - whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, - model.GalaxySession.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == email), + whereclause=sa.and_( model.User.table.c.email == email ), from_obj=[ sa.join( model.Job.table, model.User.table ) ] ) trends = dict() @@ -720,7 +716,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): all_jobs_per_tool = sa.select( ( model.Job.table.c.tool_id.label( 'tool_id' ), model.Job.table.c.id.label( 'id' ), - self.select_month( model.Job.table.c.create_time ).label( 'date' ) ), + self.select_day( model.Job.table.c.create_time ).label( 'date' ) ), whereclause=model.Job.table.c.user_id != monitor_user_id, from_obj=[ model.Job.table ] ) @@ -798,7 +794,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): group_by=[ 'tool_id' ], order_by=[ _order ] ) - all_jobs_per_tool_errors = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), + all_jobs_per_tool_errors = sa.select( ( self.select_day( model.Job.table.c.create_time ).label( 'date' ), model.Job.table.c.id.label( 'id' ), model.Job.table.c.tool_id.label( 'tool_id' ) ), whereclause=sa.and_( model.Job.table.c.state == 'error', @@ -865,16 +861,18 @@ class Jobs( BaseUIController, ReportQueryBuilder ): order_by=[ _order ] ) # Use to make sparkline - all_jobs_for_tool = sa.select( ( self.select_month(model.Job.table.c.create_time).label('date'), model.Job.table.c.id.label('id') ), - whereclause=sa.and_( model.Job.table.c.tool_id == tool_id, - model.Job.table.c.user_id != monitor_user_id ), + all_jobs_for_tool = sa.select( ( self.select_month(model.Job.table.c.create_time).label('month'), + self.select_day(model.Job.table.c.create_time).label('day'), + model.Job.table.c.id.label('id') ), + whereclause=sa.and_( model.Job.table.c.tool_id == tool_id, + model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ] ) trends = dict() for job in all_jobs_for_tool.execute(): - job_day = int(job.date.strftime("%-d")) - 1 - job_month = int(job.date.strftime("%-m")) - job_month_name = job.date.strftime("%B") - job_year = job.date.strftime("%Y") + job_day = int(job.day.strftime("%-d")) - 1 + job_month = int(job.month.strftime("%-m")) + job_month_name = job.month.strftime("%B") + job_year = job.month.strftime("%Y") key = str( job_month_name + job_year) try: diff --git a/templates/webapps/reports/jobs_per_month_all.mako b/templates/webapps/reports/jobs_per_month_all.mako index 0b8a08ccdca..fcb5d9ce348 100644 --- a/templates/webapps/reports/jobs_per_month_all.mako +++ b/templates/webapps/reports/jobs_per_month_all.mako @@ -14,7 +14,7 @@ ${get_css()}

Jobs Per Month

-
Click Month to view details.
+
Click Month to view details. Graph goes from the 1st to the last of the month.
${job[0]} ${job[1]}${job[1]} ${job[0]}${job[0]} ${job[1]}${job[0]} ${job[1]}
%if len( jobs ) == 0: diff --git a/templates/webapps/reports/jobs_tool_per_month.mako b/templates/webapps/reports/jobs_tool_per_month.mako index 8d5eea5ad78..2bedfc24010 100644 --- a/templates/webapps/reports/jobs_tool_per_month.mako +++ b/templates/webapps/reports/jobs_tool_per_month.mako @@ -50,7 +50,7 @@ ${get_css()} %endif - ${make_sparkline(key, trends[key], "line", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ day")} <% ctr += 1 %> diff --git a/templates/webapps/reports/jobs_user_per_month.mako b/templates/webapps/reports/jobs_user_per_month.mako index d18d8c5235c..3ad804d040c 100644 --- a/templates/webapps/reports/jobs_user_per_month.mako +++ b/templates/webapps/reports/jobs_user_per_month.mako @@ -48,7 +48,7 @@ ${get_css()} %endif - ${make_sparkline(key, trends[key], "line", "/ day")} + ${make_sparkline(key, trends[key], "bar", "/ day")} <% ctr += 1 %> From 88471eb21b6b22c416ae9f6dd19cca8322b3e75c Mon Sep 17 00:00:00 2001 From: Airistotal Date: Fri, 26 Jun 2015 10:09:55 -0500 Subject: [PATCH 14/68] Fix where days/weeks/... reverted to days when sorting columns. Refactored time_period code into function. Applied sparklines to workflows pages. --- .../webapps/reports/controllers/jobs.py | 57 ++++------- .../webapps/reports/controllers/workflows.py | 95 ++++++++++++++++++- templates/webapps/reports/index.mako | 2 +- .../webapps/reports/jobs_errors_per_tool.mako | 6 +- templates/webapps/reports/jobs_per_tool.mako | 6 +- templates/webapps/reports/jobs_per_user.mako | 4 +- .../webapps/reports/jobs_user_per_month.mako | 4 +- .../reports/workflows_per_month_all.mako | 9 ++ .../webapps/reports/workflows_per_user.mako | 19 +++- .../reports/workflows_user_per_month.mako | 8 ++ 10 files changed, 155 insertions(+), 55 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 409edf6c80f..460fcbcb48b 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -52,6 +52,22 @@ def sorter(default_sort_id, kwd): return SortSpec(sort_id, order, arrow, _order) +def get_spark_time( time_period ): + _time_period = 0 + + if time_period == "days": + _time_period = 1.0 + elif time_period == "weeks": + _time_period = 7.0 + elif time_period == "months": + _time_period = 30.0 + elif time_period == "years": + _time_period = 365.0 + else: + time_period = "days" + _time_period = 1.0 + + return time_period, _time_period class SpecifiedDateListGrid( grids.Grid ): @@ -454,10 +470,8 @@ class Jobs( BaseUIController, ReportQueryBuilder ): jobs = [] for row in jobs_by_month.execute(): - month = int(row.date.strftime("%-m")) month_name = row.date.strftime("%B") year = int(row.date.strftime("%Y")) - wday, day_range = calendar.monthrange(year, month) jobs.append( ( row.date.strftime( "%Y-%m" ), @@ -557,17 +571,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): arrow = specs.arrow _order = specs.exc_order time_period = kwd.get('spark_time') - if time_period == "days": - _time_period = 1.0 - elif time_period == "weeks": - _time_period = 7.0 - elif time_period == "months": - _time_period = 30.0 - elif time_period == "years": - _time_period = 365.0 - else: - time_period = "days" - _time_period = 1.0 + time_period, _time_period = get_spark_time( time_period ) limit = 30 jobs = [] @@ -689,18 +693,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): arrow = specs.arrow _order = specs.exc_order time_period = kwd.get('spark_time') - if time_period == "days": - _time_period = 1.0 - elif time_period == "weeks": - _time_period = 7.0 - elif time_period == "months": - _time_period = 30.0 - elif time_period == "years": - _time_period = 365.0 - else: - time_period = "days" - _time_period = 1.0 - + time_period, _time_period = get_spark_time( time_period ) limit = 30 # In case we don't know which is the monitor user we will query for all jobs @@ -770,19 +763,9 @@ class Jobs( BaseUIController, ReportQueryBuilder ): arrow = specs.arrow _order = specs.exc_order time_period = kwd.get('spark_time') - if time_period == "days": - _time_period = 1.0 - elif time_period == "weeks": - _time_period = 7.0 - elif time_period == "months": - _time_period = 30.0 - elif time_period == "years": - _time_period = 365.0 - else: - time_period = "days" - _time_period = 1.0 - + time_period, _time_period = get_spark_time( time_period ) limit = 30 + # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index 562a1a55619..ef9c0abd7e2 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -1,14 +1,16 @@ import calendar -from datetime import date, timedelta +from datetime import datetime, date, timedelta from galaxy import eggs from galaxy import model, util from galaxy.model.orm import and_ +from math import floor from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids eggs.require( "SQLAlchemy >= 0.4" ) +import re import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder -from galaxy.webapps.reports.controllers.jobs import sorter +from galaxy.webapps.reports.controllers.jobs import sorter, get_spark_time import logging log = logging.getLogger( __name__ ) @@ -152,20 +154,46 @@ class Workflows( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order - q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), + + q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ), + sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), from_obj=[ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ), order_by=[ _order ] ) + + all_workflows = sa.select( ( self.select_day( model.StoredWorkflow.table.c.create_time ).label( 'date' ), + model.StoredWorkflow.table.c.id ) ) + + trends = dict() + for workflow in all_workflows.execute(): + workflow_day = int(workflow.date.strftime("%-d")) - 1 + workflow_month = int(workflow.date.strftime("%-m")) + workflow_month_name = workflow.date.strftime("%B") + workflow_year = workflow.date.strftime("%Y") + key = str( workflow_month_name + workflow_year) + + try: + trends[key][workflow_day] += 1 + except KeyError: + workflow_year = int(workflow_year) + wday, day_range = calendar.monthrange(workflow_year, workflow_month) + trends[key] = [0] * day_range + trends[key][workflow_day] += 1 + workflows = [] for row in q.execute(): + month_name = row.date.strftime("%B") + year = int(row.date.strftime("%Y")) + workflows.append( ( row.date.strftime( "%Y-%m" ), row.total_workflows, - row.date.strftime( "%B" ), - row.date.strftime( "%Y" ) ) ) + month_name, + year ) ) return trans.fill_template( '/webapps/reports/workflows_per_month_all.mako', order=order, arrow=arrow, sort_id=sort_id, + trends=trends, workflows=workflows, message=message ) @@ -177,12 +205,42 @@ class Workflows( BaseUIController, ReportQueryBuilder ): order = specs.order arrow = specs.arrow _order = specs.exc_order + time_period = kwd.get('spark_time') + time_period, _time_period = get_spark_time( time_period ) + limit=30 + workflows = [] q = sa.select( ( model.User.table.c.email.label( 'user_email' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), from_obj=[ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], group_by=[ 'user_email' ], order_by=[ _order ] ) + + all_workflows_per_user = sa.select( ( model.User.table.c.email.label( 'user_email' ), + self.select_day( model.StoredWorkflow.table.c.create_time ).label('date'), + model.StoredWorkflow.table.c.id ), + from_obj=[ sa.outerjoin( model.StoredWorkflow.table, + model.User.table ) ] ) + currday = datetime.today() + trends = dict() + for workflow in all_workflows_per_user.execute(): + curr_user = re.sub(r'\W+', '', workflow.user_email) + try: + day = currday - workflow.date + except TypeError: + day = datetime.date(currday) - datetime.date(workflow.date) + + day = day.days + container = floor(day / _time_period) + container = int(container) + try: + if container < limit: + trends[curr_user][container] += 1 + except KeyError: + trends[curr_user] = [0] * limit + if container < limit: + trends[curr_user][container] += 1 + for row in q.execute(): workflows.append( ( row.user_email, row.total_workflows ) ) @@ -190,6 +248,9 @@ class Workflows( BaseUIController, ReportQueryBuilder ): order=order, arrow=arrow, sort_id=sort_id, + limit=limit, + trends=trends, + time_period=time_period, workflows=workflows, message=message ) @@ -204,12 +265,35 @@ class Workflows( BaseUIController, ReportQueryBuilder ): _order = specs.exc_order email = util.restore_text( params.get( 'email', '' ) ) user_id = trans.security.decode_id( params.get( 'id', '' ) ) + q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), whereclause=model.StoredWorkflow.table.c.user_id == user_id, from_obj=[ model.StoredWorkflow.table ], group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ), order_by=[ _order ] ) + + all_workflows_user_month = sa.select( ( self.select_day( model.StoredWorkflow.table.c.create_time ).label( 'date' ), + model.StoredWorkflow.table.c.id ), + whereclause=model.StoredWorkflow.table.c.user_id == user_id, + from_obj=[ model.StoredWorkflow.table ] ) + + trends = dict() + for workflow in all_workflows_user_month.execute(): + workflow_day = int(workflow.date.strftime("%-d")) - 1 + workflow_month = int(workflow.date.strftime("%-m")) + workflow_month_name = workflow.date.strftime("%B") + workflow_year = workflow.date.strftime("%Y") + key = str( workflow_month_name + workflow_year) + + try: + trends[key][workflow_day] += 1 + except KeyError: + workflow_year = int(workflow_year) + wday, day_range = calendar.monthrange(workflow_year, workflow_month) + trends[key] = [0] * day_range + trends[key][workflow_day] += 1 + workflows = [] for row in q.execute(): workflows.append( ( row.date.strftime( "%Y-%m" ), @@ -221,6 +305,7 @@ class Workflows( BaseUIController, ReportQueryBuilder ): order=order, arrow=arrow, sort_id=sort_id, + trends=trends, workflows=workflows, message=message ) diff --git a/templates/webapps/reports/index.mako b/templates/webapps/reports/index.mako index 8a259dad093..c372d3ec438 100644 --- a/templates/webapps/reports/index.mako +++ b/templates/webapps/reports/index.mako @@ -53,7 +53,7 @@
Jobs in error per month
Jobs per user
Jobs per tool
-
Errors per tool
+
Errors per tool
diff --git a/templates/webapps/reports/jobs_errors_per_tool.mako b/templates/webapps/reports/jobs_errors_per_tool.mako index 9b0bb819288..dbf23d06f00 100644 --- a/templates/webapps/reports/jobs_errors_per_tool.mako +++ b/templates/webapps/reports/jobs_errors_per_tool.mako @@ -28,17 +28,17 @@ ${get_css()} %else: %if is_user_jobs_only: %else: %endif diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako index a6725de8b61..f0cc4ac8b7c 100644 --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -27,17 +27,17 @@ ${get_css()} %else: %if is_user_jobs_only: %else: %endif diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako index 95a1eec659e..f5252211e48 100644 --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -27,11 +27,11 @@ ${get_css()} %else: diff --git a/templates/webapps/reports/jobs_user_per_month.mako b/templates/webapps/reports/jobs_user_per_month.mako index 3ad804d040c..6b045916153 100644 --- a/templates/webapps/reports/jobs_user_per_month.mako +++ b/templates/webapps/reports/jobs_user_per_month.mako @@ -3,7 +3,9 @@ <%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> -<% from galaxy import util %> +<% + from galaxy import util +%> %if message: ${render_msg( message, 'done' )} diff --git a/templates/webapps/reports/workflows_per_month_all.mako b/templates/webapps/reports/workflows_per_month_all.mako index 23f21d65167..2416b135abe 100644 --- a/templates/webapps/reports/workflows_per_month_all.mako +++ b/templates/webapps/reports/workflows_per_month_all.mako @@ -1,11 +1,14 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> %if message: ${render_msg( message, 'done' )} %endif +${spark_css()} +${jqs_style()} ${get_css()}
@@ -27,6 +30,7 @@ ${get_css()} <% ctr = 0 %> %for workflow in workflows: + <% key = str(workflow[2]) + str(workflow[3]) %> <% month = workflow[0] total = workflow[1] @@ -38,6 +42,11 @@ ${get_css()} %endif
+ %try: + ${make_sparkline(key, trends[key], "bar", "/ day")} + %except KeyError: + %endtry + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/workflows_per_user.mako b/templates/webapps/reports/workflows_per_user.mako index cf0596322a1..20ea9419b9c 100644 --- a/templates/webapps/reports/workflows_per_user.mako +++ b/templates/webapps/reports/workflows_per_user.mako @@ -1,40 +1,48 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> +<%! + import re + from galaxy import util +%> %if message: ${render_msg( message, 'done' )} %endif +${spark_css()} +${jqs_style()} ${get_css()}

Workflows Per User

+
Graph goes from present to past ${make_spark_settings( "jobs", "per_user", limit, sort_id, order, time_period )}
There are no jobs.
${job[2]} ${job[3]} ${job[1]}
${job[2]} ${job[3]} ${job[1]}
- ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'errors_per_tool', 'Tool ID')} + ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'errors_per_tool', 'Tool ID', spark_time=time_period)} ${arrow} - ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User Jobs in Error')} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User Jobs in Error', spark_time=time_period)} ${arrow} - ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User and Monitor Jobs in Error')} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User and Monitor Jobs in Error', spark_time=time_period)} ${arrow}
- ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'per_tool', 'Tool ID')} + ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'per_tool', 'Tool ID', spark_time=time_period)} ${arrow} - ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User Jobs')} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User Jobs', spark_time=time_period)} ${arrow} - ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User and Monitor Jobs')} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User and Monitor Jobs', spark_time=time_period)} ${arrow}
- ${get_sort_url(sort_id, order, 'user_email', 'jobs', 'per_user', 'User')} + ${get_sort_url(sort_id, order, 'user_email', 'jobs', 'per_user', 'User', spark_time=time_period)} ${arrow} - ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_user', 'Total Jobs')} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_user', 'Total Jobs', spark_time=time_period)} ${arrow}
${month} ${total}
%if len( workflows ) == 0: %else: <% ctr = 0 %> %for workflow in workflows: <% - from galaxy import util email = workflow[0] total = workflow[1] user = trans.sa_session.query( trans.model.User ) \ .filter_by( email=email ) \ .one() + key = re.sub(r'\W+', '', workflow[0]) %> %if ctr % 2 == 1: @@ -43,6 +51,11 @@ ${get_css()} %endif + %try: + ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])} + %except KeyError: + %endtry + <% ctr += 1 %> %endfor diff --git a/templates/webapps/reports/workflows_user_per_month.mako b/templates/webapps/reports/workflows_user_per_month.mako index eb895740b46..f43266cc93f 100644 --- a/templates/webapps/reports/workflows_user_per_month.mako +++ b/templates/webapps/reports/workflows_user_per_month.mako @@ -1,5 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <% @@ -10,6 +11,7 @@ ${render_msg( message, 'done' )} %endif +${jqs_style()} ${get_css()} <% @@ -19,6 +21,9 @@ ${get_css()}

Workflows per month for user "${_email}"

+

+

Graph goes from first of the month to the last

+

There are no workflows
- ${get_sort_url(sort_id, order, 'user_email', 'workflows', 'per_user', 'User')} + ${get_sort_url(sort_id, order, 'user_email', 'workflows', 'per_user', 'User', spark_time=time_period)} ${arrow} - ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_user', 'Total Workflows')} + ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_user', 'Total Workflows', spark_time=time_period)} ${arrow}
${email} ${total}
%if len( workflows ) == 0: @@ -36,6 +41,7 @@ ${get_css()} <% ctr = 0 %> %for workflow in workflows: <% + key = workflow[2] + workflow[3] month = workflow[0] total = workflow[1] %> @@ -46,6 +52,8 @@ ${get_css()} %endif + ${make_sparkline(key, trends[key], "bar", "/ day")} + <% ctr += 1 %> %endfor From 263f6341274b06d60eb7e08d8bd834ad0b567c41 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Fri, 26 Jun 2015 10:17:21 -0500 Subject: [PATCH 15/68] Fixed up whitespaces --- lib/galaxy/webapps/reports/controllers/jobs.py | 2 ++ lib/galaxy/webapps/reports/controllers/workflows.py | 6 +++--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 460fcbcb48b..85131da4591 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -52,6 +52,7 @@ def sorter(default_sort_id, kwd): return SortSpec(sort_id, order, arrow, _order) + def get_spark_time( time_period ): _time_period = 0 @@ -69,6 +70,7 @@ def get_spark_time( time_period ): return time_period, _time_period + class SpecifiedDateListGrid( grids.Grid ): class JobIdColumn( grids.IntegerColumn ): diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index ef9c0abd7e2..41424e71934 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -160,7 +160,7 @@ class Workflows( BaseUIController, ReportQueryBuilder ): from_obj=[ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ), order_by=[ _order ] ) - + all_workflows = sa.select( ( self.select_day( model.StoredWorkflow.table.c.create_time ).label( 'date' ), model.StoredWorkflow.table.c.id ) ) @@ -207,7 +207,7 @@ class Workflows( BaseUIController, ReportQueryBuilder ): _order = specs.exc_order time_period = kwd.get('spark_time') time_period, _time_period = get_spark_time( time_period ) - limit=30 + limit = 30 workflows = [] q = sa.select( ( model.User.table.c.email.label( 'user_email' ), @@ -272,7 +272,7 @@ class Workflows( BaseUIController, ReportQueryBuilder ): from_obj=[ model.StoredWorkflow.table ], group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ), order_by=[ _order ] ) - + all_workflows_user_month = sa.select( ( self.select_day( model.StoredWorkflow.table.c.create_time ).label( 'date' ), model.StoredWorkflow.table.c.id ), whereclause=model.StoredWorkflow.table.c.user_id == user_id, From 328da98823722bb28ab09aa1caa00ca6085327c6 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Tue, 30 Jun 2015 09:46:50 -0500 Subject: [PATCH 16/68] Refactored and added styling --- client/galaxy/style/less/base.less | 29 +++++++++++++++++++ static/style/blue/base.css | 6 ++++ templates/spark_base.mako | 15 ---------- .../webapps/reports/jobs_errors_per_tool.mako | 10 +++---- .../webapps/reports/jobs_per_month_all.mako | 7 +++-- .../reports/jobs_per_month_in_error.mako | 7 +++-- templates/webapps/reports/jobs_per_tool.mako | 10 +++---- templates/webapps/reports/jobs_per_user.mako | 8 ++--- .../reports/jobs_specified_month_all.mako | 9 +++--- .../jobs_specified_month_in_error.mako | 9 +++--- .../webapps/reports/jobs_tool_per_month.mako | 7 +++-- .../webapps/reports/jobs_user_per_month.mako | 5 ++-- .../reports/registered_users_per_month.mako | 4 +-- .../registered_users_specified_month.mako | 4 +-- .../reports/requests_per_month_all.mako | 4 +-- .../webapps/reports/requests_per_user.mako | 4 +-- .../reports/requests_user_per_month.mako | 4 +-- .../reports/users_last_access_date.mako | 4 +-- .../reports/users_user_disk_usage.mako | 4 +-- .../reports/workflows_per_month_all.mako | 8 ++--- .../webapps/reports/workflows_per_user.mako | 8 ++--- .../reports/workflows_user_per_month.mako | 5 ++-- 22 files changed, 99 insertions(+), 72 deletions(-) diff --git a/client/galaxy/style/less/base.less b/client/galaxy/style/less/base.less index 80e8444b404..da5e65074e8 100644 --- a/client/galaxy/style/less/base.less +++ b/client/galaxy/style/less/base.less @@ -1705,3 +1705,32 @@ div.toolTitleNoSection #for_bears { display: none; } + +// ============================================================================ Reports Webapp + +.dir_arrow { + visibility: hidden +} + +#spark_time_select { + display: inline-block; +} + +#spark_select { + height: 23px; + width: 30px; + padding: 0; + border-radius: 2px; +} + +.quarter_width { + width: 25%; +} + +.third_width { + width: 30%; +} + +.half_width { + width: 50% +} diff --git a/static/style/blue/base.css b/static/style/blue/base.css index f1d6e219277..985db37d3f5 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2377,3 +2377,9 @@ div.toolTitleNoSection{padding-bottom:5px;font-weight:bold} .icon-button.chevron-expand:hover{background-image:url(sprite-fugue.png);background-position:0px -336px;width:16px;height:16px;height:16px} .icon-button.chevron-expand{background-image:url(sprite-fugue.png);background-position:0px -320px;width:16px;height:16px;height:16px} #for_bears{display:none} +.dir_arrow{visibility:hidden} +#spark_time_select{display:inline-block} +#spark_select{height:23px;width:30px;padding:0;border-radius:2px} +.quarter_width{width:25%} +.third_width{width:30%} +.half_width{width:50%} diff --git a/templates/spark_base.mako b/templates/spark_base.mako index ea19597f6b1..33c4c642052 100644 --- a/templates/spark_base.mako +++ b/templates/spark_base.mako @@ -8,21 +8,6 @@ -<%def name="spark_css()"> - - - <%def name="make_spark_settings( controller, action, limit, sort_id, order, time_period )">
diff --git a/templates/webapps/reports/jobs_errors_per_tool.mako b/templates/webapps/reports/jobs_errors_per_tool.mako index dbf23d06f00..28defe9c22c 100644 --- a/templates/webapps/reports/jobs_errors_per_tool.mako +++ b/templates/webapps/reports/jobs_errors_per_tool.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <%! import re @@ -10,7 +10,6 @@ ${render_msg( message, 'done' )} %endif -${spark_css()} ${jqs_style()} ${get_css()} @@ -27,21 +26,22 @@ ${get_css()}
%else: - %if is_user_jobs_only: - %else: - %endif + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_per_month_all.mako b/templates/webapps/reports/jobs_per_month_all.mako index fcb5d9ce348..7cd4bf29d4c 100644 --- a/templates/webapps/reports/jobs_per_month_all.mako +++ b/templates/webapps/reports/jobs_per_month_all.mako @@ -20,21 +20,22 @@ ${get_css()} %else: - %if is_user_jobs_only: - %else: - %endif + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_per_month_in_error.mako b/templates/webapps/reports/jobs_per_month_in_error.mako index 742fd1e3d79..5c58b33b4aa 100644 --- a/templates/webapps/reports/jobs_per_month_in_error.mako +++ b/templates/webapps/reports/jobs_per_month_in_error.mako @@ -20,21 +20,22 @@ ${get_css()} %else: - %if is_user_jobs_only: - %else: - %endif + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako index f0cc4ac8b7c..b6c840fbfb7 100644 --- a/templates/webapps/reports/jobs_per_tool.mako +++ b/templates/webapps/reports/jobs_per_tool.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <%! import re @@ -10,7 +10,6 @@ ${render_msg( message, 'done' )} %endif -${spark_css()} ${jqs_style()} ${get_css()} @@ -26,21 +25,22 @@ ${get_css()} %else: - %if is_user_jobs_only: - %else: - %endif + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako index f5252211e48..c7886cfd380 100644 --- a/templates/webapps/reports/jobs_per_user.mako +++ b/templates/webapps/reports/jobs_per_user.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <%! import re @@ -10,7 +10,6 @@ ${render_msg( message, 'done' )} %endif -${spark_css()} ${jqs_style()} ${get_css()} @@ -26,14 +25,15 @@ ${get_css()} %else: - - + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_specified_month_all.mako b/templates/webapps/reports/jobs_specified_month_all.mako index 69b97d4492a..cb4f021dccf 100644 --- a/templates/webapps/reports/jobs_specified_month_all.mako +++ b/templates/webapps/reports/jobs_specified_month_all.mako @@ -20,22 +20,23 @@ ${get_css()} %else: - - + %if is_user_jobs_only: - %else: - %endif + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_specified_month_in_error.mako b/templates/webapps/reports/jobs_specified_month_in_error.mako index 807205b0019..daf8b0506bf 100644 --- a/templates/webapps/reports/jobs_specified_month_in_error.mako +++ b/templates/webapps/reports/jobs_specified_month_in_error.mako @@ -19,22 +19,23 @@ ${get_css()} %else: - - + %if is_user_jobs_only: - %else: - %endif + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_tool_per_month.mako b/templates/webapps/reports/jobs_tool_per_month.mako index 2bedfc24010..58e159f030c 100644 --- a/templates/webapps/reports/jobs_tool_per_month.mako +++ b/templates/webapps/reports/jobs_tool_per_month.mako @@ -24,21 +24,22 @@ ${get_css()} %else: - %if is_user_jobs_only: - %else: - %endif + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/jobs_user_per_month.mako b/templates/webapps/reports/jobs_user_per_month.mako index 6b045916153..d254d477ea5 100644 --- a/templates/webapps/reports/jobs_user_per_month.mako +++ b/templates/webapps/reports/jobs_user_per_month.mako @@ -31,14 +31,15 @@ ${get_css()} %else: - - + <% ctr = 0 %> %for job in jobs: diff --git a/templates/webapps/reports/registered_users_per_month.mako b/templates/webapps/reports/registered_users_per_month.mako index 5b54030f52a..8653a7741b6 100644 --- a/templates/webapps/reports/registered_users_per_month.mako +++ b/templates/webapps/reports/registered_users_per_month.mako @@ -17,11 +17,11 @@ ${get_css()} %else: - - diff --git a/templates/webapps/reports/registered_users_specified_month.mako b/templates/webapps/reports/registered_users_specified_month.mako index 0f63a3da3ce..f912d6aca36 100644 --- a/templates/webapps/reports/registered_users_specified_month.mako +++ b/templates/webapps/reports/registered_users_specified_month.mako @@ -14,8 +14,8 @@ %else: - - + + <% ctr = 0 %> %for user in users: diff --git a/templates/webapps/reports/requests_per_month_all.mako b/templates/webapps/reports/requests_per_month_all.mako index 2cd67314e45..a36ced7e8ee 100644 --- a/templates/webapps/reports/requests_per_month_all.mako +++ b/templates/webapps/reports/requests_per_month_all.mako @@ -13,8 +13,8 @@ %else: - - + + <% ctr = 0 %> %for request in requests: diff --git a/templates/webapps/reports/requests_per_user.mako b/templates/webapps/reports/requests_per_user.mako index 0eff425889f..f2727b0e6df 100644 --- a/templates/webapps/reports/requests_per_user.mako +++ b/templates/webapps/reports/requests_per_user.mako @@ -13,8 +13,8 @@ %else: - - + + <% ctr = 0 %> %for request in requests: diff --git a/templates/webapps/reports/requests_user_per_month.mako b/templates/webapps/reports/requests_user_per_month.mako index e3a78a52118..b3d5a2823ca 100644 --- a/templates/webapps/reports/requests_user_per_month.mako +++ b/templates/webapps/reports/requests_user_per_month.mako @@ -20,11 +20,11 @@ ${get_css()} %else: - - diff --git a/templates/webapps/reports/users_last_access_date.mako b/templates/webapps/reports/users_last_access_date.mako index 9a0b31ae5dc..a3564792e05 100644 --- a/templates/webapps/reports/users_last_access_date.mako +++ b/templates/webapps/reports/users_last_access_date.mako @@ -34,11 +34,11 @@ ${get_css()}
There are no workflows for user "${_email}"
${month} ${total}
There are no jobs in the error state.
+ ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'errors_per_tool', 'Tool ID', spark_time=time_period)} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User Jobs in Error', spark_time=time_period)} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'errors_per_tool', 'User and Monitor Jobs in Error', spark_time=time_period)} ${arrow}
There are no jobs.
+ ${get_sort_url(sort_id, order, 'date', 'jobs', 'per_month_all', 'Month')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_all', 'User Jobs')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_all', 'User and Monitor Jobs')} ${arrow}
There are no jobs in the error state.
+ ${get_sort_url(sort_id, order, 'date', 'jobs', 'per_month_in_error', 'Month')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_in_error', 'User Jobs')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_month_in_error', 'User and Monitor Jobs')} ${arrow}
There are no jobs.
+ ${get_sort_url(sort_id, order, 'tool_id', 'jobs', 'per_tool', 'Tool ID', spark_time=time_period)} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User Jobs', spark_time=time_period)} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_tool', 'User and Monitor Jobs', spark_time=time_period)} ${arrow}
There are no jobs.
+ ${get_sort_url(sort_id, order, 'user_email', 'jobs', 'per_user', 'User', spark_time=time_period)} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'per_user', 'Total Jobs', spark_time=time_period)} ${arrow}
There are no jobs for ${month_label} ${year_label}
Day + Day ${get_sort_url(sort_id, order, 'date', 'jobs', 'specified_month_all', 'Date')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_all', 'User Jobs')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_all', 'User and Monitor Jobs')} ${arrow}
There are no jobs in the error state for ${month_label} ${year_label}
Day + Day ${get_sort_url(sort_id, order, 'date', 'jobs', 'specified_month_in_error', 'Date')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_in_error', 'User Jobs in Error')} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'specified_month_in_error', 'User and Monitor Jobs in Error')} ${arrow}
There are no jobs for tool "${tool_id}"
+ ${get_sort_url(sort_id, order, 'date', 'jobs', 'tool_per_month', 'Month', tool_id=tool_id)} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'tool_per_month', 'User Jobs', tool_id=tool_id)} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'tool_per_month', 'User and Monitor Jobs', tool_id=tool_id)} ${arrow}
There are no jobs for user "${ _email }"
+ ${get_sort_url(sort_id, order, 'date', 'jobs', 'user_per_month', 'Month', email=email )} ${arrow} + ${get_sort_url(sort_id, order, 'total_jobs', 'jobs', 'user_per_month', 'Total Jobs', email=email)} ${arrow}
There are no registered users
+ ${get_sort_url(sort_id, order, 'date', 'users', 'registered_users_per_month', 'Month')} ${arrow} + ${get_sort_url(sort_id, order, 'num_users', 'users', 'registered_users_per_month', 'Number of Registrations')} ${arrow}
There are no user registrations for ${month_label} ${year_label}
DayNew RegistrationsDayNew Registrations
There are no requests
MonthTotalMonthTotal
There are no requests
UserTotal RequestsUserTotal Requests
There are no requests for user "${util.restore_text( email )}"
+ ${get_sort_url(sort_id, order, 'date', 'users' 'requests_users_per_month', 'Month')} ${arrow} Total + Total ${get_sort_url(sort_id, order, 'num_users', 'users' 'requests_users_per_month', 'Month')} ${arrow}
%if users: - - diff --git a/templates/webapps/reports/users_user_disk_usage.mako b/templates/webapps/reports/users_user_disk_usage.mako index d2511140f6c..c232bf1dcc6 100644 --- a/templates/webapps/reports/users_user_disk_usage.mako +++ b/templates/webapps/reports/users_user_disk_usage.mako @@ -27,11 +27,11 @@ ${get_css()}
+ ${get_sort_url(sort_id, order, 'zero', 'users', 'last_access_date', 'Email', days_not_logged_in=days_not_logged_in)} ${arrow} + ${get_sort_url(sort_id, order, 'one', 'users', 'last_access_date', 'Date of last Login', days_not_logged_in=days_not_logged_in)} ${arrow}
%if users: - - diff --git a/templates/webapps/reports/workflows_per_month_all.mako b/templates/webapps/reports/workflows_per_month_all.mako index 2416b135abe..4b0fdf24496 100644 --- a/templates/webapps/reports/workflows_per_month_all.mako +++ b/templates/webapps/reports/workflows_per_month_all.mako @@ -1,13 +1,12 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings" /> %if message: ${render_msg( message, 'done' )} %endif -${spark_css()} ${jqs_style()} ${get_css()} @@ -19,14 +18,15 @@ ${get_css()} %else: - - + <% ctr = 0 %> %for workflow in workflows: diff --git a/templates/webapps/reports/workflows_per_user.mako b/templates/webapps/reports/workflows_per_user.mako index 20ea9419b9c..6299aeb2d3d 100644 --- a/templates/webapps/reports/workflows_per_user.mako +++ b/templates/webapps/reports/workflows_per_user.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings, spark_css" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings" /> <%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> <%! import re @@ -11,7 +11,6 @@ ${render_msg( message, 'done' )} %endif -${spark_css()} ${jqs_style()} ${get_css()} @@ -24,15 +23,16 @@ ${get_css()} %else: - - + <% ctr = 0 %> %for workflow in workflows: diff --git a/templates/webapps/reports/workflows_user_per_month.mako b/templates/webapps/reports/workflows_user_per_month.mako index f43266cc93f..6d2f50cd084 100644 --- a/templates/webapps/reports/workflows_user_per_month.mako +++ b/templates/webapps/reports/workflows_user_per_month.mako @@ -29,14 +29,15 @@ ${get_css()} %else: - - + <% ctr = 0 %> %for workflow in workflows: From 860c39b48c37ca4bb37c2be555b983d1cd95f8a7 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Tue, 30 Jun 2015 10:44:06 -0500 Subject: [PATCH 17/68] Added new Runs per workflow page --- .../webapps/reports/controllers/workflows.py | 69 +++++++++++++++++++ templates/webapps/reports/index.mako | 1 + .../reports/workflows_per_workflow.mako | 65 +++++++++++++++++ 3 files changed, 135 insertions(+) create mode 100644 templates/webapps/reports/workflows_per_workflow.mako diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index 562a1a55619..ac6ea5b56f6 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -223,6 +223,75 @@ class Workflows( BaseUIController, ReportQueryBuilder ): sort_id=sort_id, workflows=workflows, message=message ) + + @web.expose + def per_workflow( self, trans, **kwd ): + message = '' + + params = util.Params( kwd ) + specs = sorter( 'workflow_name', kwd ) + sort_id = specs.sort_id + order = specs.order + arrow = specs.arrow + _order = specs.exc_order + time_period = kwd.get('spark_time') + time_period, _time_period = get_spark_time( time_period ) + limit = 30 + + # In case we don't know which is the monitor user we will query for all jobs + + q = sa.select( ( model.Workflow.table.c.id.label( 'workflow_id' ), + sa.func.min(model.Workflow.table.c.name).label( 'workflow_name' ), + sa.func.count( model.WorkflowInvocation.table.c.id ).label( 'total_runs' ) ), + from_obj=[ model.Workflow.table, + model.WorkflowInvocation.table ], + whereclause=sa.and_( model.WorkflowInvocation.table.c.workflow_id==model.Workflow.table.c.id ), + group_by=[ model.Workflow.table.c.id ], + order_by=[ _order ] + ) + + all_runs_per_workflow = sa.select( ( model.Workflow.table.c.id.label( 'workflow_id' ), + model.Workflow.table.c.name.label( 'workflow_name' ), + self.select_day( model.WorkflowInvocation.table.c.create_time ).label( 'date' ) ), + from_obj=[ model.Workflow.table, + model.WorkflowInvocation.table ], + whereclause=sa.and_( model.WorkflowInvocation.table.c.workflow_id==model.Workflow.table.c.id ) ) + + currday = date.today() + trends = dict() + for run in all_runs_per_workflow.execute(): + curr_tool = re.sub(r'\W+', '', str(run.workflow_id)) + try: + day = currday - run.date + except TypeError: + day = currday - datetime.date(run.date) + + day = day.days + container = floor(day / _time_period) + container = int(container) + try: + if container < limit: + trends[curr_tool][container] += 1 + except KeyError: + trends[curr_tool] = [0] * limit + if container < limit: + trends[curr_tool][container] += 1 + + runs = [] + for row in q.execute(): + runs.append( ( row.workflow_name, + row.total_runs, + row.workflow_id) ) + + return trans.fill_template( '/webapps/reports/workflows_per_workflow.mako', + order=order, + arrow=arrow, + sort_id=sort_id, + limit=limit, + time_period=time_period, + trends=trends, + runs=runs, + message=message) # ---- Utility methods ------------------------------------------------------- diff --git a/templates/webapps/reports/index.mako b/templates/webapps/reports/index.mako index 0ab41755770..5f8c72f34fb 100644 --- a/templates/webapps/reports/index.mako +++ b/templates/webapps/reports/index.mako @@ -74,6 +74,7 @@
+
Runs per Workflows
Workflows per month
Workflows per user
diff --git a/templates/webapps/reports/workflows_per_workflow.mako b/templates/webapps/reports/workflows_per_workflow.mako new file mode 100644 index 00000000000..0dc1c59a617 --- /dev/null +++ b/templates/webapps/reports/workflows_per_workflow.mako @@ -0,0 +1,65 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/spark_base.mako" import="jqs_style, make_sparkline, make_spark_settings" /> +<%namespace file="/sorting_base.mako" import="get_sort_url, get_css" /> +<%! + import re +%> + +%if message: + ${render_msg( message, 'done' )} +%endif + +${jqs_style()} +${get_css()} + + +
+
+

Runs per Workflow

+
+ Graph goes from present to past ${make_spark_settings( 'workflows', 'per_workflow', limit, sort_id, order, time_period )} +
+
+ ${get_sort_url(sort_id, order, 'email', 'users', 'user_disk_usage', 'Email')} + ${get_sort_url(sort_id, order, 'disk_usage', 'users', 'user_disk_usage', 'Disk Usage')} ${arrow}
There are no workflows
+ ${get_sort_url(sort_id, order, 'date', 'workflows', 'per_month_all', 'Month')} ${arrow} + ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_month_all', 'Total')} ${arrow}
There are no workflows
+ ${get_sort_url(sort_id, order, 'user_email', 'workflows', 'per_user', 'User', spark_time=time_period)} ${arrow} + ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'per_user', 'Total Workflows', spark_time=time_period)} ${arrow}
There are no workflows for user "${_email}"
+ ${get_sort_url(sort_id, order, 'date', 'workflows', 'user_per_month', 'Month', email=util.sanitize_text( email ))} ${arrow} + ${get_sort_url(sort_id, order, 'total_workflows', 'workflows', 'user_per_month', 'Total', email=util.sanitize_text( email ))} ${arrow}
+ %if len( runs ) == 0: + + %else: + + + + + + + <% ctr = 0 %> + %for run in runs: + <% key = re.sub(r'\W+', '', str(run[2])) %> + %if ctr % 2 == 1: + + %else: + + %endif + + + + %try: + ${make_sparkline(key, trends[key], "bar", "/ " + time_period[:-1])} + %except KeyError: + %endtry + + + <% ctr += 1 %> + %endfor + %endif +
There are no runs.
+ ${get_sort_url(sort_id, order, 'workflow_id', 'workflows', 'per_workflow', 'Workflow ID', spark_time=time_period)} + ${arrow} + + ${get_sort_url(sort_id, order, 'workflow_name', 'workflows', 'per_workflow', 'Workflow Name', spark_time=time_period)} + ${arrow} + + ${get_sort_url(sort_id, order, 'total_runs', 'workflows', 'per_workflow', 'Workflow Runs', spark_time=time_period)} + ${arrow} +
${run[2]}${run[0]}${run[1]}
+
+
+ From 33154aaac535fcac0c1a1b6ee9aa0617736862ba Mon Sep 17 00:00:00 2001 From: Airistotal Date: Tue, 30 Jun 2015 10:50:06 -0500 Subject: [PATCH 18/68] Fixed formatting --- lib/galaxy/webapps/reports/controllers/workflows.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index 5232323a10e..b11ced0d3fc 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -308,12 +308,11 @@ class Workflows( BaseUIController, ReportQueryBuilder ): trends=trends, workflows=workflows, message=message ) - + @web.expose def per_workflow( self, trans, **kwd ): message = '' - params = util.Params( kwd ) specs = sorter( 'workflow_name', kwd ) sort_id = specs.sort_id order = specs.order @@ -330,17 +329,16 @@ class Workflows( BaseUIController, ReportQueryBuilder ): sa.func.count( model.WorkflowInvocation.table.c.id ).label( 'total_runs' ) ), from_obj=[ model.Workflow.table, model.WorkflowInvocation.table ], - whereclause=sa.and_( model.WorkflowInvocation.table.c.workflow_id==model.Workflow.table.c.id ), + whereclause=sa.and_( model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id ), group_by=[ model.Workflow.table.c.id ], - order_by=[ _order ] - ) + order_by=[ _order ] ) all_runs_per_workflow = sa.select( ( model.Workflow.table.c.id.label( 'workflow_id' ), model.Workflow.table.c.name.label( 'workflow_name' ), self.select_day( model.WorkflowInvocation.table.c.create_time ).label( 'date' ) ), from_obj=[ model.Workflow.table, model.WorkflowInvocation.table ], - whereclause=sa.and_( model.WorkflowInvocation.table.c.workflow_id==model.Workflow.table.c.id ) ) + whereclause=sa.and_( model.WorkflowInvocation.table.c.workflow_id == model.Workflow.table.c.id ) ) currday = date.today() trends = dict() From 1b23081d41e28eccbd1f6dc4326e8f8340ba73c0 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 17 Jul 2015 14:00:39 +0100 Subject: [PATCH 19/68] Refactor reports styling out into its own less file. This was it doesn't need to be loaded for Galaxy. --- client/galaxy/style/less/base.less | 29 ---------------------- client/galaxy/style/less/reports.less | 28 +++++++++++++++++++++ client/grunt-tasks/style.js | 5 ++-- static/style/blue/base.css | 6 ----- static/style/blue/reports.css | 6 +++++ templates/webapps/reports/base_panels.mako | 6 +++++ 6 files changed, 43 insertions(+), 37 deletions(-) create mode 100644 client/galaxy/style/less/reports.less create mode 100644 static/style/blue/reports.css diff --git a/client/galaxy/style/less/base.less b/client/galaxy/style/less/base.less index da5e65074e8..80e8444b404 100644 --- a/client/galaxy/style/less/base.less +++ b/client/galaxy/style/less/base.less @@ -1705,32 +1705,3 @@ div.toolTitleNoSection #for_bears { display: none; } - -// ============================================================================ Reports Webapp - -.dir_arrow { - visibility: hidden -} - -#spark_time_select { - display: inline-block; -} - -#spark_select { - height: 23px; - width: 30px; - padding: 0; - border-radius: 2px; -} - -.quarter_width { - width: 25%; -} - -.third_width { - width: 30%; -} - -.half_width { - width: 50% -} diff --git a/client/galaxy/style/less/reports.less b/client/galaxy/style/less/reports.less new file mode 100644 index 00000000000..ddb102759e0 --- /dev/null +++ b/client/galaxy/style/less/reports.less @@ -0,0 +1,28 @@ +// ============================================================================ Reports Webapp + +.dir_arrow { + visibility: hidden +} + +#spark_time_select { + display: inline-block; +} + +#spark_select { + height: 23px; + width: 30px; + padding: 0; + border-radius: 2px; +} + +.quarter_width { + width: 25%; +} + +.third_width { + width: 30%; +} + +.half_width { + width: 50% +} diff --git a/client/grunt-tasks/style.js b/client/grunt-tasks/style.js index 47be772bf8d..97dad713735 100644 --- a/client/grunt-tasks/style.js +++ b/client/grunt-tasks/style.js @@ -20,7 +20,8 @@ module.exports = function( grunt ){ 'masthead', 'library', 'trackster', - 'circster' + 'circster', + 'reports' ]; @@ -79,4 +80,4 @@ module.exports = function( grunt ){ }); grunt.registerTask( 'style', [ 'sprite', 'less-site-config', 'less', 'clean' ] ); -}; \ No newline at end of file +}; diff --git a/static/style/blue/base.css b/static/style/blue/base.css index 985db37d3f5..f1d6e219277 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2377,9 +2377,3 @@ div.toolTitleNoSection{padding-bottom:5px;font-weight:bold} .icon-button.chevron-expand:hover{background-image:url(sprite-fugue.png);background-position:0px -336px;width:16px;height:16px;height:16px} .icon-button.chevron-expand{background-image:url(sprite-fugue.png);background-position:0px -320px;width:16px;height:16px;height:16px} #for_bears{display:none} -.dir_arrow{visibility:hidden} -#spark_time_select{display:inline-block} -#spark_select{height:23px;width:30px;padding:0;border-radius:2px} -.quarter_width{width:25%} -.third_width{width:30%} -.half_width{width:50%} diff --git a/static/style/blue/reports.css b/static/style/blue/reports.css new file mode 100644 index 00000000000..cc14661617f --- /dev/null +++ b/static/style/blue/reports.css @@ -0,0 +1,6 @@ +.dir_arrow{visibility:hidden} +#spark_time_select{display:inline-block} +#spark_select{height:23px;width:30px;padding:0;border-radius:2px} +.quarter_width{width:25%} +.third_width{width:30%} +.half_width{width:50%} diff --git a/templates/webapps/reports/base_panels.mako b/templates/webapps/reports/base_panels.mako index d2c3f3623ff..84bd5624026 100644 --- a/templates/webapps/reports/base_panels.mako +++ b/templates/webapps/reports/base_panels.mako @@ -1,5 +1,11 @@ <%inherit file="/base/base_panels.mako"/> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "reports" )} + + + ## Default title <%def name="title()">Galaxy Reports From 1ac9e5f05492e16a0cdd1409875efb6aec94d9cd Mon Sep 17 00:00:00 2001 From: Airistotal Date: Fri, 17 Jul 2015 14:33:34 -0500 Subject: [PATCH 20/68] Fixed import clash --- lib/galaxy/webapps/reports/controllers/jobs.py | 1 - lib/galaxy/webapps/reports/controllers/workflows.py | 1 - 2 files changed, 2 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index f5413c20f11..713c7b40afe 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -12,7 +12,6 @@ from sqlalchemy import and_, not_, or_ from galaxy import model, util from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids -from galaxy.model.orm import and_, not_, or_ from math import floor import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index 78c1cf45d1e..66270290f53 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -7,7 +7,6 @@ import sqlalchemy as sa from sqlalchemy import and_ from galaxy import model, util -from galaxy.model.orm import and_ from math import floor from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids From 6f4eeb28e3ea8bba34e80b6543b837f2ee834a5b Mon Sep 17 00:00:00 2001 From: Airistotal Date: Fri, 17 Jul 2015 14:41:10 -0500 Subject: [PATCH 21/68] Removed duplicate import --- lib/galaxy/webapps/reports/controllers/jobs.py | 1 - lib/galaxy/webapps/reports/controllers/workflows.py | 1 - 2 files changed, 2 deletions(-) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 713c7b40afe..755e42a9573 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -16,7 +16,6 @@ from math import floor import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import re -import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder log = logging.getLogger( __name__ ) diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index 66270290f53..4fdc9f92aca 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -12,7 +12,6 @@ from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids eggs.require( "SQLAlchemy >= 0.4" ) import re -import sqlalchemy as sa from galaxy.webapps.reports.controllers.query import ReportQueryBuilder from galaxy.webapps.reports.controllers.jobs import sorter, get_spark_time From e55c5e5d9d4d5bf878570ebe9d8b1803f3404204 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Tue, 28 Jul 2015 08:36:13 -0400 Subject: [PATCH 22/68] Fix the ChangeDirectory.execute_step() method and enhance the "directory" recipe step classes to perform within the temporary working directory created by the InstallEnvironment.make_tmp_dir() method (via the use of a new TMP_WORK_DIR reserved word in recipes) in addition to the $INSTALL_DIR reserved word (which has always been supported in recipes). This commit grew out of a fix for the following code in the ChangeDirectory.execute_step() method, which does not perform as the comment describes: ================= # Change directory to a directory above the current working directory, but within the defined work_dir. dir = target_directory.replace( os.path.realpath( work_dir ), '' ).lstrip( '/' ) ================== The resulting directory is always within the current working directory rather than "above" it. The new TMP_WORK_DIR reserved word points to the actual temporary working directory, so recipes now have a way to do perform actions within that directory during the compilation and installation process. --- .../tool_dependencies/recipe/step_handler.py | 79 +++++++++++++------ 1 file changed, 55 insertions(+), 24 deletions(-) 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 248d2a4c051..df81eaa923f 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 @@ -248,7 +248,31 @@ class RecipeStep( object ): raise "Unimplemented Method" -class AssertDirectoryExecutable( RecipeStep ): +class DirectoryRecipeStep( RecipeStep ): + """ + Class for handling recipe steps related to directory actions during the + installation process. Recipes that use the TMP_WORK_DIR reserved word + enable sub-classes (e.g., MakeDirectory, ChangeDirectory, etc) to perform + actions via the subclass's execute_step() method within the temporary + working directory created by the InstallEnvironment.make_tmp_dir() method. + This mirrors the same behavior that results from the use of the $INSTALL_DIR + keyword, where the subclasses perform the same directory actions within + the installation environment rather than the working environment. + """ + + def set_directory_path( self, work_dir, current_dir, target_dir ): + """ + This method currently replaces the TMP_WORK_DIR keyword with the path + to the temporary working directory. + """ + if target_dir.startswith( 'TMP_WORK_DIR' ): + target_dir = target_dir.replace( 'TMP_WORK_DIR', os.path.realpath( work_dir ) ) + elif current_dir is not None: + target_dir = os.path.join( current_dir, target_dir ) + return os.path.normpath( target_dir ) + + +class AssertDirectoryExecutable( DirectoryRecipeStep ): def __init__( self, app ): self.app = app @@ -277,10 +301,11 @@ class AssertDirectoryExecutable( RecipeStep ): Since this class is not used in the initial download stage, no recipe step filtering is performed here, and None values are always returned for filtered_actions and dir. """ - if os.path.isabs( action_dict[ 'full_path' ] ): - full_path = action_dict[ 'full_path' ] + tmp_path = self.set_directory_path( work_dir, current_dir, action_dict[ 'full_path' ] ) + if os.path.isabs( tmp_path ): + full_path = tmp_path else: - full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + full_path = os.path.join( current_dir, tmp_path ) if not self.assert_directory_executable( full_path=full_path ): status = self.app.install_model.ToolDependency.installation_status.ERROR error_message = 'The path %s is not a directory or is not executable by the owner.' % str( full_path ) @@ -298,7 +323,7 @@ class AssertDirectoryExecutable( RecipeStep ): return action_dict -class AssertDirectoryExists( RecipeStep ): +class AssertDirectoryExists( DirectoryRecipeStep ): def __init__( self, app ): self.app = app @@ -323,10 +348,11 @@ class AssertDirectoryExists( RecipeStep ): class is not used in the initial download stage, no recipe step filtering is performed here, and None values are always returned for filtered_actions and dir. """ - if os.path.isabs( action_dict[ 'full_path' ] ): - full_path = action_dict[ 'full_path' ] + tmp_path = self.set_directory_path( work_dir, current_dir, action_dict[ 'full_path' ] ) + if os.path.isabs( tmp_path ): + full_path = tmp_path else: - full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + full_path = os.path.join( current_dir, tmp_path ) if not self.assert_directory_exists( full_path=full_path ): status = self.app.install_model.ToolDependency.installation_status.ERROR error_message = 'The path %s is not a directory or does not exist.' % str( full_path ) @@ -476,7 +502,7 @@ class Autoconf( RecipeStep ): return action_dict -class ChangeDirectory( RecipeStep ): +class ChangeDirectory( DirectoryRecipeStep ): def __init__( self, app ): self.app = app @@ -489,15 +515,13 @@ class ChangeDirectory( RecipeStep ): no recipe step filtering is performed here and a None value is return for filtered_actions. However, the new dir value is returned since it is needed for later steps. """ - target_directory = os.path.realpath( os.path.normpath( os.path.join( current_dir, action_dict[ 'directory' ] ) ) ) - if target_directory.startswith( os.path.realpath( current_dir ) ) and os.path.exists( target_directory ): - # Change directory to a directory within the current working directory. - dir = target_directory - elif target_directory.startswith( os.path.realpath( work_dir ) ) and os.path.exists( target_directory ): - # Change directory to a directory above the current working directory, but within the defined work_dir. - dir = target_directory.replace( os.path.realpath( work_dir ), '' ).lstrip( '/' ) + target_directory = self.set_directory_path( work_dir, current_dir, action_dict[ 'directory' ] ) + if target_directory.startswith( os.path.realpath( work_dir ) ) and os.path.exists( target_directory ): + # Change directory to a directory either above or within current_dir, + # which is within the defined work_dir. + dir = os.path.normpath( target_directory ) else: - log.debug( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.', target_directory ) + log.debug( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.' % str( target_directory ) ) dir = current_dir return tool_dependency, None, dir @@ -760,7 +784,7 @@ class DownloadFile( Download, RecipeStep ): return action_dict -class MakeDirectory( RecipeStep ): +class MakeDirectory( DirectoryRecipeStep ): def __init__( self, app ): self.app = app @@ -772,10 +796,11 @@ class MakeDirectory( RecipeStep ): Make a directory on disk. Since this class is not used in the initial download stage, no recipe step filtering is performed here, and None values are always returned for filtered_actions and dir. """ - if os.path.isabs( action_dict[ 'full_path' ] ): - full_path = action_dict[ 'full_path' ] + tmp_dir = self.set_directory_path( work_dir, current_dir, action_dict[ 'full_path' ] ) + if os.path.isabs( tmp_dir ): + full_path = tmp_dir else: - full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + full_path = os.path.join( current_dir, tmp_dir ) self.make_directory( full_path=full_path ) return tool_dependency, None, None @@ -821,7 +846,7 @@ class MakeInstall( RecipeStep ): return action_dict -class MoveDirectoryFiles( RecipeStep ): +class MoveDirectoryFiles( DirectoryRecipeStep ): def __init__( self, app ): self.app = app @@ -833,9 +858,15 @@ class MoveDirectoryFiles( RecipeStep ): Move a directory of files. Since this class is not used in the initial download stage, no recipe step filtering is performed here, and None values are always returned for filtered_actions and dir. """ + source_dir = self.set_directory_path( work_dir, + current_dir, + action_dict[ 'source_directory' ] ) + destination_dir = self.set_directory_path( work_dir, + current_dir, + action_dict[ 'destination_directory' ] ) self.move_directory_files( current_dir=current_dir, - source_dir=os.path.join( action_dict[ 'source_directory' ] ), - destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) ) + source_dir=source_dir, + destination_dir=destination_dir ) return tool_dependency, None, None def move_directory_files( self, current_dir, source_dir, destination_dir ): From 2c2f49bf8e980ff7879452f0073ec755906f5591 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Wed, 29 Jul 2015 13:57:34 -0400 Subject: [PATCH 23/68] Visualizations, trackster: allow the user to add the dataset launched from as a new track in an existing trackster visualization; add utils/query-string-parsing.js for pulling query params from the query string --- .../scripts/utils/query-string-parsing.js | 21 +++++ client/galaxy/scripts/viz/trackster.js | 84 +++++++++++++++++-- .../trackster/config/trackster.xml | 1 + static/maps/utils/query-string-parsing.js.map | 1 + static/maps/viz/trackster.js.map | 2 +- static/scripts/utils/query-string-parsing.js | 2 + static/scripts/viz/trackster.js | 2 +- 7 files changed, 106 insertions(+), 7 deletions(-) create mode 100644 client/galaxy/scripts/utils/query-string-parsing.js create mode 100644 static/maps/utils/query-string-parsing.js.map create mode 100644 static/scripts/utils/query-string-parsing.js diff --git a/client/galaxy/scripts/utils/query-string-parsing.js b/client/galaxy/scripts/utils/query-string-parsing.js new file mode 100644 index 00000000000..8b5ec29433d --- /dev/null +++ b/client/galaxy/scripts/utils/query-string-parsing.js @@ -0,0 +1,21 @@ +define([], function(){ +// ============================================================================ +function get( key, queryString ){ + queryString = queryString || window.location.search.substr( 1 ); + var keyRegex = new RegExp( key + '=([^&#$]+)' ), + matches = queryString.match( keyRegex ); + if( !matches || !matches.length ){ + return undefined; + } + matches = matches.splice( 1 ); + if( matches.length === 1 ){ + return matches[0]; + } + return matches; +} + +// ============================================================================ + return { + get : get + }; +}); diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js index 02d162ca472..3131070c79c 100644 --- a/client/galaxy/scripts/viz/trackster.js +++ b/client/galaxy/scripts/viz/trackster.js @@ -31,8 +31,8 @@ require( }); // trackster viewer -define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ], - function(_, base, tracks, visualization, mod_icon_btn) { +define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button", "utils/query-string-parsing" ], + function(_, base, tracks, visualization, mod_icon_btn, query_string ) { /** * User interface controls for trackster */ @@ -401,11 +401,84 @@ var TracksterView = Backbone.View.extend( // hide right panel force_right_panel("hide"); + // check if id is available - if (galaxy_config.app.id) + if (galaxy_config.app.id){ this.view_existing(); - else + } else if( query_string.get( 'dataset_id' ) ){ + this.choose_existing_or_new(); + } else { this.view_new(); + } + }, + + choose_existing_or_new : function () { + var self = this; + var dbkey = query_string.get( 'dbkey' ), + listTracksParams = {}, + dataset_params = { + dbkey : dbkey, + dataset_id : query_string.get( 'dataset_id' ), + hda_ldda : query_string.get( 'hda_ldda' ) + }; + if (dbkey){ + listTracksParams[ 'f-dbkey' ] = dbkey; + } + $.ajax({ + url: galaxy_config.root + 'visualization/list_tracks?' + $.param( listTracksParams ), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + + success: function(table_html) { + console.debug( 'success' ); + function view_in_saved(){ + // Show new modal with saved visualizations. + Galaxy.modal.show({ + title : "Add Data to Saved Visualization", + body : table_html, + buttons : { + "Cancel": function() { + // go back to the first choice + show_choice(); + }, + "Add to visualization": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + dataset_params.id = vis_id; + window.location = galaxy_config.root + "visualization/trackster?" + $.param(dataset_params); + }); + } + } + }); + } + function show_choice(){ + Galaxy.modal.show({ + title : "View Data in a New or Saved Visualization?", + // either have text in here or have to remove body and the header/footer margins + body : ( + // TODO: yay. inline styles. thanks, galaxy + '

    You can add this dataset as:' + + "
  • a new track to one of your existing, saved Trackster " + + "sessions if they share the genome build: " + dbkey + "
    • " + + "
  • or create a new session with this dataset as the only track
    • " + + "

" + ), + buttons : { + "Cancel": function() { + window.location = galaxy_config.root + "visualization/list"; + }, + "View in saved visualization": function() { + view_in_saved(); + }, + "View in new visualization": function() { + self.view_new(); + } + } + }); + } + show_choice(); + } + }); }, // view @@ -459,7 +532,8 @@ var TracksterView = Backbone.View.extend( }); // select default - if (galaxy_config.app.default_dbkey) { + var dbkeys_in_genomes = response.map( function( r ){ return r[1]; }); + if (galaxy_config.app.default_dbkey && _.contains(dbkeys_in_genomes,galaxy_config.app.default_dbkey)) { $("#new-dbkey").val( galaxy_config.app.default_dbkey ); } diff --git a/config/plugins/visualizations/trackster/config/trackster.xml b/config/plugins/visualizations/trackster/config/trackster.xml index 02e06e73e52..2d63a12854b 100644 --- a/config/plugins/visualizations/trackster/config/trackster.xml +++ b/config/plugins/visualizations/trackster/config/trackster.xml @@ -15,6 +15,7 @@ None dataset_id hda_ldda + dbkey diff --git a/static/maps/utils/query-string-parsing.js.map b/static/maps/utils/query-string-parsing.js.map new file mode 100644 index 00000000000..d094099a2ac --- /dev/null +++ b/static/maps/utils/query-string-parsing.js.map @@ -0,0 +1 @@ +{"version":3,"file":"query-string-parsing.js","sources":["../../src/utils/query-string-parsing.js"],"names":["define","get","key","queryString","window","location","search","substr","keyRegex","RegExp","matches","match","length","splice","undefined"],"mappings":"AAAAA,UAAW,WAEX,QAASC,GAAKC,EAAKC,GACfA,EAAcA,GAAeC,OAAOC,SAASC,OAAOC,OAAQ,EAC5D,IAAIC,GAAW,GAAIC,QAAQP,EAAM,cAC7BQ,EAAUP,EAAYQ,MAAOH,EACjC,OAAKE,IAAYA,EAAQE,QAGzBF,EAAUA,EAAQG,OAAQ,GACH,IAAnBH,EAAQE,OACDF,EAAQ,GAEZA,GANII,OAUX,OACIb,IAAMA"} \ No newline at end of file diff --git a/static/maps/viz/trackster.js.map b/static/maps/viz/trackster.js.map index 83d0ceaa2fe..99be99d004d 100644 --- a/static/maps/viz/trackster.js.map +++ b/static/maps/viz/trackster.js.map @@ -1 +1 @@ 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").addClass("position").appendTo(e),g=($("").text(a).appendTo(f).click(function(){return view.go_to(a),!1}),$("
").text(b).appendTo(e));if(c){{var h=$("
").addClass("delete-icon-container").prependTo(e).click(function(){return e.slideUp("fast"),e.remove(),view.has_changes=!0,!1});$("").addClass("icon-button delete").appendTo(h)}g.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return view.has_changes=!0,e},create_visualization:function(b,d,e,f,g){var h=this,i=new c.TracksterView(a.extend(b,{header:!1}));return i.editor=!0,$.when(i.load_chroms_deferred).then(function(a){if(d){var b=d.chrom,j=d.start,k=d.end,l=d.overview;b&&void 0!==j&&k?i.change_chrom(b,j,k):i.change_chrom(a[0].chrom)}else i.change_chrom(a[0].chrom);if(e)for(var m=0;m"),$("#right-border").click(function(){view.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():this.view_new()},view_existing:function(){var a=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:a.title,vis_id:a.vis_id,dbkey:a.dbkey},a.viewport,a.tracks,a.bookmarks,!0),this.init_editor()},view_new:function(){var a=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(b){Galaxy.modal.show({title:"New Visualization",body:a.template_view_new(b),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){a.create_browser($("#new-title").val(),$("#new-dbkey").val()),Galaxy.modal.hide()}}}),galaxy_config.app.default_dbkey&&$("#new-dbkey").val(galaxy_config.app.default_dbkey),$("#new-title").focus(),$("select[name='dbkey']").select2(),$("#overlay").css("overflow","auto")}})},template_view_new:function(a){for(var b='
Is the build not listed here? Add a Custom Build
'},create_browser:function(a,b){$(document).trigger("convert_to_values"),view=ui.create_visualization({container:$("#center .unified-panel-body"),name:a,dbkey:b},galaxy_config.app.gene_region),this.init_editor(),view.editor=!0},init_editor:function(){$("#center .unified-panel-title").text(view.config.get_value("name")+" ("+view.dbkey+")"),galaxy_config.app.add_dataset&&$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(a){view.add_drawable(c.object_from_template(a,view,view))}}),$("#add-bookmark-button").click(function(){var a=view.chrom+":"+view.low+"-"+view.high,b="Bookmark description";return ui.add_bookmark(a,b,!0)}),ui.init_keyboard_nav(view),$(window).on("beforeunload",function(){return view.has_changes?"There are unsaved changes to your visualization that will be lost if you leave this page.":void 0})}});return{TracksterUI:f,GalaxyApp:g}}); +var ui=null,view=null,browser_router=null;require(["utils/utils","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating"],function(a){a.cssLoadFile("static/style/jquery.rating.css"),a.cssLoadFile("static/style/autocomplete_tagging.css"),a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),a.cssLoadFile("static/style/library.css"),a.cssLoadFile("static/style/trackster.css")}),define(["libs/underscore","base","viz/trackster/tracks","viz/visualization","mvc/ui/icon-button","utils/query-string-parsing"],function(a,b,c,d,e,f){var g=b.Base.extend({initialize:function(a){this.baseURL=a},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var a=[];$(".bookmark").each(function(){a.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var b=view.overview_drawable?view.overview_drawable.config.get_value("name"):null,c={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:b},bookmarks:a};return $.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(c)}}).success(function(a){Galaxy.modal.hide(),view.vis_id=a.vis_id,view.has_changes=!1,window.history.pushState({},"",a.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var b=this,f=e.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){d.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(b){a.each(b,function(a){view.add_drawable(c.object_from_template(a,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new c.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==$("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=b.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){b.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){b.handle_unsaved_changes(view)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=f,f},add_bookmarks:function(){{var a=this;this.baseURL}Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"}),$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(b){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:b,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var b,c=$(this).val();b="id"===$(this).attr("name")?{hda_id:c}:{ldda_id:c},$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:b,dataType:"json"}).then(function(b){for(i=0;i").addClass("bookmark").appendTo(d),f=$("
").addClass("position").appendTo(e),g=($("").text(a).appendTo(f).click(function(){return view.go_to(a),!1}),$("
").text(b).appendTo(e));if(c){{var h=$("
").addClass("delete-icon-container").prependTo(e).click(function(){return e.slideUp("fast"),e.remove(),view.has_changes=!0,!1});$("").addClass("icon-button delete").appendTo(h)}g.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return view.has_changes=!0,e},create_visualization:function(b,d,e,f,g){var h=this,i=new c.TracksterView(a.extend(b,{header:!1}));return i.editor=!0,$.when(i.load_chroms_deferred).then(function(a){if(d){var b=d.chrom,j=d.start,k=d.end,l=d.overview;b&&void 0!==j&&k?i.change_chrom(b,j,k):i.change_chrom(a[0].chrom)}else i.change_chrom(a[0].chrom);if(e)for(var m=0;m"),$("#right-border").click(function(){view.resize_window()}),force_right_panel("hide"),galaxy_config.app.id?this.view_existing():f.get("dataset_id")?this.choose_existing_or_new():this.view_new()},choose_existing_or_new:function(){var a=this,b=f.get("dbkey"),c={},d={dbkey:b,dataset_id:f.get("dataset_id"),hda_ldda:f.get("hda_ldda")};b&&(c["f-dbkey"]=b),$.ajax({url:galaxy_config.root+"visualization/list_tracks?"+$.param(c),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){function e(){Galaxy.modal.show({title:"Add Data to Saved Visualization",body:c,buttons:{Cancel:function(){f()},"Add to visualization":function(){$(parent.document).find("input[name=id]:checked").each(function(){var a=$(this).val();d.id=a,window.location=galaxy_config.root+"visualization/trackster?"+$.param(d)})}}})}function f(){Galaxy.modal.show({title:"View Data in a New or Saved Visualization?",body:'

    You can add this dataset as:
  • a new track to one of your existing, saved Trackster sessions if they share the genome build: '+b+"
  • or create a new session with this dataset as the only track

",buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},"View in saved visualization":function(){e()},"View in new visualization":function(){a.view_new()}}})}console.debug("success"),f()}})},view_existing:function(){var a=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:a.title,vis_id:a.vis_id,dbkey:a.dbkey},a.viewport,a.tracks,a.bookmarks,!0),this.init_editor()},view_new:function(){var b=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(c){Galaxy.modal.show({title:"New Visualization",body:b.template_view_new(c),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){b.create_browser($("#new-title").val(),$("#new-dbkey").val()),Galaxy.modal.hide()}}});var d=c.map(function(a){return a[1]});galaxy_config.app.default_dbkey&&a.contains(d,galaxy_config.app.default_dbkey)&&$("#new-dbkey").val(galaxy_config.app.default_dbkey),$("#new-title").focus(),$("select[name='dbkey']").select2(),$("#overlay").css("overflow","auto")}})},template_view_new:function(a){for(var b='
Is the build not listed here? Add a Custom Build
'},create_browser:function(a,b){$(document).trigger("convert_to_values"),view=ui.create_visualization({container:$("#center .unified-panel-body"),name:a,dbkey:b},galaxy_config.app.gene_region),this.init_editor(),view.editor=!0},init_editor:function(){$("#center .unified-panel-title").text(view.config.get_value("name")+" ("+view.dbkey+")"),galaxy_config.app.add_dataset&&$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(a){view.add_drawable(c.object_from_template(a,view,view))}}),$("#add-bookmark-button").click(function(){var a=view.chrom+":"+view.low+"-"+view.high,b="Bookmark description";return ui.add_bookmark(a,b,!0)}),ui.init_keyboard_nav(view),$(window).on("beforeunload",function(){return view.has_changes?"There are unsaved changes to your visualization that will be lost if you leave this page.":void 0})}});return{TracksterUI:g,GalaxyApp:h}}); //# sourceMappingURL=../../maps/viz/trackster.js.map \ No newline at end of file From 91a29d8a6af6f26c556b6655a0697c3524554783 Mon Sep 17 00:00:00 2001 From: "y.hoogstrate@erasmusmc.nl" Date: Thu, 30 Jul 2015 12:06:07 +0200 Subject: [PATCH 24/68] extract_genomic_dna support for 2bit files from Local data --- tools/extract/extract_genomic_dna.py | 22 ++++++++++++++++++---- tools/extract/extract_genomic_dna.xml | 10 +++++----- 2 files changed, 23 insertions(+), 9 deletions(-) mode change 100644 => 100755 tools/extract/extract_genomic_dna.py diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py old mode 100644 new mode 100755 index a5018934224..3b23ea739f5 --- a/tools/extract/extract_genomic_dna.py +++ b/tools/extract/extract_genomic_dna.py @@ -4,7 +4,7 @@ usage: %prog $input $out_file1 -1, --cols=N,N,N,N,N: Columns for start, end, strand in input file -d, --dbkey=N: Genome build of input file -o, --output_format=N: the data type of the output file - -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc + -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc or twobit.loc -I, --interpret_features: if true, complete features are interpreted when input is GFF -F, --fasta=: genomic sequences to use for extraction -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format. @@ -35,17 +35,31 @@ def reverse_complement( s ): return "".join( reversed_s ) def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ): + # Checks for the presence of *.nib files matching the dbkey within alignseq.loc seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR seq_path = '' for line in open( seq_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: + if len( fields) >= 3 and fields[1] == dbkey: + print "Using *.nib genomic reference files" seq_path = fields[2].strip() break + + # If no entry in aligseq.loc was found, check for the presence of a *.2bit file in twobit.loc + if seq_path == '': + seq_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR + seq_path = '' + for line in open( seq_file ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( "#" ) and line.endswith( '.2bit' ): + fields = line.split( '\t' ) + if len(fields) >= 2 and fields[0] == dbkey: + print "Using a *.2bit genomic reference file" + seq_path = fields[1].strip() + break + return seq_path def __main__(): diff --git a/tools/extract/extract_genomic_dna.xml b/tools/extract/extract_genomic_dna.xml index d568d84835a..69847cd77c4 100644 --- a/tools/extract/extract_genomic_dna.xml +++ b/tools/extract/extract_genomic_dna.xml @@ -29,7 +29,7 @@ - + @@ -39,10 +39,10 @@ - - - - + + + + From 6ce94ce7e6b54f50720cc9559477d3b8035527a5 Mon Sep 17 00:00:00 2001 From: "y.hoogstrate@erasmusmc.nl" Date: Thu, 30 Jul 2015 13:12:51 +0200 Subject: [PATCH 25/68] Fixed comments --- tools/extract/extract_genomic_dna.py | 31 ++++++++++++---------------- 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py index 3b23ea739f5..72d672ed97c 100755 --- a/tools/extract/extract_genomic_dna.py +++ b/tools/extract/extract_genomic_dna.py @@ -37,30 +37,25 @@ def reverse_complement( s ): def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ): # Checks for the presence of *.nib files matching the dbkey within alignseq.loc seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR - seq_path = '' - for line in open( seq_file ): + for line in open(seq_file): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): fields = line.split( '\t' ) if len( fields) >= 3 and fields[1] == dbkey: print "Using *.nib genomic reference files" - seq_path = fields[2].strip() - break - - # If no entry in aligseq.loc was found, check for the presence of a *.2bit file in twobit.loc - if seq_path == '': - seq_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR - seq_path = '' - for line in open( seq_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( "#" ) and line.endswith( '.2bit' ): - fields = line.split( '\t' ) - if len(fields) >= 2 and fields[0] == dbkey: - print "Using a *.2bit genomic reference file" - seq_path = fields[1].strip() - break + return fields[2].strip() - return seq_path + # If no entry in aligseq.loc was found, check for the presence of a *.2bit file in twobit.loc + seq_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR + for line in open( seq_file ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( "#" ) and line.endswith( '.2bit' ): + fields = line.split( '\t' ) + if len(fields) >= 2 and fields[0] == dbkey: + print "Using a *.2bit genomic reference file" + return fields[1].strip() + + return '' def __main__(): # From bb4588aaaf268e56baf3e8d35e5f8cbc1979207b Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Thu, 30 Jul 2015 09:43:57 -0400 Subject: [PATCH 26/68] Managers, history: replace _get_history_data with proper serializers --- lib/galaxy/managers/histories.py | 17 ++++++--- .../webapps/galaxy/controllers/history.py | 37 ++++++++++--------- lib/galaxy/webapps/galaxy/controllers/page.py | 16 ++++---- lib/galaxy/webapps/galaxy/controllers/root.py | 9 +++-- 4 files changed, 47 insertions(+), 32 deletions(-) diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index ef8933f3478..5451a52a245 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -321,14 +321,21 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer return state - def serialize_contents( self, history, *args, **context ): + def serialize_contents( self, history, key, trans=None, **context ): contents_dictionaries = [] for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ): contents_dict = {} + if isinstance( content, model.HistoryDatasetAssociation ): - contents_dict = self.hda_serializer.serialize_to_view( content, view='detailed', **context ) - # elif isinstance( content, model.HistoryDatasetCollectionAssociation ): - # contents_dict = self._serialize_collection( trans, content ) + contents_dict = self.hda_serializer.serialize_to_view( content, + view='detailed', trans=trans, **context ) + # TODO: work out: shouldn't history annotations *always* use user=history.user? why anything else? + hda_annotation = self.hda_serializer.serialize_annotation( content, 'annotation', user=history.user ) + contents_dict[ 'annotation' ] = hda_annotation + + elif isinstance( content, model.HistoryDatasetCollectionAssociation ): + contents_dict = self._serialize_collection( trans, content ) + contents_dictionaries.append( contents_dict ) return contents_dictionaries @@ -341,7 +348,7 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer id=self.app.security.encode_id( collection.id ), ) return collections_util.dictify_dataset_collection_instance( dataset_collection_instance, - security=self.app.security, parent=dataset_collection_instance.history, view="element" ) + security=self.app.security, parent=dataset_collection_instance.history, view="element" ) class HistoryDeserializer( sharable.SharableModelDeserializer, deletable.PurgableDeserializerMixin ): diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index 6a4068db785..f04a3f60396 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -564,9 +564,10 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI unencoded_history_id = self.decode_id( id ) history_to_view = self.history_manager.get_accessible( unencoded_history_id, trans.user, current_history=trans.history ) - history_data = self.history_manager._get_history_data( trans, history_to_view ) - history_dictionary = history_data[ 'history' ] - hda_dictionaries = history_data[ 'contents' ] + history_dictionary = self.history_serializer.serialize_to_view( history_to_view, + view='detailed', user=trans.user, trans=trans ) + contents = self.history_serializer.serialize_contents( history_to_view, + 'contents', trans=trans, user=trans.user ) jobs = ( trans.sa_session.query( trans.app.model.Job ) .filter( trans.app.model.Job.user == history_to_view.user ) @@ -583,7 +584,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI tools[ tool_id ] = tool.to_dict( trans, io_details=True, link_details=True ) return trans.fill_template( "history/structure.mako", historyId=history_dictionary[ 'id' ], - history=history_dictionary, hdas=hda_dictionaries, jobs=jobs, tools=tools, **kwargs ) + history=history_dictionary, hdas=contents, jobs=jobs, tools=tools, **kwargs ) @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): @@ -599,16 +600,18 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI use_panels = galaxy.util.string_as_bool( use_panels ) history_dictionary = {} - hda_dictionaries = [] + contents = [] user_is_owner = False try: - history_to_view = self.history_manager.get_accessible( self.decode_id( id ), trans.user, current_history=trans.history ) + history_to_view = self.history_manager.get_accessible( self.decode_id( id ), trans.user, + current_history=trans.history ) user_is_owner = history_to_view.user == trans.user # include all datasets: hidden, deleted, and purged - history_data = self.history_manager._get_history_data( trans, history_to_view ) - history_dictionary = history_data[ 'history' ] - hda_dictionaries = history_data[ 'contents' ] + history_dictionary = self.history_serializer.serialize_to_view( history_to_view, + view='detailed', user=trans.user, trans=trans ) + contents = self.history_serializer.serialize_contents( history_to_view, + 'contents', trans=trans, user=trans.user ) except Exception, exc: user_id = str( trans.user.id ) if trans.user else '(anonymous)' @@ -621,8 +624,8 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI return trans.show_error_message( error_msg, use_panels=use_panels ) return trans.fill_template_mako( "history/view.mako", - history=history_dictionary, hdas=hda_dictionaries, user_is_owner=user_is_owner, - show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) + history=history_dictionary, hdas=contents, user_is_owner=user_is_owner, + show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) @web.expose def view_multiple( self, trans, include_deleted_histories=False, order='update' ): @@ -683,19 +686,19 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI # create ownership flag for template, dictify models user_is_owner = trans.user == history.user - history_data = self.history_manager._get_history_data( trans, history ) - history_dict = history_data[ 'history' ] - hda_dicts = history_data[ 'contents' ] + history_dictionary = self.history_serializer.serialize_to_view( history, + view='detailed', user=trans.user, trans=trans ) + contents = self.history_serializer.serialize_contents( history, 'contents', trans=trans, user=trans.user ) - history_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, history ) + history_dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, history ) # note: adding original annotation since this is published - get_dict returns user-based annos # for hda_dict in hda_dicts: # hda_dict[ 'annotation' ] = hda.annotation # dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) return trans.stream_template_mako( "history/display.mako", item=history, item_data=[], - user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts, - user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + user_is_owner=user_is_owner, history_dict=history_dictionary, hda_dicts=contents, + user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) # ......................................................................... sharing & publishing @web.expose diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index a99aeba6472..6f3e0ea4d22 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -302,6 +302,7 @@ class PageController( BaseUIController, SharableMixin, def __init__( self, app ): super( PageController, self ).__init__( app ) self.history_manager = managers.histories.HistoryManager( app ) + self.history_serializer = managers.histories.HistorySerializer( self.app ) self.hda_manager = managers.hdas.HDAManager( app ) @web.expose @@ -755,15 +756,16 @@ class PageController( BaseUIController, SharableMixin, history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) # include all datasets: hidden, deleted, and purged - history_data = self.history_manager._get_history_data( trans, history ) - history_dictionary = history_data[ 'history' ] - hda_dictionaries = history_data[ 'contents' ] + history_dictionary = self.history_serializer.serialize_to_view( history, + view='detailed', user=trans.user, trans=trans ) + contents = self.history_serializer.serialize_contents( history, 'contents', trans=trans, user=trans.user ) history_dictionary[ 'annotation' ] = history.annotation - filled = trans.fill_template( "history/embed.mako", item=history, - user_is_owner=user_is_owner, - history_dict=history_dictionary, - hda_dicts=hda_dictionaries ) + filled = trans.fill_template( "history/embed.mako", + item=history, + user_is_owner=user_is_owner, + history_dict=history_dictionary, + hda_dicts=contents ) return filled def _get_embedded_visualization_html( self, trans, id ): diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index a80a714f797..9af41eb7ef0 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -26,6 +26,7 @@ class RootController( BaseUIController, UsesAnnotations ): def __init__( self, app ): super( RootController, self ).__init__( app ) self.history_manager = managers.histories.HistoryManager( app ) + self.history_serializer = managers.histories.HistorySerializer( self.app ) @web.expose def default(self, trans, target1=None, target2=None, **kwd): @@ -124,9 +125,11 @@ class RootController( BaseUIController, UsesAnnotations ): history_dictionary = {} hda_dictionaries = [] try: - history_data = self.history_manager._get_history_data( trans, trans.get_history( create=True ) ) - history_dictionary = history_data[ 'history' ] - hda_dictionaries = history_data[ 'contents' ] + history = trans.get_history( create=True ) + history_dictionary = self.history_serializer.serialize_to_view( history, + view='detailed', user=trans.user, trans=trans ) + hda_dictionaries = self.history_serializer.serialize_contents( history, + 'contents', trans=trans, user=trans.user ) except Exception, exc: user_id = str( trans.user.id ) if trans.user else '(anonymous)' From 8644b21808fd779c062e1fbd475b8912845226d8 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Thu, 30 Jul 2015 10:00:26 -0400 Subject: [PATCH 27/68] Managers, history: remove _get_history_data; rename hdas -> contents in altered templates and web methods --- lib/galaxy/managers/histories.py | 49 ------------------- .../webapps/galaxy/controllers/history.py | 13 ++--- lib/galaxy/webapps/galaxy/controllers/page.py | 2 +- lib/galaxy/webapps/galaxy/controllers/root.py | 8 +-- templates/webapps/galaxy/history/display.mako | 5 +- templates/webapps/galaxy/history/embed.mako | 2 +- .../webapps/galaxy/history/structure.mako | 4 +- templates/webapps/galaxy/history/view.mako | 6 +-- templates/webapps/galaxy/root/history.mako | 12 ++--- 9 files changed, 23 insertions(+), 78 deletions(-) diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index 5451a52a245..e9030cc8797 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -122,55 +122,6 @@ class HistoryManager( sharable.SharableModelManager, deletable.PurgableManagerMi """ return self.set_current( trans, self.by_id( history_id ) ) -# TODO: replace or move to serializer - def _get_history_data( self, trans, history ): - """ - Returns a dictionary containing ``history`` and ``contents``, serialized - history and an array of serialized history contents respectively. - """ - # TODO: instantiate here? really? - history_serializer = HistorySerializer( self.app ) - hda_serializer = hdas.HDASerializer( self.app ) - history_dictionary = {} - contents_dictionaries = [] - try: - history_dictionary = history_serializer.serialize_to_view( history, view='detailed', - user=trans.user, trans=trans ) - - for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ): - contents_dict = {} - if isinstance( content, model.HistoryDatasetAssociation ): - contents_dict = hda_serializer.serialize_to_view(content, view='detailed', user=trans.user, trans=trans ) - hda_annotation = hda_serializer.serialize_annotation( content, 'annotation', user=history.user ) - contents_dict[ 'annotation' ] = hda_annotation - elif isinstance( content, model.HistoryDatasetCollectionAssociation ): - try: - service = self.app.dataset_collections_service - collection = service.get_dataset_collection_instance( - trans=trans, - instance_type='history', - id=self.app.security.encode_id( content.id ), - ) - serializer = collections_util.dictify_dataset_collection_instance - contents_dict = serializer( collection, - security=self.app.security, - parent=collection.history, - view="element" ) - except Exception, exc: - log.exception( "Error in history API at listing dataset collection: %s", exc ) - # TODO: return some dict with the error - contents_dictionaries.append( contents_dict ) - - except Exception, exc: - user_id = str( trans.user.id ) if trans.user else '(anonymous)' - log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) - message = ( 'An error occurred getting the history data from the server. ' - 'Please contact a Galaxy administrator if the problem persists.' ) - history_dictionary[ 'error' ] = message - - return { 'history': history_dictionary, - 'contents': contents_dictionaries } - # container interface def _filter_to_contained( self, container, content_class ): return content_class.history == container diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index f04a3f60396..1a519ad99cb 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -562,7 +562,8 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI unencoded_history_id = trans.history.id if id: unencoded_history_id = self.decode_id( id ) - history_to_view = self.history_manager.get_accessible( unencoded_history_id, trans.user, current_history=trans.history ) + history_to_view = self.history_manager.get_accessible( unencoded_history_id, trans.user, + current_history=trans.history ) history_dictionary = self.history_serializer.serialize_to_view( history_to_view, view='detailed', user=trans.user, trans=trans ) @@ -570,8 +571,8 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI 'contents', trans=trans, user=trans.user ) jobs = ( trans.sa_session.query( trans.app.model.Job ) - .filter( trans.app.model.Job.user == history_to_view.user ) - .filter( trans.app.model.Job.history_id == unencoded_history_id ) ).all() + .filter( trans.app.model.Job.user == history_to_view.user ) + .filter( trans.app.model.Job.history_id == unencoded_history_id ) ).all() jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs ) tools = {} @@ -584,7 +585,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI tools[ tool_id ] = tool.to_dict( trans, io_details=True, link_details=True ) return trans.fill_template( "history/structure.mako", historyId=history_dictionary[ 'id' ], - history=history_dictionary, hdas=contents, jobs=jobs, tools=tools, **kwargs ) + history=history_dictionary, contents=contents, jobs=jobs, tools=tools, **kwargs ) @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): @@ -624,7 +625,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI return trans.show_error_message( error_msg, use_panels=use_panels ) return trans.fill_template_mako( "history/view.mako", - history=history_dictionary, hdas=contents, user_is_owner=user_is_owner, + history=history_dictionary, contents=contents, user_is_owner=user_is_owner, show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) @web.expose @@ -697,7 +698,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI # dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) return trans.stream_template_mako( "history/display.mako", item=history, item_data=[], - user_is_owner=user_is_owner, history_dict=history_dictionary, hda_dicts=contents, + user_is_owner=user_is_owner, history_dict=history_dictionary, content_dicts=contents, user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) # ......................................................................... sharing & publishing diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 6f3e0ea4d22..43050a8b4cf 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -765,7 +765,7 @@ class PageController( BaseUIController, SharableMixin, item=history, user_is_owner=user_is_owner, history_dict=history_dictionary, - hda_dicts=contents ) + content_dicts=contents ) return filled def _get_embedded_visualization_html( self, trans, id ): diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index 9af41eb7ef0..74388e74dc7 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -123,12 +123,12 @@ class RootController( BaseUIController, UsesAnnotations ): show_deleted = string_as_bool_or_none( show_deleted ) history_dictionary = {} - hda_dictionaries = [] + content_dictionaries = [] try: history = trans.get_history( create=True ) history_dictionary = self.history_serializer.serialize_to_view( history, view='detailed', user=trans.user, trans=trans ) - hda_dictionaries = self.history_serializer.serialize_contents( history, + content_dictionaries = self.history_serializer.serialize_contents( history, 'contents', trans=trans, user=trans.user ) except Exception, exc: @@ -138,8 +138,8 @@ class RootController( BaseUIController, UsesAnnotations ): 'Please contact a Galaxy administrator if the problem persists.' ) return trans.fill_template_mako( "root/history.mako", - history=history_dictionary, hdas=hda_dictionaries, - show_deleted=show_deleted, show_hidden=show_hidden ) + history=history_dictionary, contents=content_dictionaries, + show_deleted=show_deleted, show_hidden=show_hidden ) # ---- Dataset display / editing ---------------------------------------- @web.expose diff --git a/templates/webapps/galaxy/history/display.mako b/templates/webapps/galaxy/history/display.mako index 82bf1636059..977ae417e09 100644 --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -46,7 +46,7 @@
-${ galaxy_client.load( app='app', historyId=historyId, history=history, hdas=hdas, jobs=jobs, tools=tools ) } +${ galaxy_client.load( app='app', historyId=historyId, history=history, contents=contents, jobs=jobs, tools=tools ) } diff --git a/templates/webapps/galaxy/history/view.mako b/templates/webapps/galaxy/history/view.mako index 807ce39fa54..baca4dac391 100644 --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -167,7 +167,7 @@ a.btn { var hasMasthead = ${ 'true' if use_panels else 'false' }, userIsOwner = ${ 'true' if user_is_owner else 'false' }, historyJSON = ${ h.dumps( history ) }, - hdaJSON = ${ h.dumps( hdas ) }, + contentsJSON = ${ h.dumps( contents ) }, panelToUse = ( userIsOwner )? //TODO: change class names ({ location: 'mvc/history/history-panel-edit', className: 'HistoryPanelEdit' }): @@ -190,11 +190,11 @@ a.btn { if( hasMasthead ){ $( '#center' ).css( 'overflow', 'auto' ); } - + var panelClass = panelMod[ panelToUse.className ], // history module is already in the dpn chain from the panel. We can re-scope it here. historyModel = require( 'mvc/history/history-model' ), - history = new historyModel.History( historyJSON, hdaJSON ); + history = new historyModel.History( historyJSON, contentsJSON ); window.historyPanel = new panelClass({ show_deleted : ${show_deleted_json}, diff --git a/templates/webapps/galaxy/root/history.mako b/templates/webapps/galaxy/root/history.mako index 0750f93720a..2223ce06f2a 100644 --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -20,28 +20,22 @@ $(function(){ -${ galaxy_client.load( app='app', history=history, hdas=hdas, show_deleted=show_deleted, show_hidden=show_hidden ) } +${ galaxy_client.load( app='app', history=history, contents=contents, + show_deleted=show_deleted, show_hidden=show_hidden ) } From 45fb7f8994bbbcc21505379f37a46d8608390c89 Mon Sep 17 00:00:00 2001 From: Airistotal Date: Thu, 30 Jul 2015 09:18:19 -0500 Subject: [PATCH 28/68] Moved styles to reports.less Added import to base.less to include reports.less --- client/galaxy/style/less/base.less | 11 +- client/galaxy/style/less/reports.less | 113 ++++++++++++++++-- .../webapps/reports/controllers/jobs.py | 2 +- static/style/blue/base.css | 4 +- static/style/blue/reports.css | 7 +- templates/page_base.mako | 87 -------------- templates/sorting_base.mako | 4 - templates/spark_base.mako | 10 -- .../webapps/reports/jobs_errors_per_tool.mako | 3 +- .../webapps/reports/jobs_per_month_all.mako | 3 +- .../reports/jobs_per_month_in_error.mako | 3 +- templates/webapps/reports/jobs_per_tool.mako | 3 +- templates/webapps/reports/jobs_per_user.mako | 3 +- .../reports/jobs_specified_month_all.mako | 3 +- .../jobs_specified_month_in_error.mako | 3 +- .../webapps/reports/jobs_tool_per_month.mako | 3 +- .../webapps/reports/jobs_user_per_month.mako | 3 +- .../reports/workflows_per_month_all.mako | 3 +- .../webapps/reports/workflows_per_user.mako | 3 +- .../reports/workflows_per_workflow.mako | 3 +- .../reports/workflows_user_per_month.mako | 3 +- 21 files changed, 123 insertions(+), 154 deletions(-) diff --git a/client/galaxy/style/less/base.less b/client/galaxy/style/less/base.less index 8dad18887c1..72dfbd62e78 100644 --- a/client/galaxy/style/less/base.less +++ b/client/galaxy/style/less/base.less @@ -4,6 +4,9 @@ // Galaxy specific variables @import "galaxy_variables.less"; +// Galaxy Report Webapp +@import "reports"; + @white: #fff; @black: #000; @@ -134,14 +137,6 @@ body { #left-border { left: 250px; } -.reports-panel-container { - position: absolute; - top: @panel_header_height; - bottom: 10px; - overflow: scroll; - width: 100%; - padding: 10px; -} #center { left:250 + @border-default-color_padding; right: 250 + @border-default-color_padding; diff --git a/client/galaxy/style/less/reports.less b/client/galaxy/style/less/reports.less index ddb102759e0..1a4d26ec6b0 100644 --- a/client/galaxy/style/less/reports.less +++ b/client/galaxy/style/less/reports.less @@ -1,13 +1,19 @@ // ============================================================================ Reports Webapp - -.dir_arrow { - visibility: hidden +// ======================================================== Left ============== +.reports-panel-container { + position: absolute; + /*From base.less, top should be @panel_header_height*/ + top: 30px; + bottom: 10px; + overflow: scroll; + width: 100%; + padding: 10px; } +// ======================================================== SparkLines ======== #spark_time_select { display: inline-block; } - #spark_select { height: 23px; width: 30px; @@ -15,14 +21,101 @@ border-radius: 2px; } -.quarter_width { - width: 25%; +.jqstooltip { + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; + } + +// ======================================================== Sorting =========== +.dir_arrow { + visibility: hidden } +// ======================================================== Paging ============ +// ======================================== Pages ============================= +#back_button, #next_button, #curr_button, .miss_pages, .page_button { + position: relative; + float: left; + height: 24px; + width: 23px; + margin: 0 -1px 0 0; + padding-top: 2.5px; + border: 1px solid #bfbfbf; + z-index: 0; +} + +#back_button { + cursor: pointer; + border-top-left-radius: 3px; + border-bottom-left-radius: 3px; +} + +#curr_button { + background: #ebd9b2; + border: 1px solid #5f6990; + z-index: 1; +} + +#formHeader > tbody > tr { + vertical-align: middle; +} + +#next_button { + cursor: pointer; + border-top-right-radius: 3px; + border-bottom-right-radius: 3px; +} + +#page_selector { + cursor: default; + position: relative; + text-align: center; +} + + + +.page_button > a { + text-decoration: none; + padding: 8px; + margin: -8px; + height: 100%; + width: 100%; +} +// ======================================== Entry Selector ==================== +#entries_edit { + position: relative; + padding: 0; + width: 36px; + height: 20px; + text-align: center; + border: 1px solid black; + border-radius: 3px; + z-index: 6; +} + +#entry_submit { + cursor: default; + position: relative; + display: inline-block; + border: 1px solid black; + padding: 0; + width: 22px; + height: 22px; + border-radius: 11px; + background-color: #ebd9b2; + text-align: center; + opacity: 0.0; + z-index: 0; +} + +// ======================================================== Misc. ============= +.half_width { + width: 50% +} .third_width { width: 30%; } - -.half_width { - width: 50% -} +.quarter_width { + width: 25%; +} \ No newline at end of file diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index ac5f50977fe..6638ab815cb 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -288,7 +288,7 @@ class Jobs( BaseUIController, ReportQueryBuilder ): if "entries" in kwd: entries = int(kwd.get( 'entries' )) else: - entries = 50 + entries = 25 limit = entries * 4 if "offset" in kwd: diff --git a/static/style/blue/base.css b/static/style/blue/base.css index 312a11dcd11..e94d8b88702 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1,4 +1,4 @@ -/*! normalize.css v2.1.0 | MIT License | git.io/normalize */article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,video{display:inline-block}audio:not([controls]){display:none;height:0}[hidden]{display:none}html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}a:focus{outline:thin dotted}a:active,a:hover{outline:0}h1{font-size:2em;margin:.67em 0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:bold}dfn{font-style:italic}hr{-moz-box-sizing:content-box;box-sizing:content-box;height:0}mark{background:#ff0;color:#000}code,kbd,pre,samp{font-family:monospace,serif;font-size:1em}pre{white-space:pre-wrap}q{quotes:"\201C" "\201D" "\2018" "\2019"}small{font-size:80%}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:baseline}sup{top:-0.5em}sub{bottom:-0.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:0}fieldset{border:1px solid #c0c0c0;margin:0 2px;padding:.35em .625em .75em}legend{border:0;padding:0}button,input,select,textarea{font-family:inherit;font-size:100%;margin:0}button,input{line-height:normal}button,select{text-transform:none}button,html input[type="button"],input[type="reset"],input[type="submit"]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}input[type="checkbox"],input[type="radio"]{box-sizing:border-box;padding:0}input[type="search"]{-webkit-appearance:textfield;-moz-box-sizing:content-box;-webkit-box-sizing:content-box;box-sizing:content-box}input[type="search"]::-webkit-search-cancel-button,input[type="search"]::-webkit-search-decoration{-webkit-appearance:none}button::-moz-focus-inner,input::-moz-focus-inner{border:0;padding:0}textarea{overflow:auto;vertical-align:top}table{border-collapse:collapse;border-spacing:0}@media print{*{text-shadow:none !important;color:#000 !important;background:transparent !important;box-shadow:none !important}a,a:visited{text-decoration:underline}a[href]:after{content:" (" attr(href) ")"}abbr[title]:after{content:" (" attr(title) ")"}.ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:""}pre,blockquote{border:1px solid #999;page-break-inside:avoid}thead{display:table-header-group}tr,img{page-break-inside:avoid}img{max-width:100% 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.text-and-autocomplete-select:after{border-top-color:#fff}.icon-button.general-question{background:url(question-octagon-frame.png) no-repeat;float:right;margin-top:3px;margin-right:4px}.icon-button.tag-question{background:url(question-balloon.png) no-repeat;float:right;margin-top:3px;margin-right:4px}.icon-button.tag{background-image:url(sprite-fugue.png);background-position:-16px -112px;width:16px;height:16px}.icon-button.tags{background-image:url(sprite-fugue.png);background-position:-32px -112px;width:16px;height:16px}.icon-button.tag--plus{background-image:url(sprite-fugue.png);background-position:0 -112px;width:16px;height:16px}.icon-button.toggle-expand{background-image:url(sprite-fugue.png);background-position:-80px -112px;width:16px;height:16px}.icon-button.toggle{background-image:url(sprite-fugue.png);background-position:-48px -112px;width:16px;height:16px}.icon-button.toggle:hover{background-image:url(sprite-fugue.png);background-position:-96px -112px;width:16px;height:16px}.icon-button.arrow-circle{background-image:url(sprite-fugue.png);background-position:-32px 0;width:16px;height:16px}.icon-button.chevron{background-image:url(sprite-fugue.png);background-position:-32px -64px;width:16px;height:16px}.icon-button.bug{background-image:url(sprite-fugue.png);background-position:-64px -32px;width:16px;height:16px}.icon-button.disk{background-image:url(sprite-fugue.png);background-position:-16px -80px;width:16px;height:16px}.icon-button.information{background-image:url(sprite-fugue.png);background-position:-96px -80px;width:16px;height:16px}.icon-button.annotate{background-image:url(sprite-fugue.png);background-position:-112px -96px;width:16px;height:16px}.icon-button.go-to-full-screen{background-image:url(sprite-fugue.png);background-position:0 0;width:16px;height:16px}.icon-button.import{background-image:url(sprite-fugue.png);background-position:-112px -80px;width:16px;height:16px}.icon-button.plus-button{background-image:url(sprite-fugue.png);background-position:-112px -48px;width:16px;height:16px}.icon-button.plus-button:hover{background-image:url(sprite-fugue.png);background-position:-112px -64px;width:16px;height:16px}.icon-button.gear{background-image:url(sprite-fugue.png);background-position:-96px 0;width:16px;height:16px}.icon-button.chart_curve{background-image:url(sprite-fugue.png);background-position:-64px -48px;width:16px;height:16px}.icon-button.disk--arrow{background-image:url(sprite-fugue.png);background-position:-80px -64px;width:16px;height:16px}.icon-button.disk--arrow:hover{background-image:url(sprite-fugue.png);background-position:0 -80px;width:16px;height:16px}.icon-button.cross-circle{background-image:url(sprite-fugue.png);background-position:-80px 0;width:16px;height:16px}.icon-button.cross-circle:hover{background-image:url(sprite-fugue.png);background-position:-80px -16px;width:16px;height:16px}.icon-button.arrow-split{background-image:url(sprite-fugue.png);background-position:-16px -32px;width:16px;height:16px}.icon-button.arrow-split:hover{background-image:url(sprite-fugue.png);background-position:-32px -32px;width:16px;height:16px}.icon-button.chevron-expand:hover{background-image:url(sprite-fugue.png);background-position:-16px -64px;width:16px;height:16px}.icon-button.chevron-expand{background-image:url(sprite-fugue.png);background-position:0 -64px;width:16px;height:16px}#for_bears{display:none} \ No newline at end of file diff --git a/static/style/blue/reports.css b/static/style/blue/reports.css index cc14661617f..be512d2cb21 100644 --- a/static/style/blue/reports.css +++ b/static/style/blue/reports.css @@ -1,6 +1 @@ -.dir_arrow{visibility:hidden} -#spark_time_select{display:inline-block} -#spark_select{height:23px;width:30px;padding:0;border-radius:2px} -.quarter_width{width:25%} -.third_width{width:30%} -.half_width{width:50%} +.reports-panel-container{position:absolute;top:30px;bottom:10px;overflow:scroll;width:100%;padding:10px}#spark_time_select{display:inline-block}#spark_select{height:23px;width:30px;padding:0;border-radius:2px}.jqstooltip{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}.dir_arrow{visibility:hidden}#back_button,#next_button,#curr_button,.miss_pages,.page_button{position:relative;float:left;height:24px;width:23px;margin:0 -1px 0 0;padding-top:2.5px;border:1px solid #bfbfbf;z-index:0}#back_button{cursor:pointer;border-top-left-radius:3px;border-bottom-left-radius:3px}#curr_button{background:#ebd9b2;border:1px solid #5f6990;z-index:1}#formHeader>tbody>tr{vertical-align:middle}#next_button{cursor:pointer;border-top-right-radius:3px;border-bottom-right-radius:3px}#page_selector{cursor:default;position:relative;text-align:center}.page_button>a{text-decoration:none;padding:8px;margin:-8px;height:100%;width:100%}#entries_edit{position:relative;padding:0;width:36px;height:20px;text-align:center;border:1px solid black;border-radius:3px;z-index:6}#entry_submit{cursor:default;position:relative;display:inline-block;border:1px solid black;padding:0;width:22px;height:22px;border-radius:11px;background-color:#ebd9b2;text-align:center;opacity:0;z-index:0}.half_width{width:50%}.third_width{width:30%}.quarter_width{width:25%} \ No newline at end of file diff --git a/templates/page_base.mako b/templates/page_base.mako index 76f4490ec79..5e5d7c16e4c 100644 --- a/templates/page_base.mako +++ b/templates/page_base.mako @@ -14,7 +14,6 @@ <%def name="get_pages( sort_id, order, page_specs, *args, **kwargs )"> ## Creates the page buttons ${get_page_script()} - ${get_page_css()}
↞
@@ -61,92 +60,6 @@
-<%def name="get_page_css()"> - <%doc> - Page Styling - - - - <%doc> - Entry Styling - - - - <%def name="get_page_script()">