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view.json for visualizeR rangesExplorer
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{ | |
"version": "2.98.0", | |
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"" | |
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"url": "modules/types/edition/slick_grid/", | |
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] | |
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"newRows" | |
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], | |
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"title": "Dartaset Selector (click on row)", | |
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"title": "Dartaset Selector (click on row)", | |
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"icon": "", | |
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100, | |
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{ | |
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"" | |
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"" | |
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} | |
], | |
"title": "Dartaset Selector (click on row)", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/slick_grid/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
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{ | |
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[ | |
"newRows" | |
] | |
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[ | |
{ | |
"name": "label", | |
"jpath": [ | |
"label" | |
], | |
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"formatter": "typerenderer", | |
"copyFormatter": "default", | |
"visibility": "both", | |
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"editorOptions": "", | |
"hideColumn": [] | |
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] | |
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{ | |
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255, | |
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"clickMode": "text" | |
} | |
] | |
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[ | |
{ | |
"getter": [] | |
} | |
] | |
], | |
"actionOutButtons": [ | |
[ | |
{} | |
] | |
], | |
"data": [ | |
{ | |
"saveInView": [ | |
[] | |
], | |
"varname": [ | |
"" | |
], | |
"data": [ | |
"[]" | |
] | |
} | |
] | |
} | |
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"top": 23 | |
}, | |
"size": { | |
"width": 14, | |
"height": 15 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Select analysis (click on row)", | |
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255, | |
255, | |
255, | |
0 | |
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"name": "Default layer" | |
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}, | |
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}, | |
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"title": "Select analysis (click on row)", | |
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255, | |
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"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
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"top": 23 | |
}, | |
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"height": 27 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Select analysis (click on row)", | |
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255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
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}, | |
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}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Select analysis (click on row)", | |
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255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 42, | |
"top": 23 | |
}, | |
"size": { | |
"width": 14, | |
"height": 27 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Select analysis (click on row)", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 3, | |
"vars_in": [ | |
{ | |
"rel": "list", | |
"name": "selectedDataSets" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"vars_out": [ | |
{ | |
"event": "onSelect", | |
"rel": "row", | |
"jpath": [ | |
"data" | |
], | |
"name": "selectedData" | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
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] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Export Data" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Select analysis (click on row)", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"\nAPI.loading('computeStatistics','Please wait while we compute basic statistics for the chosen data');\n\n// you need to leave some time to display the message\n// we use setImmediate to achieve this\n\nsetImmediate(getStats);\n\n\nfunction getStats() {\nlet selectedData = API.getData('selectedData')\nlet varNames = Object.keys(selectedData[0])\n\n\nlet x = new Array\nlet s = new Array\nObject.keys(selectedData[0]).forEach(e => {\n x.push([[e], selectedData.map(col => col[e])])\n s.push({\"index\": e,\n \"indicator\": {\n \"type\": \"sparkline\",\n \"value\": selectedData.map(col => col[e]),\n \"_options\": {\n \"type\": \"box\",\n \"raw\": false,\n \"minValue\": -50,\n \"maxValue\": 20,\n \"boxLineColor\": \"black\",\n \"boxFillColor\": \"lightgrey\",\n \"whiskerColor\": \"black\",\n \"medianColor\": \"red\",\n \"lineColor\": \"black\",\n \"target\": [],\n \"targetColor\": \"green\"\n }\n }})\n})\n\n\nconsole.log('calculate indicators executed')\n\nAPI.createData('selectedDataMatrix', s)\nAPI.createData('x', x)\nAPI.createData('varNames', varNames)\n\n API.stopLoading('computeStatistics');\n}\n" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 1, | |
"top": 76 | |
}, | |
"size": { | |
"width": 60, | |
"height": 30 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "calculate indicators", | |
"bgColor": [ | |
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255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
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"top": 0 | |
}, | |
"size": { | |
"width": 60, | |
"height": 24 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "calculate indicators", | |
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255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
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}, | |
"size": { | |
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}, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
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"help": { | |
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}, | |
"size": { | |
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}, | |
"zIndex": 0, | |
"display": false, | |
"title": "calculate indicators", | |
"bgColor": [ | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 1, | |
"top": 76 | |
}, | |
"size": { | |
"width": 60, | |
"height": 30 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "calculate indicators", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 4, | |
"vars_in": [ | |
{ | |
"rel": "inputValue", | |
"name": "selectedData" | |
} | |
], | |
"actions_in": [ | |
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], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "calculate indicators", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/slick_grid/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"slickCheck": [ | |
[ | |
"enableCellNavigation", | |
"rowNumbering", | |
"forceFitColumns", | |
"highlightScroll", | |
"forgetLastActive", | |
"filterColumns", | |
"editable", | |
"keepSelected" | |
] | |
], | |
"copyPaste": [ | |
[] | |
], | |
"copyPasteOptions": [ | |
[ | |
"newRows" | |
] | |
], | |
"autoColumns": [ | |
[] | |
], | |
"toolbar": [ | |
[] | |
], | |
"colorjpath": [ | |
[] | |
], | |
"slick.defaultColumnWidth": [ | |
null | |
], | |
"slick.rowHeight": [ | |
"30" | |
], | |
"slick.headerRowHeight": [ | |
30 | |
], | |
"slick.selectionModel": [ | |
"row" | |
], | |
"idProperty": [ | |
"" | |
], | |
"filterType": [ | |
"pref" | |
], | |
"filterRow": [ | |
"// Documentation: https://github.com/NPellet/visualizer/blob/46b40ca86345f8fa313563bf9c6ecb80ba323101/src/modules/types/edition/slick_grid/view.js#L1695-L1735" | |
], | |
"customJpaths": [ | |
"" | |
] | |
} | |
], | |
"cols": [ | |
[ | |
{ | |
"name": "label", | |
"jpath": [ | |
"index" | |
], | |
"editor": "none", | |
"forceType": "", | |
"formatter": "typerenderer", | |
"copyFormatter": "default", | |
"visibility": "both", | |
"rendererOptions": "", | |
"editorOptions": "", | |
"width": 86, | |
"hideColumn": [] | |
}, | |
{ | |
"name": "indicator", | |
"jpath": [ | |
"indicator" | |
], | |
"editor": "none", | |
"forceType": "", | |
"formatter": "typerenderer", | |
"copyFormatter": "default", | |
"visibility": "both", | |
"rendererOptions": "", | |
"editorOptions": "", | |
"width": 129, | |
"hideColumn": [] | |
} | |
] | |
], | |
"actionCols": [ | |
[ | |
{ | |
"name": "help", | |
"icon": "fa-question", | |
"backgroundColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"color": [ | |
0, | |
0, | |
0, | |
1 | |
], | |
"action": "getHelp", | |
"position": "end", | |
"clickMode": "text", | |
"isAction": true | |
} | |
] | |
], | |
"groupings": [ | |
[ | |
{ | |
"getter": [] | |
} | |
] | |
], | |
"actionOutButtons": [ | |
[ | |
{} | |
] | |
], | |
"data": [ | |
{ | |
"saveInView": [ | |
[] | |
], | |
"varname": [ | |
"" | |
], | |
"data": [ | |
"[]" | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 23, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Metabolites selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 1, | |
"top": 36 | |
}, | |
"size": { | |
"width": 35, | |
"height": 39 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Metabolites indicators", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 23, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Metabolites selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 23, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Metabolites selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 23, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Metabolites selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 5, | |
"vars_in": [ | |
{ | |
"rel": "list", | |
"name": "selectedDataMatrix" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"vars_out": [ | |
{ | |
"event": "onRowsSelect", | |
"rel": "rows", | |
"jpath": [], | |
"name": "selectedIndicators" | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Export Data" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Metabolites selector", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/chart/statistics/parallel_coordinates/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"colJPath": [ | |
"element" | |
], | |
"options": [ | |
[ | |
"hide", | |
"brush", | |
"shadow" | |
] | |
], | |
"brushMode": [ | |
"1D-axes-multi" | |
], | |
"predicate": [ | |
"and" | |
] | |
} | |
], | |
"cols": [ | |
[ | |
{} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 24, | |
"top": 0 | |
}, | |
"size": { | |
"width": 121, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Click and drag on the variable axis to filter sample within a range", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 37, | |
"top": 2 | |
}, | |
"size": { | |
"width": 86, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Click and drag on the variable axis to select sample within a range", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"spectra": { | |
"position": { | |
"left": 40, | |
"top": 0 | |
}, | |
"size": { | |
"width": 121, | |
"height": 24 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Click and drag on the variable axis to filter sample within a range", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 24, | |
"top": 0 | |
}, | |
"size": { | |
"width": 121, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Click and drag on the variable axis to filter sample within a range", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 24, | |
"top": 0 | |
}, | |
"size": { | |
"width": 121, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Click and drag on the variable axis to filter sample within a range", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 6, | |
"vars_in": [ | |
{ | |
"rel": "value", | |
"name": "selectedData" | |
}, | |
{ | |
"rel": "columns", | |
"name": "parallelVariablesLabels" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"vars_out": [ | |
{ | |
"event": "onBrushSelection", | |
"rel": "flagResult", | |
"jpath": [], | |
"name": "selectedParallel" | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
185, | |
27, | |
27, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Show fullscreen", | |
"Export Data", | |
"Print" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Click and drag on the variable axis to filter sample within a range", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"let selectedIndicators = API.getData('selectedIndicators')\n\nlet parallelVariablesLabels = []\nselectedIndicators.map(x => {\n parallelVariablesLabels.push({\"name\" : x.index, \"jpath\" : \"element.\" + x.index})\n})\n\nAPI.createData('parallelVariablesLabels', parallelVariablesLabels)\n\nconsole.log('create parallel executed')\n\n\n" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 62, | |
"top": 76 | |
}, | |
"size": { | |
"width": 68, | |
"height": 25 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "create parallel variables", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 25 | |
}, | |
"size": { | |
"width": 60, | |
"height": 21 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "create parallel variables", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"spectra": { | |
"position": { | |
"left": 62, | |
"top": 76 | |
}, | |
"size": { | |
"width": 68, | |
"height": 25 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "create parallel variables", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 62, | |
"top": 76 | |
}, | |
"size": { | |
"width": 68, | |
"height": 25 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "create parallel variables", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 62, | |
"top": 76 | |
}, | |
"size": { | |
"width": 68, | |
"height": 25 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "create parallel variables", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 7, | |
"vars_in": [ | |
{ | |
"rel": "inputValue", | |
"name": "selectedIndicators" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "create parallel variables", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"//let selectedSample = API.getData('selectedParallel');\n//let selectedMarkers = API.getData('selectedMarkers').resurrect();\nlet metadata = API.getData('selectedMetadata');\nlet s = new Array();\n\n//let s = selectedSample.reduce(\n// (out, bool, index) => bool ? out.concat(metadata[index]) : out, \n//[]\n//)\n\nswitch(this.variable) {\n case 'selectedParallel':\n //selectedParallel is a boolean filter\n let selectedSample = API.getData('selectedParallel');\n s = selectedSample.reduce(\n (out, bool, index) => bool ? out.concat(metadata[index]) : out, \n []\n )\n break;\n case 'selectedMarkers':\n //selectedMarkers is a list an array with index\n let selectedMarkers = API.getData('selectedMarkers').resurrect();\n console.log(selectedMarkers);\n s = metadata.filter((v,i,a) => selectedMarkers.includes(i + 1));\n break;\n}\n\n\nAPI.createData('selectedSamples', s)\n\nconsole.log('sample selector executed')\n\n\n//let s2 = []\n//selectedSample.forEach( (e, i) => {\n// if (e) {s2.push(metadata[i])}\n//})\n\n//let selectedMetadata = metadata[s]\n//let m = metadata.filter( (x, i) => {\n// if (s.includes(i)) {return i}\n//}\n//)\n\n\n" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 38, | |
"top": 27 | |
}, | |
"size": { | |
"width": 50, | |
"height": 36 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "sample selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 47 | |
}, | |
"size": { | |
"width": 60, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "sample selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"spectra": { | |
"position": { | |
"left": 29, | |
"top": 11 | |
}, | |
"size": { | |
"width": 72, | |
"height": 36 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "sample selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 38, | |
"top": 27 | |
}, | |
"size": { | |
"width": 50, | |
"height": 36 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "sample selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 38, | |
"top": 27 | |
}, | |
"size": { | |
"width": 50, | |
"height": 36 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "sample selector", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 8, | |
"vars_in": [ | |
{ | |
"rel": "inputValue", | |
"name": "selectedParallel" | |
}, | |
{ | |
"rel": "inputValue", | |
"name": "selectedMarkers" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Show fullscreen" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "sample selector", | |
"zindex": 19 | |
}, | |
{ | |
"url": "modules/types/edition/slick_grid/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"slickCheck": [ | |
[ | |
"enableCellNavigation", | |
"rowNumbering", | |
"forceFitColumns", | |
"highlightScroll", | |
"forgetLastActive", | |
"filterColumns", | |
"editable" | |
] | |
], | |
"copyPaste": [ | |
[ | |
"active" | |
] | |
], | |
"copyPasteOptions": [ | |
[ | |
"newRows", | |
"readOnly" | |
] | |
], | |
"autoColumns": [ | |
[] | |
], | |
"toolbar": [ | |
[ | |
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}, | |
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}, | |
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}, | |
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} | |
}, | |
"id": 12, | |
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{} | |
], | |
"actions_in": [ | |
{ | |
"rel": "execute", | |
"name": "boxplotButton" | |
}, | |
{ | |
"rel": "execute", | |
"name": "invertButton" | |
}, | |
{ | |
"rel": "execute", | |
"name": "resetSelectionButton" | |
} | |
], | |
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{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
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{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Show fullscreen" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "box plot calculator", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Compute / Refresh Boxplot" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
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0, | |
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] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
null | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
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"Default layer": { | |
"position": { | |
"left": 159, | |
"top": -1 | |
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"size": { | |
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"height": 5 | |
}, | |
"zIndex": 0, | |
"display": true, | |
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255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 15, | |
"top": 85 | |
}, | |
"size": { | |
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"height": 8 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
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"left": 124, | |
"top": 22 | |
}, | |
"size": { | |
"width": 17, | |
"height": 5 | |
}, | |
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"display": false, | |
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255, | |
255, | |
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"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 124, | |
"top": 22 | |
}, | |
"size": { | |
"width": 17, | |
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"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 124, | |
"top": 22 | |
}, | |
"size": { | |
"width": 17, | |
"height": 5 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 13, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "boxplotButton" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 36 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Invert selection" | |
], | |
"onLabel": [ | |
"invert selection" | |
], | |
"offLabel": [ | |
"restore selection" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"invert" | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 133, | |
"top": 16 | |
}, | |
"size": { | |
"width": 12, | |
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}, | |
"zIndex": 0, | |
"display": true, | |
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255, | |
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"wrapper": false, | |
"created": true, | |
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}, | |
"admin": { | |
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"left": 0, | |
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"display": true, | |
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255, | |
255, | |
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"wrapper": true, | |
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}, | |
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255, | |
255, | |
255, | |
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], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 127, | |
"top": 26 | |
}, | |
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"width": 12, | |
"height": 5 | |
}, | |
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255, | |
255, | |
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], | |
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"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 14, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "invertButton" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
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100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
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{ | |
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[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
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{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 34 | |
}, | |
{ | |
"url": "modules/types/edition/rich_text/", | |
"configuration": { | |
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"group": [ | |
{ | |
"editable": [ | |
[ | |
"isEditable" | |
] | |
], | |
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0 | |
], | |
"modifyInVariable": [ | |
[] | |
], | |
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[ | |
"yes" | |
] | |
], | |
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[] | |
], | |
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255, | |
255, | |
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}, | |
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255, | |
255, | |
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}, | |
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"left": 157, | |
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}, | |
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"width": 27, | |
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}, | |
"zIndex": 0, | |
"display": true, | |
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255, | |
255, | |
255, | |
0 | |
], | |
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"created": true, | |
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}, | |
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"top": 0 | |
}, | |
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"height": 20 | |
}, | |
"zIndex": 0, | |
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255, | |
255, | |
255, | |
0 | |
], | |
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"created": true, | |
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}, | |
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"left": 0, | |
"top": 0 | |
}, | |
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"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
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255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 15, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
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{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
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{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"richtext": "<p>to do:</p>\n\n<p><s>fix inverse selection</s></p>\n\n<p><s>reset selection</s></p>\n\n<p><s>boxplot without selection</s></p>\n\n<p> </p>\n\n<p><s>upload target</s></p>\n\n<p>loadings pca</p>\n\n<p>color pca / select groups for color</p>\n\n<p>check for zero deviation in columns</p>\n\n<p> </p>\n\n<p>correlation matrix between selected Parallels</p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"var {Matrix, MatrixStat: Stat, ArrayStat} = ML;\nconst computeMean = ArrayStat.mean;\nconst computeVariance = ArrayStat.variance;\nconst mean = Stat.mean;\nconst stdev = Stat.standardDeviation;\nvar spectraDataSet = [];\nvar matrixYData = [];\nvar actionName, actionValue\n\nlet d = API.getData('data')\nlet highlights = d[0].metadata.map(x=>x._highlight)\n\nswitch(this.variable) {\n case 'csvParameters':\n actionName = 'csvParameters';\n break;\n default:\n actionName = this.action.name;\n actionValue = this.action.value;\n}\n\nswitch (actionName) {\n case \"PCA\":\n //get the matrix\n matrixYData = API.getData(\"selectedIndicators\").map(x=>x.indicator.value);\n matrixYData = transpose(matrixYData);\n\n //check for number of columns\n if (matrixYData[0].length < 2) {\n API.createData('errorMessage', 'Select at least 2 indicators(metabolites)');\n break;\n };\n \n // get parameters for PCA\n let pcaPlotParam = API.getData(\"pcaPlot\").resurrect();\n \n let pca = PCA(matrixYData, {\n nComponents: pcaPlotParam.numberOfEigenVectors,\n threshold: pcaPlotParam.threshold,\n maxIterations: pcaPlotParam.maxIterations,\n scale: true,\n center: true\n });\n \n plotResult(pca.T, pcaPlotParam, 'pcaResult');\n plotResult(pca.P, pcaPlotParam, 'pcaResultLoadings');\n break;\n \n case 'plotResult':\n var {x, y} = actionValue.data;\n var indexs = actionValue.indexs;\n var dataClass = actionValue.dataClass;\n if (!dataClass) {\n dataClass = new Array(x.length).fill([1]);\n }\n var l = x.length;\n let nbClasses = dataClass[0].length;\n var result = {\n title: 'main plot',\n data: [\n {\n x: x,\n y: y,\n type: 'scatter',\n info: Array.from({length: x.length}, (v, k) => k+1),\n styles: {\n unselected: new Array(x.length),\n selected: new Array(x.length)\n }\n }\n ]\n };\n var selectedScale = chroma.scale(['green', 'black']).domain([0, nbClasses - 1]).mode('hsl');\n var unselectedScale = chroma.scale(['red', 'blue']).domain([0, nbClasses - 1]).mode('hsl');\n console.log(unselectedScale(0).toString());\n \n let unselected = result.data[0].styles.unselected;\n let selected = result.data[0].styles.selected;\n \n for (let i = 0; i < l; i++) {\n for (let j = 0; j < nbClasses; j++) {\n if(dataClass[i][j] === 1) {\n unselected[i] = {\n fill: unselectedScale(j).toString(),\n shape: \"circle\",\n cx: 0,\n cy: 0,\n r: 3,\n height: \"5px\",\n width: \"5px\",\n stroke: \"transparent\"\n };\n selected[i] = {\n fill: selectedScale(j).toString(),\n shape: \"circle\",\n cx: 0,\n cy: 0,\n r: 3,\n height: \"5px\",\n width: \"5px\",\n stroke: \"transparent\"\n };\n j = nbClasses;\n };\n // info[i] = {index: indexs[i]};\n }\n }\n API.createData(actionValue.varName, result);\n if (actionValue.varName == 'pcaResult' ) {\n API.createData(actionValue.varName + 'ellipse', predictEllipse(x, y, 5, 0.95, 1024));\n }\n break;\n}\n\nfunction plotResult(prediction, pcaPlot, varName) {\n var x = prediction.getColumn(pcaPlot.pcx - 1);\n var y = prediction.getColumn(pcaPlot.pcy - 1);\n var dataClass = new Array(x.length).fill([0, 0, 0, 1]);\n //console.log(dataClass);\n dataClass[0] = [1, 0,0, 0];\n dataClass[1] = [0, 1,0, 0];\n dataClass[2] = [0, 0,1, 0];\n //API.createData('dataToPlot', {data: {x, y}, varName, dataClass});\n API.doAction('plotResult', {data: {x, y}, varName, dataClass});\n}\n\nfunction adjustData(dataSet, options) {\n if (Array.isArray(dataSet[0])) {\n dataSet = Matrix.checkMatrix(dataSet);\n } else if (Array.isArray(dataSet)) {\n dataSet = new Matrix(dataSet.map(a => {\n return [a];\n }));\n } else {\n throw new Error('Invalid data type for dataSet');\n }\n const {\n means = Stat.mean(dataSet),\n std = Stat.standardDeviation(dataSet, means, true)\n } = options;\n\n return [dataSet, means, std];\n}\n\nfunction normal(x) {\n if (!Array.isArray(x)) {\n throw new Error('The input should be an array');\n } else if (!Array.isArray(x[0])) {\n return vectorNormalization(x);\n } else {\n return matrixNormalization(x);\n }\n}\n\nfunction vectorNormalization(data) {\n let mean = computeMean(data);\n let std = computeVariance(data, true);\n\n let ans = new Array(data.length);\n if (std === 0) {\n for (let i = 0; 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"display": false, | |
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"fontFamily": [ | |
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}, | |
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"group": [ | |
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"[{\"ID\":\"Creatine\",\"title\":\"Creatine\",\"text\":[]},{\"ID\":\"Glucose\",\"title\":\"Glucose\",\"text\":[]},{\"ID\":\"D_Galactose_alpha\",\"title\":\"D_Galactose_alpha\",\"text\":[]},{\"ID\":\"D_Lactose\",\"title\":\"D_Lactose\",\"text\":[]},{\"ID\":\"Alanine\",\"title\":\"Alanine\",\"text\":[]},{\"ID\":\"Lactate\",\"title\":\"Lactate\",\"text\":[]},{\"ID\":\"Acetate\",\"title\":\"Acetate\",\"text\":[]},{\"ID\":\"Succinate\",\"title\":\"Succinate\",\"text\":[]},{\"ID\":\"Citrate\",\"title\":\"Citrate\",\"text\":[]},{\"ID\":\"Dimethylamine\",\"title\":\"Dimethylamine\",\"text\":[]},{\"ID\":\"Trimethylamine\",\"title\":\"Trimethylamine\",\"text\":[]},{\"ID\":\"Betaine\",\"title\":\"Betaine\",\"text\":[]},{\"ID\":\"Glycine\",\"title\":\"Glycine\",\"text\":[]},{\"ID\":\"Fumaric_acid\",\"title\":\"Fumaric_acid\",\"text\":[]},{\"ID\":\"Formate\",\"title\":\"Formate\",\"text\":[]},{\"ID\":\"X1_Methylnicotinamide\",\"title\":\"X1_Methylnicotinamide\",\"text\":[]},{\"ID\":\"Dimethylglycine\",\"title\":\"Dimethylglycine\",\"text\":[]},{\"ID\":\"Myo_Inositol\",\"title\":\"Myo_Inositol\",\"text\":[]},{\"ID\":\"Taurine\",\"title\":\"Taurine\",\"text\":[]},{\"ID\":\"Hippurate\",\"title\":\"Hippurate\",\"text\":[{\"p\":\"Hippurate is the glycine conjugate of benzoic acid and is synthesised in both the liver and renal cortex. Other minor routes of synthesis of benzoic acid in humans include basic metabolism of protein catabolism or from metabolism of quinic acid via the shikimate pathway in the gastrointestine (Pero et al 2010 D.O.I. 10.2174/157488410790410588) It is typically associated with bacterial metabolism of dietary phenolics. The absence of hippurate in the urine of new-born infants is consistent with the involvement of the gut bacteria in its synthesis. Hippurate was first identified in horse (hippos) urine in 1829 by Liebig and is one of the highest concentration aromatic compounds in human urine. It is associated with lean muscle mass, low body weight and is inversely associated with blood pressure. 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] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 92, | |
"top": 36 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 123, | |
"top": 23 | |
}, | |
"size": { | |
"width": 24, | |
"height": 23 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 58, | |
"top": 18 | |
}, | |
"size": { | |
"width": 24, | |
"height": 23 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Upload your data", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 29, | |
"vars_out": [ | |
{ | |
"event": "onRead", | |
"rel": "data", | |
"jpath": [], | |
"name": "droppedData" | |
} | |
], | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Upload your data", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"\nlet actionName, actionValue;\nlet data = [];\nlet customMethod;\n\nswitch(this.variable) {\n case 'droppedData':\n actionName = 'droppedData';\n actionValue = API.getData(actionName).resurrect();\n break\n default:\n actionName = this.action.name;\n actionValue = this.action.value;\n}\n\nswitch(actionName) {\n case 'droppedData':\n \n //var zipFile = actionValue;\n //var jsZip = new JSZip();\n //let zip = await jsZip.loadAsync(actionValue.content);\n //let res = await zip.files['rangesExplorer.data.json'].async('string');\n \n //API.createData('res', JSON.parse(res));\n //console.log('zip executed');\n \n switch (String(Object.keys(actionValue))) {\n case 'parseXlsx':\n var metadata = [];\n xlsxParser.fromDataAsync(actionValue.content).then((result) => {\n var sheets = result.sheets();\n var template = {}, temp = {};\n for (let sheet of sheets) {\n let name = sheet.name().toLowerCase().replace(/\\s/g, '');\n template[name] = {};\n temp[name] = sheet;\n let currentSheet = template[name];\n let minCol = sheet.row(1).minUsedColumnNumber();\n let maxCol = sheet.row(1).maxUsedColumnNumber() + 1;\n let headers = sheet.row(1)._cells.map((cell) => cell._value.replace(/\\s/g, ''));\n for (let i = minCol; i < maxCol; i++) {\n currentSheet[headers[i]] = null;\n }\n }\n temp.main.forEachExistingRow((_, i) => {\n metadata[i] = JSON.parse(JSON.stringify(template));\n for (let key in template) {\n let sheet = temp[key];\n let currentMetadata = metadata[i];\n let currentSheet = currentMetadata[key];\n let column = 1;\n if (sheet.row(i)._cells.length === 0) return;\n for (let header in currentSheet) {\n currentSheet[header] = sheet.row(i)._cells[column++]._value;\n }\n }\n })\n metadata = metadata.slice(2);\n var metadataList = {};\n metadata.forEach((m, i, array) => {\n let highlight = Math.random();\n let key = m.main.SampleID.replace(/\\./g, '_').toLowerCase();\n m._highlight = highlight;\n metadataList[key] = {\n index: i,\n _highlight: highlight\n }\n return;\n });\n \n API.createData('metadataList', metadataList);\n API.createData('metadata', metadata);\n });\n break;\n \n case 'csvFile':\n customMethod = Papa.parse(actionValue.csvFile.content, {\n header: true,\n delimiter: \",\"\n });\n \n //API.createData('customMethod', data);\n extractCSV(customMethod);\n break;\n }\n \n case 'download':\n var string = \",Creatinine,Creatine,Glucose,Alanine,Lactate,Acetate,Succinate,Citrate,Dimethylamine,Trimethylamine\\nAirwave_1_10_1Custom,10.77096162,0.149213248,0.219200053,,,0.114529688,0.107564026,2.809720562,0.290457802,0.001393114\\nAirwave_1_100_1Custom,2.316093057,0.01303475,0.054474036,,,0.031174903,0.039852373,1.039391475,0.073301503,0.001408082\\nAirwave_6_30_1Custom,13.30611001,0.191876443,0.231654052,,,0.060562254,0.052609127,1.318416998,0.441306889,0.008132261\\nAirwave_38_90_1Custom,11.85137551,0.13781424,0.208870282,,,0.05917576,0.033497749,3.370650175,0.257927047,0.001422446\";\n var toDownload = new Blob([string], {type: 'text/plain'});\n fileSaver(toDownload, 'ExampleFile.csv');\n break;\n \n case 'downloadTemplate':\n var string = \",Creatinine,Creatine,Glucose,Alanine,Lactate,Acetate,Succinate,Citrate,Dimethylamine,Trimethylamine,Betaine,Glycine,Formate,Methylnicotinamide,Dimethylglycine,Taurine,Hippurate,Hydroxybutyric_acid,Valine,Methylhistidine,Sarcosine,Trigonelline,Tartrate,Guanidinoacetate,Ethanol,Paracetamol,Paracetamol_glucuronide,X1_Hydroxyisovalerate,X3_Hydroxyisovalerate,Isoleucine,Leucine,X4_Hydroxyphenylacetate,Glutamine,Glycolate,X3_Aminoisobutyrate,Tyrosine,Pantothenic_acid,X4_Hydroxyhippuric_acid\\nAirwave_1_10_1,10.77096162,0.149213248,0.219200053,0.46928622,0.151093488,0.114529688,0.107564026,2.809720562,0.290457802,0.001393114,0.157630721,0.85743617,0.117838248,0.08022949,0.050912889,1.631998796,0.801086358,0,0.054591478,0,0,0.12843978,0.056903813,0.561631098,0,0,0,0.001524958,0.08380798,0.012319695,0.054196726,0.079207377,0,0.62164627,0.166112223,0,0.096905673,0\";\n var toDownload = new Blob([string], {type: 'text/plain'});\n fileSaver(toDownload, 'TemplateFile.csv');\n break;\n \n}\n\nconsole.log('parse csv executed with action: ' + actionName);\n\n\nfunction extractCSV(customMethod) {\n //var customMethod = API.getData('customMethod').resurrect();\n var customDescriptors = getDescriptors(customMethod);\n console.log(customDescriptors)\n var customData = cleanData(customMethod);\n console.log(customData)\n var customName = customData.map(d => d.sampleid);\n console.log(customName)\n let custom = ({customName: customName, customData: customData});\n API.createData('customData', custom);\n \n let data = API.getData('selectedData');\n let metadata = API.getData('selectedMetadata');\n \n //let customData = API.getData('customData').customData;\n //let customName = API.getData('customData').customName;\n \n customData.map((x, i) => data.push(completeCustomData(data, x, customName[i])));\n API.createData('selectedData', data);\n console.log(data.length);\n \n customData.map((x, i) => metadata.push(completeCustomMetadata(metadata, customName[i])));\n API.createData('selectedMetadata', metadata);\n console.log(metadata.length);\n \n API.switchToLayer(\"Default layer\");\n\n}\n\nfunction getDescriptors(input) {\n let result = [];\n for (let i of input.meta.fields) {\n if (i === '') continue;\n let name = i.replace(/\\./g, '_').toLowerCase();\n result.push({\n name,\n jpath: 'element.' + name,\n });\n }\n return result;\n}\n\nfunction cleanData(input, factor = 1) {\n var data = JSON.parse(JSON.stringify(input.data));\n if (input.errors.length > 0) {\n let errors = input.errors.filter((a) => a.row !== undefined);\n errors.sort((a, b) => a.row + b.row).forEach((e) => {\n data.splice(e.row, 1);\n });\n }\n \n return data.map((e, index) => {\n let result = {}\n let keys = Object.keys(e);\n for (let i = 1; i < keys.length; i++) {\n let name = keys[i].replace(/\\./g, '_').toLowerCase();\n result[name] = Number(e[keys[i]]) * factor;\n };\n result['sampleid'] = e[''].replace(/\\./g, '_').toLowerCase();;\n return result;\n })\n}\n\nfunction clone(input) {\n return JSON.parse(JSON.stringify(input));\n}\n\nfunction completeCustomData(data, custom, customName) {\n let result = {};\n let labels = Object.keys(data[0]);\n let customKeys = Object.keys(custom).map(x => x.toLowerCase());\n let labelsLC = labels.map(x => x.toLowerCase());\n labelsLC.map((x, i) => (customKeys.indexOf(x) != -1) ? result[labels[i]] = custom[x] : result[labels[i]] = 0);\n result[\"_highlight\"] = data.length + 1;\n result[\"_row\"] = customName;\n return result;\n}\n\nfunction completeCustomMetadata(metadata, customName) {\n let result = {};\n let labels = Object.keys(metadata[0]);\n labels.map((x, i) => result[labels[i]] = null);\n result[\"SampleID\"] = customName;\n result[\"_highlight\"] = metadata.length + 1;\n result[\"_row\"] = customName;\n return result;\n}\n\nfunction clone(input) {\n return JSON.parse(JSON.stringify(input));\n}\n\n" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{ | |
"lib": "jszip", | |
"alias": "JSZip" | |
}, | |
{ | |
"lib": "xlsxParser", | |
"alias": "xlsxParser" | |
}, | |
{ | |
"lib": "Papa-parser", | |
"alias": "Papa" | |
}, | |
{ | |
"lib": "file-saver", | |
"alias": "fileSaver" | |
} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 130 | |
}, | |
"size": { | |
"width": 60, | |
"height": 16 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Download / upload executor", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 79, | |
"top": 47 | |
}, | |
"size": { | |
"width": 68, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 79, | |
"top": 26 | |
}, | |
"size": { | |
"width": 68, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Download / upload executor", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 30, | |
"vars_in": [ | |
{ | |
"rel": "inputValue", | |
"name": "droppedData" | |
} | |
], | |
"actions_in": [ | |
{ | |
"rel": "execute", | |
"name": "download" | |
}, | |
{ | |
"rel": "execute", | |
"name": "extractCSV" | |
}, | |
{ | |
"rel": "execute", | |
"name": "downloadTemplate" | |
} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Show fullscreen" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Download / upload executor", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Download example file" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"download" | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 124, | |
"top": 5 | |
}, | |
"size": { | |
"width": 20, | |
"height": 15 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 15, | |
"top": 18 | |
}, | |
"size": { | |
"width": 20, | |
"height": 7 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Download example file", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 31, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "download" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Download example file", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/rich_text/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"editable": [ | |
[ | |
"isEditable" | |
] | |
], | |
"debouncing": [ | |
0 | |
], | |
"modifyInVariable": [ | |
[] | |
], | |
"storeInView": [ | |
[ | |
"yes" | |
] | |
], | |
"autoHeight": [ | |
[] | |
], | |
"bgColor": [ | |
[ | |
255, | |
255, | |
255, | |
1 | |
] | |
], | |
"postit": [ | |
[] | |
], | |
"html": [ | |
[ | |
"yes" | |
] | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 109, | |
"top": 47 | |
}, | |
"size": { | |
"width": 25, | |
"height": 37 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Upload" | |
} | |
}, | |
"id": 32, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"richtext": "<p><span style=\"font-size:104px\"> 3</span></p>\n\n<p><span style=\"font-size:12px\">It may take a while to read and extract your data. If successful you will be redirected to the main panel of this application that is "Browser".</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">You can use the following button to navigate into the application.</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">Browser allows to browse the data and is the default or landing layer.</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">Spectra allows you to select samples and see the original spectra.</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">Upload allows you to upload your custom data.</span></p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/rich_text/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"editable": [ | |
[ | |
"isEditable" | |
] | |
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"modifyInVariable": [ | |
[] | |
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"storeInView": [ | |
[ | |
"yes" | |
] | |
], | |
"autoHeight": [ | |
[] | |
], | |
"bgColor": [ | |
[ | |
255, | |
255, | |
255, | |
1 | |
] | |
], | |
"postit": [ | |
[] | |
], | |
"html": [ | |
[ | |
"yes" | |
] | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
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"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
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"spectra": { | |
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"left": 0, | |
"top": 0 | |
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"size": { | |
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"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
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"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
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"title": "", | |
"bgColor": [ | |
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"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
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"top": 48 | |
}, | |
"size": { | |
"width": 26, | |
"height": 27 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Upload" | |
} | |
}, | |
"id": 33, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"richtext": "<p><span style=\"font-size:104px\"> 1</span></p>\n\n<p><span style=\"font-size:12px\">First, download the example file (CSV format). Open it with MS Excel or LibreOffice and add the values corresponding to the metabolites. Add as many rows as necessary but, please, do not alter the column names. Columns can be deleted if unnecessary, except the first one that should contain a unique identifier for each sample.</span></p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/rich_text/", | |
"configuration": { | |
"sections": {}, | |
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"group": [ | |
{ | |
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0 | |
], | |
"modifyInVariable": [ | |
[] | |
], | |
"storeInView": [ | |
[ | |
"yes" | |
] | |
], | |
"autoHeight": [ | |
[] | |
], | |
"bgColor": [ | |
[ | |
255, | |
255, | |
255, | |
1 | |
] | |
], | |
"postit": [ | |
[] | |
], | |
"html": [ | |
[ | |
"yes" | |
] | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
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"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
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"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
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"bgColor": [ | |
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"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
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}, | |
"size": { | |
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"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
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255, | |
255, | |
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], | |
"wrapper": true, | |
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}, | |
"spectra": { | |
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"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
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"bgColor": [ | |
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255, | |
255, | |
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"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
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"top": 0 | |
}, | |
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"height": 20 | |
}, | |
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"display": false, | |
"title": "", | |
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255, | |
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255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
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"left": 57, | |
"top": 48 | |
}, | |
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"width": 26, | |
"height": 27 | |
}, | |
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"display": true, | |
"title": "", | |
"bgColor": [ | |
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255, | |
255, | |
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], | |
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"name": "Upload" | |
} | |
}, | |
"id": 34, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"richtext": "<p><span style=\"font-size:104px\"> 2</span></p>\n\n<p><span style=\"font-size:12px\">Once done, save the file in CSV format and drop it into the area for that purpose. You can also click in the area to display the file selector tool of your OS.</span></p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Download template file" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"downloadTemplate" | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
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255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
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"name": "Default layer" | |
}, | |
"admin": { | |
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"width": 20, | |
"height": 20 | |
}, | |
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255, | |
255, | |
255, | |
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], | |
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}, | |
"spectra": { | |
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}, | |
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255, | |
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"wrapper": true, | |
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}, | |
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"position": { | |
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"top": 5 | |
}, | |
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}, | |
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"created": true, | |
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}, | |
"Upload": { | |
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"top": 27 | |
}, | |
"size": { | |
"width": 20, | |
"height": 7 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Download example file", | |
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255, | |
255, | |
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], | |
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"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 35, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "downloadTemplate" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
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100, | |
100, | |
100, | |
1 | |
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} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Download example file", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"let a = API.getData('data');\nfunction test(){\n let errorMessage = \"3dd\";\n console.log(errorMessage);\n API.createData('errorMessage', errorMessage);\n}\nsetTimeout(test, 100);" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
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"Default layer": { | |
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}, | |
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}, | |
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}, | |
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}, | |
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}, | |
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"title": "", | |
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255, | |
255, | |
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], | |
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], | |
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], | |
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} | |
], | |
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} | |
], | |
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{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
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100, | |
100, | |
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"common": [ | |
{ | |
"toolbar": [ | |
[ | |
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] | |
] | |
} | |
] | |
}, | |
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{ | |
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"" | |
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"fontFamily": [ | |
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], | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Reset Selection" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
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0, | |
0, | |
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], | |
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0, | |
0, | |
0, | |
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] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"reset" | |
], | |
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[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 131, | |
"top": 49 | |
}, | |
"size": { | |
"width": 12, | |
"height": 6 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
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], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 30, | |
"top": 86 | |
}, | |
"size": { | |
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}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
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255, | |
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"name": "spectra" | |
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"top": 0 | |
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255, | |
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"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
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"top": 0 | |
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255, | |
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"name": "Upload" | |
} | |
}, | |
"id": 37, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "resetSelectionButton" | |
} | |
], | |
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"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
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100, | |
100, | |
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} | |
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{ | |
"toolbar": [ | |
[ | |
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] | |
] | |
} | |
] | |
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"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 35 | |
}, | |
{ | |
"url": "modules/types/science/spectra/spectra_displayer/", | |
"configuration": { | |
"sections": { | |
"graph": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"graph": [ | |
{ | |
"url": [ | |
"" | |
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"zoom": [ | |
"xy" | |
], | |
"wheelAction": [ | |
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], | |
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], | |
"fullOut": [ | |
"both" | |
], | |
"legend": [ | |
null | |
], | |
"legendOptions": [ | |
[ | |
"isSerieHideable", | |
"isSerieSelectable" | |
] | |
], | |
"mouseTracking": [ | |
[] | |
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"selectScatter": [ | |
[ | |
"yes" | |
] | |
], | |
"independantYZoom": [ | |
[] | |
] | |
} | |
] | |
} | |
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"axis": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"xAxis": [ | |
{ | |
"checkboxes": [ | |
[ | |
"display" | |
] | |
], | |
"label": [ | |
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], | |
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"axismodification": [ | |
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], | |
"yAxis": [ | |
{ | |
"checkboxes": [ | |
[ | |
"display" | |
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"0" | |
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], | |
"fitToAxisOnFromTo": [ | |
[] | |
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} | |
] | |
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} | |
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"series": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"series": [ | |
{ | |
"overflow": [ | |
[] | |
], | |
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] | |
} | |
] | |
} | |
} | |
], | |
"variables": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"variables": [ | |
[ | |
{ | |
"variable": "pcaResult", | |
"axis": "0", | |
"adaptTo": "none", | |
"plotcolor": [ | |
255, | |
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], | |
"strokewidth": "2", | |
"strokestyle": "2", | |
"plotcontinuous": "discrete", | |
"peakpicking": [], | |
"markers": [ | |
"markers" | |
], | |
"markerShape": "1", | |
"markerSize": 2, | |
"normalize": "none", | |
"optimizeSlots": [], | |
"tracking": [] | |
} | |
] | |
] | |
} | |
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"misc": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"misc": [ | |
{ | |
"highlightOptions": [ | |
"{}" | |
] | |
} | |
] | |
} | |
} | |
] | |
}, | |
"groups": {} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 83, | |
"top": 23 | |
}, | |
"size": { | |
"width": 29, | |
"height": 27 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Loadings", | |
"bgColor": [ | |
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255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 116, | |
"top": 38 | |
}, | |
"size": { | |
"width": 29, | |
"height": 24 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Loadings", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 41 | |
}, | |
"size": { | |
"width": 39, | |
"height": 40 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Loadings", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 57, | |
"top": 23 | |
}, | |
"size": { | |
"width": 29, | |
"height": 27 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Loadings", | |
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255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 57, | |
"top": 23 | |
}, | |
"size": { | |
"width": 29, | |
"height": 27 | |
}, | |
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"display": false, | |
"title": "Loadings", | |
"bgColor": [ | |
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255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 38, | |
"vars_in": [ | |
{ | |
"rel": "chart", | |
"name": "pcaResultLoadings" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"event": "onSelectScatter", | |
"rel": "selectedData", | |
"jpath": [], | |
"name": "selectedMarkers" | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Loadings", | |
"zindex": 0 | |
} | |
], | |
"variables": [ | |
{ | |
"varname": "data", | |
"jpath": [ | |
"data" | |
] | |
}, | |
{ | |
"varname": "spec", | |
"jpath": [ | |
"spec" | |
] | |
} | |
], | |
"aliases": [ | |
{ | |
"path": "https://www.lactame.com/lib/spectra-data/3.2.4/spectra-data.min", | |
"alias": "SD" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/nmr-predictor/1.0.8/nmr-predictor.min", | |
"alias": "Predictor" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/openchemlib/4.6.2/openchemlib-full", | |
"alias": "OCL" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/ml/HEAD/ml", | |
"alias": "ML" | |
}, | |
{ | |
"path": "https://www.lactame.com/github/cheminfo-js/visualizer-helper/3ffac8f5646dd4231c1cb33cebae970e5ee0d503/", | |
"alias": "vh" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/image-js/0.9.5/image.min", | |
"alias": "IJS" | |
}, | |
{ | |
"path": "components/papa-parse/papaparse.min", | |
"alias": "Papa-parser" | |
}, | |
{ | |
"path": "https://dl.dropboxusercontent.com/s/ky06573iww07wnd/jerzy.js?dl=0", | |
"alias": "jerzy" | |
}, | |
{ | |
"path": "https://dl.dropboxusercontent.com/s/7npg0288cesrmhu/timsort.js?dl=0", | |
"alias": "timsort" | |
}, | |
{ | |
"path": "https://dl.dropboxusercontent.com/s/100bq1kwk27yvyj/xlsx-populate.js?dl=0", | |
"alias": "xlsxParser" | |
} | |
], | |
"configuration": { | |
"title": "ranges explorer 0.5.0" | |
}, | |
"actionscripts": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"action": [ | |
{ | |
"name": [ | |
null | |
], | |
"script": [ | |
null | |
] | |
} | |
] | |
} | |
} | |
], | |
"init_script": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"general": [ | |
{ | |
"script": [ | |
"\nAPI.loading('load','Please wait while data are being downloaded');\n\n// you need to leave some time to display the message\n// we use setImmediate to achieve this\n\nsetImmediate(loadData);\n\n$.getJSON('https://gist.githubusercontent.com/jwist/a79ba94fe60dc01b91868d9c7becbd5e/raw/rangesExplorer.data.json',function(result) {\n API.createData('data',result.data);\n API.createData('spec',result.spec);\n setTimeout(selectDataSets, 1000);\n setTimeout(selectData, 10000);\n API.stopLoading('load');\n})\n\nasync function loadData() {\n API.createData('pcaPlot', {'pcx': 1, 'pcy': 2, 'numberOfEigenVectors': 3})\n\n}\n\nfunction selectDataSets() {\n let data = API.getData('data');\n API.createData('selectedMetadata', data[0].metadata);\n API.createData('selectedDataSets', data[0].data);\n}\n\nfunction selectData() {\n let data = API.getData('selectedDataSets');\n API.createData('selectedData', data[0].data);\n}\n\n\n\n\n" | |
] | |
} | |
] | |
} | |
} | |
], | |
"custom_filters": [ | |
{ | |
"sections": { | |
"modules": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"modules": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
], | |
"filtersLib": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"filters": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
], | |
"filters": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"filter": [ | |
{ | |
"name": [ | |
null | |
], | |
"script": [ | |
null | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
] | |
}, | |
"groups": {} | |
} | |
], | |
"actionfiles": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"action": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
] | |
} |
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{ | |
"version": "2.98.0", | |
"grid": { | |
"layers": { | |
"Default layer": { | |
"name": "Default layer" | |
}, | |
"admin": { | |
"name": "admin" | |
}, | |
"spectra": { | |
"name": "spectra" | |
}, | |
"help": { | |
"name": "help" | |
}, | |
"Upload": { | |
"name": "Upload" | |
} | |
}, | |
"xWidth": 10, | |
"yHeight": 10 | |
}, | |
"modules": [ | |
{ | |
"url": "modules/types/edition/object_editor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"editable": [ | |
"view" | |
], | |
"expanded": [ | |
[] | |
], | |
"storeObject": [ | |
[] | |
], | |
"displayValue": [ | |
[] | |
], | |
"searchBox": [ | |
[ | |
"search" | |
] | |
], | |
"sendButton": [ | |
[] | |
], | |
"output": [ | |
"new" | |
], | |
"storedObject": [ | |
"{}" | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 75, | |
"top": 42 | |
}, | |
"size": { | |
"width": 35, | |
"height": 38 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 155, | |
"top": 50 | |
}, | |
"size": { | |
"width": 35, | |
"height": 38 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"spectra": { | |
"position": { | |
"left": 75, | |
"top": 42 | |
}, | |
"size": { | |
"width": 35, | |
"height": 38 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 75, | |
"top": 42 | |
}, | |
"size": { | |
"width": 35, | |
"height": 38 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
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"top": 42 | |
}, | |
"size": { | |
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"height": 38 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
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255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 1, | |
"vars_in": [ | |
{ | |
"rel": "value", | |
"name": "pcaResultLoadings" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/slick_grid/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"slickCheck": [ | |
[ | |
"enableCellNavigation", | |
"rowNumbering", | |
"forceFitColumns", | |
"highlightScroll", | |
"forgetLastActive", | |
"filterColumns" | |
] | |
], | |
"copyPaste": [ | |
[] | |
], | |
"copyPasteOptions": [ | |
[ | |
"newRows" | |
] | |
], | |
"autoColumns": [ | |
[] | |
], | |
"toolbar": [ | |
[] | |
], | |
"colorjpath": [ | |
[] | |
], | |
"slick.defaultColumnWidth": [ | |
null | |
], | |
"slick.rowHeight": [ | |
null | |
], | |
"slick.headerRowHeight": [ | |
30 | |
], | |
"slick.selectionModel": [ | |
"row" | |
], | |
"idProperty": [ | |
"" | |
], | |
"filterType": [ | |
"pref" | |
], | |
"filterRow": [ | |
"// Documentation: https://github.com/NPellet/visualizer/blob/46b40ca86345f8fa313563bf9c6ecb80ba323101/src/modules/types/edition/slick_grid/view.js#L1695-L1735" | |
], | |
"customJpaths": [ | |
"" | |
] | |
} | |
], | |
"cols": [ | |
[ | |
{ | |
"name": "label", | |
"jpath": [ | |
"label" | |
], | |
"editor": "none", | |
"forceType": "", | |
"formatter": "typerenderer", | |
"copyFormatter": "default", | |
"visibility": "both", | |
"rendererOptions": "", | |
"editorOptions": "", | |
"hideColumn": [] | |
} | |
] | |
], | |
"actionCols": [ | |
[ | |
{ | |
"backgroundColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"color": [ | |
0, | |
0, | |
0, | |
1 | |
], | |
"position": "end", | |
"clickMode": "text" | |
} | |
] | |
], | |
"groupings": [ | |
[ | |
{ | |
"getter": [] | |
} | |
] | |
], | |
"actionOutButtons": [ | |
[ | |
{} | |
] | |
], | |
"data": [ | |
{ | |
"saveInView": [ | |
[] | |
], | |
"varname": [ | |
"" | |
], | |
"data": [ | |
"[]" | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 24, | |
"top": 23 | |
}, | |
"size": { | |
"width": 13, | |
"height": 15 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Dartaset Selector (click on row)", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 1, | |
"top": 2 | |
}, | |
"size": { | |
"width": 35, | |
"height": 15 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Dartaset Selector (click on row)", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"spectra": { | |
"position": { | |
"left": 24, | |
"top": 23 | |
}, | |
"size": { | |
"width": 17, | |
"height": 27 | |
}, | |
"zIndex": 0, | |
"display": false, | |
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"title": "Dartaset Selector (click on row)", | |
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}, | |
{ | |
"url": "modules/types/edition/slick_grid/", | |
"configuration": { | |
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{ | |
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"display": true, | |
"title": "Select analysis (click on row)", | |
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] | |
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"url": "modules/types/client_interaction/code_executor/", | |
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{ | |
"display": [ | |
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] | |
], | |
"execOnLoad": [ | |
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], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
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{} | |
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} | |
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"fontFamily": [ | |
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} | |
], | |
"title": "calculate indicators", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/slick_grid/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
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[ | |
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"forgetLastActive", | |
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{ | |
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}, | |
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"height": 90 | |
}, | |
"zIndex": 0, | |
"display": true, | |
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}, | |
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"height": 90 | |
}, | |
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} | |
}, | |
"id": 5, | |
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"actions_out": [ | |
{ | |
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} | |
], | |
"vars_out": [ | |
{ | |
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"rel": "rows", | |
"jpath": [], | |
"name": "selectedIndicators" | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
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100, | |
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] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Metabolites selector", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/chart/statistics/parallel_coordinates/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
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"options": [ | |
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"cols": [ | |
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"top": 0 | |
}, | |
"size": { | |
"width": 121, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Click and drag on the variable axis to filter sample within a range", | |
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255, | |
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}, | |
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"display": false, | |
"title": "Click and drag on the variable axis to select sample within a range", | |
"bgColor": [ | |
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}, | |
"size": { | |
"width": 86, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 10, | |
"vars_in": [ | |
{ | |
"rel": "value", | |
"name": "errorMessage" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Error messages", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/slick_grid/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"slickCheck": [ | |
[ | |
"enableCellNavigation", | |
"rowNumbering", | |
"forceFitColumns", | |
"highlightScroll", | |
"forgetLastActive", | |
"editable", | |
"keepSelected" | |
] | |
], | |
"copyPaste": [ | |
[] | |
], | |
"copyPasteOptions": [ | |
[ | |
"newRows" | |
] | |
], | |
"autoColumns": [ | |
[] | |
], | |
"toolbar": [ | |
[] | |
], | |
"colorjpath": [ | |
[] | |
], | |
"slick.defaultColumnWidth": [ | |
null | |
], | |
"slick.rowHeight": [ | |
"120" | |
], | |
"slick.headerRowHeight": [ | |
30 | |
], | |
"slick.selectionModel": [ | |
"row" | |
], | |
"idProperty": [ | |
"" | |
], | |
"filterType": [ | |
"pref" | |
], | |
"filterRow": [ | |
"// Documentation: https://github.com/NPellet/visualizer/blob/46b40ca86345f8fa313563bf9c6ecb80ba323101/src/modules/types/edition/slick_grid/view.js#L1695-L1735" | |
], | |
"customJpaths": [ | |
"" | |
] | |
} | |
], | |
"cols": [ | |
[ | |
{ | |
"name": "boxplot", | |
"jpath": [], | |
"editor": "none", | |
"forceType": "chart", | |
"formatter": "typerenderer", | |
"copyFormatter": "default", | |
"visibility": "main", | |
"rendererOptions": "", | |
"editorOptions": "", | |
"hideColumn": [] | |
} | |
] | |
], | |
"actionCols": [ | |
[ | |
{ | |
"backgroundColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"color": [ | |
0, | |
0, | |
0, | |
1 | |
], | |
"position": "end", | |
"clickMode": "text" | |
} | |
] | |
], | |
"groupings": [ | |
[ | |
{ | |
"getter": [] | |
} | |
] | |
], | |
"actionOutButtons": [ | |
[ | |
{} | |
] | |
], | |
"data": [ | |
{ | |
"saveInView": [ | |
[] | |
], | |
"varname": [ | |
"" | |
], | |
"data": [ | |
"[]" | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 146, | |
"top": 0 | |
}, | |
"size": { | |
"width": 42, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 84, | |
"top": 3 | |
}, | |
"size": { | |
"width": 68, | |
"height": 40 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 146, | |
"top": 0 | |
}, | |
"size": { | |
"width": 42, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 146, | |
"top": 0 | |
}, | |
"size": { | |
"width": 42, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 146, | |
"top": 0 | |
}, | |
"size": { | |
"width": 42, | |
"height": 90 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 11, | |
"vars_in": [ | |
{ | |
"rel": "list", | |
"name": "boxPlot" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Print", | |
"Show fullscreen" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"\n\n// action name is captured (boxplotButton or invert_button)\n// the first one triggers the calculation, while the second one must only\n// invert the selection\n\nlet actionName, actionValue;\n\nactionName = this.action.name;\nactionValue = this.action.value;\n\n// selectedIndicators are the metabolites selected in the PCA or parallel\n// Boxplots are only drawn for these metabolites\nlet selectedIndicators = API.getData('selectedIndicators')\nlet selectedSample = API.getData('selectedSamples')\nlet selectedSampleIDs = API.getData('selectedSampleIDs')\n\nswitch(actionName) {\n case 'invertButton':\n let metadata = API.getData('selectedMetadata');\n let s = new Array(); \n \n let selectedMarkers = selectedSample.map(x => x._highlight);\n //console.log(\"markers selected before inversion: \" + selectedMarkers);\n \n s = metadata.filter((v,i,a) => !selectedMarkers.includes(i + 1));\n //console.log(\"Samples after inversion: \" + s.map(x => x._highlight));\n\n API.createData('selectedSamples', s)\n console.log('Boxplot executed: exec with invertButton')\n break;\n \n case 'resetSelectionButton':\n API.createData('selectedSampleIDs', []);\n API.createData('errorMessage', 'selection reseted');\n break;\n \n case 'boxplotButton':\n\n if (selectedSampleIDs.length > 0) {\n let filter = selectedSampleIDs.map(x => x._highlight);\n let filterSamples = selectedSample.map(x => x._highlight);\n //console.log(filter);\n //console.log(selectedSample);\n \n var aGroup = selectedIndicators.map((x, i) => {\n return x.indicator.value.filter((e, i) => filter.includes(i+1));\n });\n \n var bGroup = selectedIndicators.map(x => {\n return x.indicator.value.filter((e, i) => !filter.includes(i+1) && filterSamples.includes(i+1));\n });\n //console.log(\"agroup: \" + aGroup);\n //console.log(\"bgroup: \" + bGroup);\n \n //console.log(bGroup)\n let bplots = []\n if (selectedSampleIDs.length > 0) {\n aGroup.forEach((x, i) => {\n bplots[i] = new Boxplot(selectedIndicators[i].index, [getBoxPlot(aGroup[i], 0), getBoxPlot(bGroup[i], 1)]);\n });\n } else {\n parallelVariables.forEach((x, i) => {\n bplots[i] = new Boxplot(selectedIndicators[i].index, [getBoxPlot(x, i)]);\n });\n }\n //let boxPlot = new Boxplot('Box plots', bplots)\n \n //let boxPlot = new Boxplot('e', [getBoxPlot(vect, 0)])\n //let boxPlot2 = new Boxplot('e', [getBoxPlot(vect, 1)])\n //console.log(bplots)\n \n //API.createData('boxPlot', [boxPlot, boxPlot2])\n API.createData('boxPlot', bplots)\n API.createData('boxPlotvertical', bplots)\n } else {\n let errorMessage = \"Please select at least one sample in the table\"\n API.createData('errorMessage', errorMessage);\n }\n break;\n}\n\nfunction Boxplot (title, boxData) {\n this.title = title,\n this.data = boxData\n}\n\nfunction BoxData (x, q1, q2, q3, whiskers, outliers) {\n this.type = 'box',\n this.orientation = 'x'\n this.maxBoxWidth = 10,\n this.defaultStyle = {\n\t \"outlierLineWidth\" : 1,\n\t \"outlierLineColor\" : 'rgb( 255, 255, 255 )',\n\t \"outlierFillColor\" : 'rgb( 0, 255, 0 )',\n\t \"outlierFillOpacity\" : 0\n\t}\n this.boxes = new Array( \n {'y' : x, \n 'Q1' : q1, \n 'Q2' : q2, \n 'Q3' : q3, \n 'whiskers' : whiskers, \n 'outliers' : outliers})\n}\n\nfunction quantile(data, q) {\n data=Array_Sort_Numbers(data);\n var pos = ((data.length) - 1) * q;\n var base = Math.floor(pos);\n var rest = pos - base;\n if( (data[base+1]!==undefined) ) {\n return data[base] + rest * (data[base+1] - data[base]);\n } else {\n return data[base];\n }\n}\n\nfunction Array_Sort_Numbers(inputarray){\n return inputarray.sort(function(a, b) {\n return a - b;\n });\n}\n\n//let vect = [.26, 0.34, 0.70, 1.75, 50.57, 1.55, 0.08, 0.42, 0.50, 3.20, 0.15, 0.49, 0.95, 0.24, 1.37, 0.17, 6.98, 0.10, 0.94, 0.38]\n\nfunction getBoxPlot(vect, idx){\n let q25 = quantile(vect, 0.25)\n let q50 = quantile(vect, 0.50)\n let q75 = quantile(vect, 0.75)\n \n let iqr = 1.5* (q75 - q25)\n let max = Math.max.apply(Math, vect)\n let min = Math.min.apply(Math, vect)\n \n let upperLimit = (max < q75 + iqr ? max : q75 + iqr)\n let lowerLimit = (min > q25 - iqr ? min : q25 - iqr)\n \n let outliers = []\n vect.forEach(e => {\n if (e > upperLimit ) {\n outliers.push(e)\n }\n if (e < lowerLimit ) {\n outliers.push(e)\n } \n } )\n \n let boxData = new BoxData(idx, q25, q50, q75, [lowerLimit, upperLimit], outliers)\n \n return boxData\n}\n\n\n" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 68 | |
}, | |
"size": { | |
"width": 60, | |
"height": 16 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "box plot calculator", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 12, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{ | |
"rel": "execute", | |
"name": "boxplotButton" | |
}, | |
{ | |
"rel": "execute", | |
"name": "invertButton" | |
}, | |
{ | |
"rel": "execute", | |
"name": "resetSelectionButton" | |
} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Show fullscreen" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "box plot calculator", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Compute / Refresh Boxplot" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
null | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 159, | |
"top": -1 | |
}, | |
"size": { | |
"width": 17, | |
"height": 5 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 15, | |
"top": 85 | |
}, | |
"size": { | |
"width": 14, | |
"height": 8 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 124, | |
"top": 22 | |
}, | |
"size": { | |
"width": 17, | |
"height": 5 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"help": { | |
"position": { | |
"left": 124, | |
"top": 22 | |
}, | |
"size": { | |
"width": 17, | |
"height": 5 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
"position": { | |
"left": 124, | |
"top": 22 | |
}, | |
"size": { | |
"width": 17, | |
"height": 5 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
} | |
}, | |
"id": 13, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "boxplotButton" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 36 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Invert selection" | |
], | |
"onLabel": [ | |
"invert selection" | |
], | |
"offLabel": [ | |
"restore selection" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"invert" | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 133, | |
"top": 16 | |
}, | |
"size": { | |
"width": 12, | |
"height": 5 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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"richtext": "<p>to do:</p>\n\n<p><s>fix inverse selection</s></p>\n\n<p><s>reset selection</s></p>\n\n<p><s>boxplot without selection</s></p>\n\n<p> </p>\n\n<p><s>upload target</s></p>\n\n<p>loadings pca</p>\n\n<p>color pca / select groups for color</p>\n\n<p>check for zero deviation in columns</p>\n\n<p> </p>\n\n<p>correlation matrix between selected Parallels</p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
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"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
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[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"var {Matrix, MatrixStat: Stat, ArrayStat} = ML;\nconst computeMean = ArrayStat.mean;\nconst computeVariance = ArrayStat.variance;\nconst mean = Stat.mean;\nconst stdev = Stat.standardDeviation;\nvar spectraDataSet = [];\nvar matrixYData = [];\nvar actionName, actionValue\n\nlet d = API.getData('data')\nlet highlights = d[0].metadata.map(x=>x._highlight)\n\nswitch(this.variable) {\n case 'csvParameters':\n actionName = 'csvParameters';\n break;\n default:\n actionName = this.action.name;\n actionValue = this.action.value;\n}\n\nswitch (actionName) {\n case \"PCA\":\n //get the matrix\n matrixYData = API.getData(\"selectedIndicators\").map(x=>x.indicator.value);\n matrixYData = transpose(matrixYData);\n\n //check for number of columns\n if (matrixYData[0].length < 2) {\n API.createData('errorMessage', 'Select at least 2 indicators(metabolites)');\n break;\n };\n \n // get parameters for PCA\n let pcaPlotParam = API.getData(\"pcaPlot\").resurrect();\n \n let pca = PCA(matrixYData, {\n nComponents: pcaPlotParam.numberOfEigenVectors,\n threshold: pcaPlotParam.threshold,\n maxIterations: pcaPlotParam.maxIterations,\n scale: true,\n center: true\n });\n \n plotResult(pca.T, pcaPlotParam, 'pcaResult');\n plotResult(pca.P, pcaPlotParam, 'pcaResultLoadings');\n break;\n \n case 'plotResult':\n var {x, y} = actionValue.data;\n var indexs = actionValue.indexs;\n var dataClass = actionValue.dataClass;\n if (!dataClass) {\n dataClass = new Array(x.length).fill([1]);\n }\n var l = x.length;\n let nbClasses = dataClass[0].length;\n var result = {\n title: 'main plot',\n data: [\n {\n x: x,\n y: y,\n type: 'scatter',\n info: Array.from({length: x.length}, (v, k) => k+1),\n styles: {\n unselected: new Array(x.length),\n selected: new Array(x.length)\n }\n }\n ]\n };\n var selectedScale = chroma.scale(['green', 'black']).domain([0, nbClasses - 1]).mode('hsl');\n var unselectedScale = chroma.scale(['red', 'blue']).domain([0, nbClasses - 1]).mode('hsl');\n console.log(unselectedScale(0).toString());\n \n let unselected = result.data[0].styles.unselected;\n let selected = result.data[0].styles.selected;\n \n for (let i = 0; i < l; i++) {\n for (let j = 0; j < nbClasses; j++) {\n if(dataClass[i][j] === 1) {\n unselected[i] = {\n fill: unselectedScale(j).toString(),\n shape: \"circle\",\n cx: 0,\n cy: 0,\n r: 3,\n height: \"5px\",\n width: \"5px\",\n stroke: \"transparent\"\n };\n selected[i] = {\n fill: selectedScale(j).toString(),\n shape: \"circle\",\n cx: 0,\n cy: 0,\n r: 3,\n height: \"5px\",\n width: \"5px\",\n stroke: \"transparent\"\n };\n j = nbClasses;\n };\n // info[i] = {index: indexs[i]};\n }\n }\n API.createData(actionValue.varName, result);\n if (actionValue.varName == 'pcaResult' ) {\n API.createData(actionValue.varName + 'ellipse', predictEllipse(x, y, 5, 0.95, 1024));\n }\n break;\n}\n\nfunction plotResult(prediction, pcaPlot, varName) {\n var x = prediction.getColumn(pcaPlot.pcx - 1);\n var y = prediction.getColumn(pcaPlot.pcy - 1);\n var dataClass = new Array(x.length).fill([0, 0, 0, 1]);\n //console.log(dataClass);\n dataClass[0] = [1, 0,0, 0];\n dataClass[1] = [0, 1,0, 0];\n dataClass[2] = [0, 0,1, 0];\n //API.createData('dataToPlot', {data: {x, y}, varName, dataClass});\n API.doAction('plotResult', {data: {x, y}, varName, dataClass});\n}\n\nfunction adjustData(dataSet, options) {\n if (Array.isArray(dataSet[0])) {\n dataSet = Matrix.checkMatrix(dataSet);\n } else if (Array.isArray(dataSet)) {\n dataSet = new Matrix(dataSet.map(a => {\n return [a];\n }));\n } else {\n throw new Error('Invalid data type for dataSet');\n }\n const {\n means = Stat.mean(dataSet),\n std = Stat.standardDeviation(dataSet, means, true)\n } = options;\n\n return [dataSet, means, std];\n}\n\nfunction normal(x) {\n if (!Array.isArray(x)) {\n throw new Error('The input should be an array');\n } else if (!Array.isArray(x[0])) {\n return vectorNormalization(x);\n } else {\n return matrixNormalization(x);\n }\n}\n\nfunction vectorNormalization(data) {\n let mean = computeMean(data);\n let std = computeVariance(data, true);\n\n let ans = new Array(data.length);\n if (std === 0) {\n for (let i = 0; i < ans.length; i++) {\n ans[i] = (data[i] - mean);\n }\n } else {\n for (let i = 0; i < ans.length; i++) {\n ans[i] = (data[i] - mean) / std;\n }\n }\n\n return ans;\n}\n\nfunction matrixNormalization(data) {\n let means = MatrixStat.mean(data, 1);\n let std = matrixStandardDeviation(data, means);\n\n let ans = new Array(data.length);\n for (let i = 0; i < data.length; i++) {\n ans[i] = new Array(data[i].length);\n for (let j = 0; j < data[i].length; j++) {\n if (std[i] === 0) {\n ans[i][j] = (data[i][j] - means[i]);\n } else {\n ans[i][j] = (data[i][j] - means[i]) / std[i];\n }\n }\n }\n return ans;\n}\n\nfunction matrixStandardDeviation(data, means) {\n return data.map(\n (row, i) => Math.sqrt(row.reduce(\n (acc, val) => acc + ((val - means[i]) * (val - means[i]))\n , 0) / (row.length - 1))\n );\n}\n\nfunction PCA(dataset, options = {}) {\n var {\n nComponents = 2,\n threshold = 1e-9,\n maxIterations = 100\n } = options;\n\n var eMatrix = _adjust(dataset, options);\n \n var r = eMatrix.rows;\n var c = eMatrix.columns;\n\n var T = Matrix.zeros(r, nComponents);\n var P = Matrix.zeros(c, nComponents);\n var eigenvalues = new Array(nComponents);\n \n for (let i = 0; i < nComponents; i++) {\n let tIndex = maxSumColIndex(eMatrix.clone().mulM(eMatrix));\n let t = eMatrix.getColumnVector(tIndex);\n \n let k = 0;\n let tNew = t.dot(t);\n for (let tOld = Number.MAX_SAFE_INTEGER; Math.abs(tOld - tNew) > threshold && k < maxIterations; k++) {\n var p = getLoading(eMatrix, t);\n t = eMatrix.mmul(p);\n tOld = tNew;\n tNew = t.dot(t);\n //console.log(t.dot(t), tNew,tOld)\n \n }\n eigenvalues[i] = tNew;\n T.setColumn(i, t);\n P.setColumn(i, p);\n eMatrix.sub(t.mmul(p.transpose()));\n }\n return {T, P};\n}\n\nfunction getLoading(e, t) {\n var m = e.columns;\n var n = e.rows;\n\n var result = new Matrix(m, 1);\n\n var Bcolj = new Array(n);\n for (var i = 0; i < m; i++) {\n var s = 0;\n for (let k = 0; k < n; k++) {\n s += e.get(k, i) * t[k][0];\n }\n result.set(i, 0, s);\n }\n return result.mul(1 / result.norm());\n}\n\nfunction maxSumColIndex(data) {\n return data.sum('column').maxIndex()[0];\n}\n\nfunction _adjust(dataset, options) {\n dataset = new Matrix(dataset);\n if (options.center) {\n const means = mean(dataset);\n const stdevs = stdev(dataset, means, true);\n // this.means = means;\n dataset.subRowVector(means);\n if (options.scale) {\n for (var i = 0; i < stdevs.length; i++) {\n if (stdevs[i] === 0) {\n throw new RangeError('Cannot scale the dataset (standard deviation is zero at index ' + i);\n }\n }\n // this.stdevs = stdevs;\n dataset.divRowVector(stdevs);\n }\n }\n return dataset;\n};\n\nfunction predictEllipse(x, y, n, alpha, nbPoints) {\n let variance = [computeVariance(x), computeVariance(y)];\n let means = [0,0];\n let elp = ellipse([0,0], variance, nbPoints)\n let c = 2 * (n-1)/n * (n+1)/(n-2);\n let F = Math.sqrt(c * 4.7374);\n elp = elp.map((point) => {\n return point.map((p, i) => F * p + means[i])\n })\n return elp;\n}\n\nfunction ellipse(center, std, nbPoints) {\n let vector = new Array(nbPoints);\n let jump = 2 * Math.PI / (nbPoints - 1);\n let t = 0;\n for (let i = 0; i < nbPoints; i++) {\n vector[i] = [center[0] + Math.sqrt(std[0]) * Math.cos(t), center[1] + Math.sqrt(std[1]) * Math.sin(t)];\n t += jump;\n }\n return vector;\n}\n\nfunction transpose(matrix) {\n return matrix[0].map((col, i) => matrix.map(row => row[i]));\n}\n" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{ | |
"lib": "ML", | |
"alias": "ML" | |
}, | |
{ | |
"lib": "src/util/ui", | |
"alias": "UI" | |
}, | |
{ | |
"lib": "jszip", | |
"alias": "JSZip" | |
}, | |
{ | |
"lib": "components/papa-parse/papaparse.min", | |
"alias": "Papa" | |
}, | |
{ | |
"lib": "SD", | |
"alias": "SD" | |
}, | |
{ | |
"lib": "chroma", | |
"alias": "chroma" | |
} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
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"height": 20 | |
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255, | |
255, | |
255, | |
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"name": "Default layer" | |
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"left": 0, | |
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}, | |
"size": { | |
"width": 60, | |
"height": 14 | |
}, | |
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"display": true, | |
"title": "compute pca", | |
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"height": 20 | |
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{} | |
], | |
"actions_in": [ | |
{ | |
"rel": "execute", | |
"name": "PCA" | |
}, | |
{ | |
"rel": "execute", | |
"name": "plotResult" | |
} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
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} | |
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"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
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100, | |
100, | |
100, | |
1 | |
] | |
} | |
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], | |
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{ | |
"toolbar": [ | |
[ | |
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"Show fullscreen" | |
] | |
] | |
} | |
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}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "compute pca", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"PCA" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
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0, | |
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0, | |
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"startState": [ | |
"off" | |
], | |
"text": [ | |
null | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 74, | |
"top": 20 | |
}, | |
"size": { | |
"width": 8, | |
"height": 7 | |
}, | |
"zIndex": 0, | |
"display": true, | |
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255, | |
255, | |
255, | |
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"wrapper": false, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 61, | |
"top": 25 | |
}, | |
"size": { | |
"width": 17, | |
"height": 7 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
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255, | |
255, | |
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"wrapper": true, | |
"created": true, | |
"name": "admin" | |
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"rel": "output", | |
"jpath": [], | |
"name": "help" | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[] | |
], | |
"script": [ | |
"let html = API.getData('html');\nlet helpText = API.getData('helpText');\n\nif(helpText == null) {\n html = `\n <h2>TEAMMATE - A simple urinary metabolite reference database and toolbox\n for analysing urine composition based on 1H NMR spectral \n profiles</h2><br>\n Authors: Torben Kimhofer<sup>1</sup>, Alejandro Bolaños<sup>2</sup>,\n Luc Patiny<sup>3</sup>, Julien Wist<sup>2</sup>, Elaine Holmes<sup>1</sup>\n <br><br><sup>1</sup>Division of Computational and Systems Medicine, Imperial College, London, UK.\n <br><sup>2</sup>Chemistry Department, Universidad del Valle, Cali, Valle, Colombia.\n <br><sup>3</sup>Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.\n `\n}\n\nUI.dialog(String(html), {'width': '600px'});\nconsole.log(\"display html help: executed\")" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{ | |
"lib": "src/util/ui", | |
"alias": "UI" | |
} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [ | |
"disable" | |
] | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 24, | |
"top": 27 | |
}, | |
"size": { | |
"width": 54, | |
"height": 44 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "display html help", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 24, | |
"top": 62 | |
}, | |
"size": { | |
"width": 54, | |
"height": 14 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 29, | |
"vars_in": [ | |
{ | |
"rel": "inputValue", | |
"name": "html" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Show fullscreen" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "display html help", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/dragdrop/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"label": [ | |
"Drop your file here" | |
], | |
"dragoverlabel": [ | |
null | |
], | |
"hoverlabel": [ | |
"Drag'n drop or paste here" | |
], | |
"fileSelectLabel": [ | |
"Select file" | |
], | |
"labelFontSize": [ | |
26 | |
], | |
"checkOptions": [ | |
[ | |
"promptAmbiguous" | |
] | |
], | |
"inputOptions": [ | |
[ | |
"allowDrop", | |
"allowPaste", | |
"allowFileInput" | |
] | |
] | |
} | |
], | |
"vars": [ | |
[ | |
{ | |
"filter": "ext", | |
"extension": "zip", | |
"filetype": "buffer", | |
"type": "", | |
"variable": "file" | |
}, | |
{ | |
"filter": "ext", | |
"extension": "xlsx", | |
"filetype": "buffer", | |
"type": "", | |
"variable": "xlsxFile" | |
}, | |
{ | |
"filter": "ext", | |
"extension": "csv", | |
"filetype": "text", | |
"type": "", | |
"variable": "csvFile" | |
} | |
] | |
], | |
"string_general": [ | |
{ | |
"askFilename": [ | |
[] | |
] | |
} | |
], | |
"string": [ | |
[ | |
{ | |
"filter": "ext", | |
"extension": "*", | |
"type": "", | |
"variable": "str" | |
} | |
] | |
], | |
"photo": [ | |
[ | |
{ | |
"variable": "photo" | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 92, | |
"top": 36 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 123, | |
"top": 23 | |
}, | |
"size": { | |
"width": 24, | |
"height": 23 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 58, | |
"top": 18 | |
}, | |
"size": { | |
"width": 24, | |
"height": 23 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Upload your data", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 30, | |
"vars_out": [ | |
{ | |
"event": "onRead", | |
"rel": "data", | |
"jpath": [], | |
"name": "droppedData" | |
} | |
], | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Upload your data", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
"\nlet actionName, actionValue;\nlet data = [];\nlet customMethod;\n\nswitch(this.variable) {\n case 'droppedData':\n actionName = 'droppedData';\n actionValue = API.getData(actionName).resurrect();\n break\n default:\n actionName = this.action.name;\n actionValue = this.action.value;\n}\n\nswitch(actionName) {\n case 'droppedData':\n \n //var zipFile = actionValue;\n //var jsZip = new JSZip();\n //let zip = await jsZip.loadAsync(actionValue.content);\n //let res = await zip.files['rangesExplorer.data.json'].async('string');\n \n //API.createData('res', JSON.parse(res));\n //console.log('zip executed');\n \n switch (String(Object.keys(actionValue))) {\n case 'parseXlsx':\n var metadata = [];\n xlsxParser.fromDataAsync(actionValue.content).then((result) => {\n var sheets = result.sheets();\n var template = {}, temp = {};\n for (let sheet of sheets) {\n let name = sheet.name().toLowerCase().replace(/\\s/g, '');\n template[name] = {};\n temp[name] = sheet;\n let currentSheet = template[name];\n let minCol = sheet.row(1).minUsedColumnNumber();\n let maxCol = sheet.row(1).maxUsedColumnNumber() + 1;\n let headers = sheet.row(1)._cells.map((cell) => cell._value.replace(/\\s/g, ''));\n for (let i = minCol; i < maxCol; i++) {\n currentSheet[headers[i]] = null;\n }\n }\n temp.main.forEachExistingRow((_, i) => {\n metadata[i] = JSON.parse(JSON.stringify(template));\n for (let key in template) {\n let sheet = temp[key];\n let currentMetadata = metadata[i];\n let currentSheet = currentMetadata[key];\n let column = 1;\n if (sheet.row(i)._cells.length === 0) return;\n for (let header in currentSheet) {\n currentSheet[header] = sheet.row(i)._cells[column++]._value;\n }\n }\n })\n metadata = metadata.slice(2);\n var metadataList = {};\n metadata.forEach((m, i, array) => {\n let highlight = Math.random();\n let key = m.main.SampleID.replace(/\\./g, '_').toLowerCase();\n m._highlight = highlight;\n metadataList[key] = {\n index: i,\n _highlight: highlight\n }\n return;\n });\n \n API.createData('metadataList', metadataList);\n API.createData('metadata', metadata);\n });\n break;\n \n case 'csvFile':\n customMethod = Papa.parse(actionValue.csvFile.content, {\n header: true,\n delimiter: \",\"\n });\n \n //API.createData('customMethod', data);\n extractCSV(customMethod);\n break;\n }\n \n case 'download':\n var string = \",Creatinine,Creatine,Glucose,Alanine,Lactate,Acetate,Succinate,Citrate,Dimethylamine,Trimethylamine\\nAirwave_1_10_1Custom,10.77096162,0.149213248,0.219200053,,,0.114529688,0.107564026,2.809720562,0.290457802,0.001393114\\nAirwave_1_100_1Custom,2.316093057,0.01303475,0.054474036,,,0.031174903,0.039852373,1.039391475,0.073301503,0.001408082\\nAirwave_6_30_1Custom,13.30611001,0.191876443,0.231654052,,,0.060562254,0.052609127,1.318416998,0.441306889,0.008132261\\nAirwave_38_90_1Custom,11.85137551,0.13781424,0.208870282,,,0.05917576,0.033497749,3.370650175,0.257927047,0.001422446\";\n var toDownload = new Blob([string], {type: 'text/plain'});\n fileSaver(toDownload, 'ExampleFile.csv');\n break;\n \n case 'downloadTemplate':\n var string = \",Creatinine,Creatine,Glucose,Alanine,Lactate,Acetate,Succinate,Citrate,Dimethylamine,Trimethylamine,Betaine,Glycine,Formate,Methylnicotinamide,Dimethylglycine,Taurine,Hippurate,Hydroxybutyric_acid,Valine,Methylhistidine,Sarcosine,Trigonelline,Tartrate,Guanidinoacetate,Ethanol,Paracetamol,Paracetamol_glucuronide,X1_Hydroxyisovalerate,X3_Hydroxyisovalerate,Isoleucine,Leucine,X4_Hydroxyphenylacetate,Glutamine,Glycolate,X3_Aminoisobutyrate,Tyrosine,Pantothenic_acid,X4_Hydroxyhippuric_acid\\nAirwave_1_10_1,10.77096162,0.149213248,0.219200053,0.46928622,0.151093488,0.114529688,0.107564026,2.809720562,0.290457802,0.001393114,0.157630721,0.85743617,0.117838248,0.08022949,0.050912889,1.631998796,0.801086358,0,0.054591478,0,0,0.12843978,0.056903813,0.561631098,0,0,0,0.001524958,0.08380798,0.012319695,0.054196726,0.079207377,0,0.62164627,0.166112223,0,0.096905673,0\";\n var toDownload = new Blob([string], {type: 'text/plain'});\n fileSaver(toDownload, 'TemplateFile.csv');\n break;\n \n}\n\nconsole.log('parse csv executed with action: ' + actionName);\n\n\nfunction extractCSV(customMethod) {\n //var customMethod = API.getData('customMethod').resurrect();\n var customDescriptors = getDescriptors(customMethod);\n console.log(customDescriptors)\n var customData = cleanData(customMethod);\n console.log(customData)\n var customName = customData.map(d => d.sampleid);\n console.log(customName)\n let custom = ({customName: customName, customData: customData});\n API.createData('customData', custom);\n \n let data = API.getData('selectedData');\n let metadata = API.getData('selectedMetadata');\n \n //let customData = API.getData('customData').customData;\n //let customName = API.getData('customData').customName;\n \n customData.map((x, i) => data.push(completeCustomData(data, x, customName[i])));\n API.createData('selectedData', data);\n console.log(data.length);\n \n customData.map((x, i) => metadata.push(completeCustomMetadata(metadata, customName[i])));\n API.createData('selectedMetadata', metadata);\n console.log(metadata.length);\n \n API.switchToLayer(\"Default layer\");\n\n}\n\nfunction getDescriptors(input) {\n let result = [];\n for (let i of input.meta.fields) {\n if (i === '') continue;\n let name = i.replace(/\\./g, '_').toLowerCase();\n result.push({\n name,\n jpath: 'element.' + name,\n });\n }\n return result;\n}\n\nfunction cleanData(input, factor = 1) {\n var data = JSON.parse(JSON.stringify(input.data));\n if (input.errors.length > 0) {\n let errors = input.errors.filter((a) => a.row !== undefined);\n errors.sort((a, b) => a.row + b.row).forEach((e) => {\n data.splice(e.row, 1);\n });\n }\n \n return data.map((e, index) => {\n let result = {}\n let keys = Object.keys(e);\n for (let i = 1; i < keys.length; i++) {\n let name = keys[i].replace(/\\./g, '_').toLowerCase();\n result[name] = Number(e[keys[i]]) * factor;\n };\n result['sampleid'] = e[''].replace(/\\./g, '_').toLowerCase();;\n return result;\n })\n}\n\nfunction clone(input) {\n return JSON.parse(JSON.stringify(input));\n}\n\nfunction completeCustomData(data, custom, customName) {\n let result = {};\n let labels = Object.keys(data[0]);\n let customKeys = Object.keys(custom).map(x => x.toLowerCase());\n let labelsLC = labels.map(x => x.toLowerCase());\n labelsLC.map((x, i) => (customKeys.indexOf(x) != -1) ? result[labels[i]] = custom[x] : result[labels[i]] = 0);\n result[\"_highlight\"] = data.length + 1;\n result[\"_row\"] = customName;\n return result;\n}\n\nfunction completeCustomMetadata(metadata, customName) {\n let result = {};\n let labels = Object.keys(metadata[0]);\n labels.map((x, i) => result[labels[i]] = null);\n result[\"SampleID\"] = customName;\n result[\"_highlight\"] = metadata.length + 1;\n result[\"_row\"] = customName;\n return result;\n}\n\nfunction clone(input) {\n return JSON.parse(JSON.stringify(input));\n}\n\n" | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{ | |
"lib": "jszip", | |
"alias": "JSZip" | |
}, | |
{ | |
"lib": "xlsxParser", | |
"alias": "xlsxParser" | |
}, | |
{ | |
"lib": "Papa-parser", | |
"alias": "Papa" | |
}, | |
{ | |
"lib": "file-saver", | |
"alias": "fileSaver" | |
} | |
] | |
], | |
"buttons": [ | |
[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 130 | |
}, | |
"size": { | |
"width": 60, | |
"height": 16 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Download / upload executor", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 79, | |
"top": 47 | |
}, | |
"size": { | |
"width": 68, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 79, | |
"top": 26 | |
}, | |
"size": { | |
"width": 68, | |
"height": 22 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "Download / upload executor", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 31, | |
"vars_in": [ | |
{ | |
"rel": "inputValue", | |
"name": "droppedData" | |
} | |
], | |
"actions_in": [ | |
{ | |
"rel": "execute", | |
"name": "download" | |
}, | |
{ | |
"rel": "execute", | |
"name": "extractCSV" | |
}, | |
{ | |
"rel": "execute", | |
"name": "downloadTemplate" | |
} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences", | |
"Show fullscreen" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Download / upload executor", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Download example file" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"download" | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 124, | |
"top": 5 | |
}, | |
"size": { | |
"width": 20, | |
"height": 15 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 15, | |
"top": 18 | |
}, | |
"size": { | |
"width": 20, | |
"height": 7 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Download example file", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "help" | |
} | |
}, | |
"id": 32, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "download" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Download example file", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/rich_text/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"editable": [ | |
[ | |
"isEditable" | |
] | |
], | |
"debouncing": [ | |
0 | |
], | |
"modifyInVariable": [ | |
[] | |
], | |
"storeInView": [ | |
[ | |
"yes" | |
] | |
], | |
"autoHeight": [ | |
[] | |
], | |
"bgColor": [ | |
[ | |
255, | |
255, | |
255, | |
1 | |
] | |
], | |
"postit": [ | |
[] | |
], | |
"html": [ | |
[ | |
"yes" | |
] | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 109, | |
"top": 47 | |
}, | |
"size": { | |
"width": 25, | |
"height": 37 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Upload" | |
} | |
}, | |
"id": 33, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"richtext": "<p><span style=\"font-size:104px\"> 3</span></p>\n\n<p><span style=\"font-size:12px\">It may take a while to read and extract your data. If successful you will be redirected to the main panel of this application that is "Browser".</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">You can use the following button to navigate into the application.</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">Browser allows to browse the data and is the default or landing layer.</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">Spectra allows you to select samples and see the original spectra.</span></p>\n\n<p> </p>\n\n<p><span style=\"font-size:12px\">Upload allows you to upload your custom data.</span></p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/rich_text/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"editable": [ | |
[ | |
"isEditable" | |
] | |
], | |
"debouncing": [ | |
0 | |
], | |
"modifyInVariable": [ | |
[] | |
], | |
"storeInView": [ | |
[ | |
"yes" | |
] | |
], | |
"autoHeight": [ | |
[] | |
], | |
"bgColor": [ | |
[ | |
255, | |
255, | |
255, | |
1 | |
] | |
], | |
"postit": [ | |
[] | |
], | |
"html": [ | |
[ | |
"yes" | |
] | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 9, | |
"top": 48 | |
}, | |
"size": { | |
"width": 26, | |
"height": 27 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Upload" | |
} | |
}, | |
"id": 34, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"richtext": "<p><span style=\"font-size:104px\"> 1</span></p>\n\n<p><span style=\"font-size:12px\">First, download the example file (CSV format). Open it with MS Excel or LibreOffice and add the values corresponding to the metabolites. Add as many rows as necessary but, please, do not alter the column names. Columns can be deleted if unnecessary, except the first one that should contain a unique identifier for each sample.</span></p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/edition/rich_text/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"editable": [ | |
[ | |
"isEditable" | |
] | |
], | |
"debouncing": [ | |
0 | |
], | |
"modifyInVariable": [ | |
[] | |
], | |
"storeInView": [ | |
[ | |
"yes" | |
] | |
], | |
"autoHeight": [ | |
[] | |
], | |
"bgColor": [ | |
[ | |
255, | |
255, | |
255, | |
1 | |
] | |
], | |
"postit": [ | |
[] | |
], | |
"html": [ | |
[ | |
"yes" | |
] | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 57, | |
"top": 48 | |
}, | |
"size": { | |
"width": 26, | |
"height": 27 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "Upload" | |
} | |
}, | |
"id": 35, | |
"vars_in": [ | |
{} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"actions_out": [ | |
{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
1 | |
] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"richtext": "<p><span style=\"font-size:104px\"> 2</span></p>\n\n<p><span style=\"font-size:12px\">Once done, save the file in CSV format and drop it into the area for that purpose. You can also click in the area to display the file selector tool of your OS.</span></p>\n", | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Download template file" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"downloadTemplate" | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "admin" | |
}, | |
"spectra": { | |
"position": { | |
"left": 0, | |
"top": 0 | |
}, | |
"size": { | |
"width": 20, | |
"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": true, | |
"created": true, | |
"name": "spectra" | |
}, | |
"help": { | |
"position": { | |
"left": 124, | |
"top": 5 | |
}, | |
"size": { | |
"width": 20, | |
"height": 15 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
0 | |
], | |
"wrapper": false, | |
"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
"left": 15, | |
"top": 27 | |
}, | |
"size": { | |
"width": 20, | |
"height": 7 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Download example file", | |
"bgColor": [ | |
255, | |
255, | |
255, | |
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{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "downloadTemplate" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
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[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
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100, | |
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100, | |
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} | |
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], | |
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{ | |
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[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Download example file", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/code_executor/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"display": [ | |
[ | |
"editor", | |
"buttons" | |
] | |
], | |
"execOnLoad": [ | |
[] | |
], | |
"asyncAwait": [ | |
[ | |
"top" | |
] | |
], | |
"script": [ | |
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] | |
} | |
], | |
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[ | |
{} | |
] | |
], | |
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[ | |
{ | |
"name": "button1", | |
"label": "Execute", | |
"hide": [], | |
"disable": [] | |
} | |
] | |
] | |
} | |
}, | |
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"Default layer": { | |
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"top": 0 | |
}, | |
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"height": 20 | |
}, | |
"zIndex": 0, | |
"display": false, | |
"title": "", | |
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255, | |
255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
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"position": { | |
"left": 65, | |
"top": 101 | |
}, | |
"size": { | |
"width": 54, | |
"height": 26 | |
}, | |
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], | |
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"created": true, | |
"name": "admin" | |
}, | |
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}, | |
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}, | |
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"width": 20, | |
"height": 20 | |
}, | |
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255, | |
255, | |
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}, | |
"Upload": { | |
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"top": 0 | |
}, | |
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}, | |
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{} | |
], | |
"actions_in": [ | |
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], | |
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{ | |
"jpath": [] | |
} | |
], | |
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"custom": [ | |
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"title": "", | |
"icon": "", | |
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} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
"Open Preferences" | |
] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 0 | |
}, | |
{ | |
"url": "modules/types/client_interaction/button_action/", | |
"configuration": { | |
"sections": {}, | |
"groups": { | |
"group": [ | |
{ | |
"toggle": [ | |
"click" | |
], | |
"label": [ | |
"Reset Selection" | |
], | |
"onLabel": [ | |
"Toggle action off" | |
], | |
"offLabel": [ | |
"Toggle action on" | |
], | |
"title": [ | |
"" | |
], | |
"onColor": [ | |
[ | |
0, | |
0, | |
0, | |
1 | |
] | |
], | |
"offColor": [ | |
[ | |
0, | |
0, | |
0, | |
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] | |
], | |
"startState": [ | |
"off" | |
], | |
"text": [ | |
"reset" | |
], | |
"askConfirm": [ | |
[] | |
], | |
"confirmText": [ | |
"Are you sure?" | |
], | |
"okLabel": [ | |
"Ok" | |
], | |
"cancelLabel": [ | |
"Cancel" | |
], | |
"content": [ | |
"" | |
], | |
"contentType": [ | |
"content" | |
], | |
"maskOpacity": [ | |
0.6 | |
] | |
} | |
] | |
} | |
}, | |
"layers": { | |
"Default layer": { | |
"position": { | |
"left": 131, | |
"top": 49 | |
}, | |
"size": { | |
"width": 12, | |
"height": 6 | |
}, | |
"zIndex": 0, | |
"display": true, | |
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255, | |
255, | |
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], | |
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"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
"left": 30, | |
"top": 86 | |
}, | |
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"height": 7 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "", | |
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], | |
"wrapper": true, | |
"created": true, | |
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"name": "spectra" | |
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"created": true, | |
"name": "help" | |
}, | |
"Upload": { | |
"position": { | |
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}, | |
"size": { | |
"width": 20, | |
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}, | |
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"bgColor": [ | |
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255, | |
255, | |
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], | |
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"created": true, | |
"name": "Upload" | |
} | |
}, | |
"id": 38, | |
"vars_in": [], | |
"actions_in": [ | |
{} | |
], | |
"actions_out": [ | |
{ | |
"event": "onClick", | |
"rel": "actionText", | |
"jpath": [], | |
"name": "resetSelectionButton" | |
} | |
], | |
"vars_out": [], | |
"toolbar": { | |
"custom": [ | |
[ | |
{ | |
"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
"color": [ | |
100, | |
100, | |
100, | |
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] | |
} | |
] | |
], | |
"common": [ | |
{ | |
"toolbar": [ | |
[ | |
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] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "", | |
"zindex": 35 | |
}, | |
{ | |
"url": "modules/types/science/spectra/spectra_displayer/", | |
"configuration": { | |
"sections": { | |
"graph": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"graph": [ | |
{ | |
"url": [ | |
"" | |
], | |
"zoom": [ | |
"xy" | |
], | |
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"none" | |
], | |
"wheelbaseline": [ | |
0 | |
], | |
"fullOut": [ | |
"both" | |
], | |
"legend": [ | |
null | |
], | |
"legendOptions": [ | |
[ | |
"isSerieHideable", | |
"isSerieSelectable" | |
] | |
], | |
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[] | |
], | |
"selectScatter": [ | |
[ | |
"yes" | |
] | |
], | |
"independantYZoom": [ | |
[] | |
] | |
} | |
] | |
} | |
} | |
], | |
"axis": [ | |
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{ | |
"checkboxes": [ | |
[ | |
"display" | |
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], | |
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"" | |
], | |
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"axismodification": [ | |
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} | |
], | |
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{ | |
"checkboxes": [ | |
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"" | |
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{ | |
"sections": {}, | |
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[ | |
{ | |
"variable": "pcaResult", | |
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], | |
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"peakpicking": [], | |
"markers": [ | |
"markers" | |
], | |
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"markerSize": 2, | |
"normalize": "none", | |
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"tracking": [] | |
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{ | |
"sections": {}, | |
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{ | |
"highlightOptions": [ | |
"{}" | |
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} | |
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] | |
}, | |
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"position": { | |
"left": 83, | |
"top": 23 | |
}, | |
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"height": 27 | |
}, | |
"zIndex": 0, | |
"display": true, | |
"title": "Loadings", | |
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255, | |
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], | |
"wrapper": true, | |
"created": true, | |
"name": "Default layer" | |
}, | |
"admin": { | |
"position": { | |
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}, | |
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}, | |
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}, | |
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}, | |
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"title": "Loadings", | |
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"created": true, | |
"name": "Default layer" | |
}, | |
"Upload": { | |
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}, | |
"size": { | |
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"height": 27 | |
}, | |
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"name": "Default layer" | |
} | |
}, | |
"id": 39, | |
"vars_in": [ | |
{ | |
"rel": "chart", | |
"name": "pcaResultLoadings" | |
} | |
], | |
"actions_in": [ | |
{} | |
], | |
"vars_out": [ | |
{ | |
"event": "onSelectScatter", | |
"rel": "selectedData", | |
"jpath": [], | |
"name": "selectedMarkers" | |
} | |
], | |
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{ | |
"jpath": [] | |
} | |
], | |
"toolbar": { | |
"custom": [ | |
[ | |
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"title": "", | |
"icon": "", | |
"action": "", | |
"position": "begin", | |
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100, | |
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100, | |
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} | |
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], | |
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{ | |
"toolbar": [ | |
[ | |
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] | |
] | |
} | |
] | |
}, | |
"css": [ | |
{ | |
"fontSize": [ | |
"" | |
], | |
"fontFamily": [ | |
"" | |
] | |
} | |
], | |
"title": "Loadings", | |
"zindex": 0 | |
} | |
], | |
"variables": [ | |
{ | |
"varname": "data", | |
"jpath": [ | |
"data" | |
] | |
}, | |
{ | |
"varname": "spec", | |
"jpath": [ | |
"spec" | |
] | |
} | |
], | |
"aliases": [ | |
{ | |
"path": "https://www.lactame.com/lib/spectra-data/3.2.4/spectra-data.min", | |
"alias": "SD" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/nmr-predictor/1.0.8/nmr-predictor.min", | |
"alias": "Predictor" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/openchemlib/4.6.2/openchemlib-full", | |
"alias": "OCL" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/ml/HEAD/ml", | |
"alias": "ML" | |
}, | |
{ | |
"path": "https://www.lactame.com/github/cheminfo-js/visualizer-helper/3ffac8f5646dd4231c1cb33cebae970e5ee0d503/", | |
"alias": "vh" | |
}, | |
{ | |
"path": "https://www.lactame.com/lib/image-js/0.9.5/image.min", | |
"alias": "IJS" | |
}, | |
{ | |
"path": "components/papa-parse/papaparse.min", | |
"alias": "Papa-parser" | |
}, | |
{ | |
"path": "https://dl.dropboxusercontent.com/s/ky06573iww07wnd/jerzy.js?dl=0", | |
"alias": "jerzy" | |
}, | |
{ | |
"path": "https://dl.dropboxusercontent.com/s/7npg0288cesrmhu/timsort.js?dl=0", | |
"alias": "timsort" | |
}, | |
{ | |
"path": "https://dl.dropboxusercontent.com/s/100bq1kwk27yvyj/xlsx-populate.js?dl=0", | |
"alias": "xlsxParser" | |
} | |
], | |
"configuration": { | |
"title": "ranges explorer 0.5.0" | |
}, | |
"actionscripts": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"action": [ | |
{ | |
"name": [ | |
null | |
], | |
"script": [ | |
null | |
] | |
} | |
] | |
} | |
} | |
], | |
"init_script": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"general": [ | |
{ | |
"script": [ | |
"\nAPI.loading('load','Please wait while we compute basic statistics for the chosen data');\n\n// you need to leave some time to display the message\n// we use setImmediate to achieve this\n\nsetImmediate(loadData);\n\nasync function loadData() {\n \n setTimeout(selectDataSets, 100);\n setTimeout(selectData, 10000);\n API.stopLoading('load');\n}\n\nAPI.createData('pcaPlot', {'pcx': 1, 'pcy': 2, 'numberOfEigenVectors': 3})\n\nfunction selectDataSets() {\n let data = API.getData('data');\n API.createData('selectedMetadata', data[0].metadata);\n API.createData('selectedDataSets', data[0].data);\n}\n\nfunction selectData() {\n let data = API.getData('selectedDataSets');\n API.createData('selectedData', data[0].data);\n}\n\n\n\n\n\n" | |
] | |
} | |
] | |
} | |
} | |
], | |
"custom_filters": [ | |
{ | |
"sections": { | |
"modules": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"modules": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
], | |
"filtersLib": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"filters": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
], | |
"filters": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"filter": [ | |
{ | |
"name": [ | |
null | |
], | |
"script": [ | |
null | |
] | |
} | |
], | |
"libs": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
] | |
}, | |
"groups": {} | |
} | |
], | |
"actionfiles": [ | |
{ | |
"sections": {}, | |
"groups": { | |
"action": [ | |
[ | |
{} | |
] | |
] | |
} | |
} | |
] | |
} |
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