From d03fc330cd91d376045d0dd028955619d914dc7e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 7 Apr 2018 10:22:33 +0000
Subject: Dear @zsloan,
This patch removes TableTools. I don't think we use it. I have compared the look and feel
of below pages and I see no difference. If that is correct we can simply ditch it by
merging this PR. Note that if we are using such functionality this package is considered
obsolete by the authors.
According to https://datatables.net/extensions/tabletools/:
This extension has now been retired and has been replaced by the
Buttons and Select extensions. The documentation is retained for
legacy reference only. New projects should use Buttons and Select in
preference to TableTools. Moving Tabletools CSS
--- a/wqflask/wqflask/static/packages/TableTools/media/css/TableTools.css
+++ b/wqflask/wqflask/static/packages/TableTools/media/css/TableTools.css
@@ -319,3 +319,8 @@ div.DTTT_collection a.DTTT_button {
line-height: 20px;
}
+.no-sort::after { display: none!important; }
+.no-sort { pointer-events: none!important;
+ cursor: default!important;
+}
+
wqflask/wqflask/templates/correlation_matrix.html:
wqflask/wqflask/templates/collections/list.html:
wqflask/wqflask/templates/search_error.html:
wqflask/wqflask/templates/corr_scatterplot.html:
wqflask/wqflask/templates/pair_scan_results.html:
---
MANIFEST.in | 9 -
.../static/packages/TableTools/alt_init.html | 520 ----
.../static/packages/TableTools/alter_buttons.html | 505 ----
.../static/packages/TableTools/bootstrap.html | 551 -----
.../static/packages/TableTools/button_text.html | 531 -----
.../static/packages/TableTools/collection.html | 522 -----
.../static/packages/TableTools/defaults.html | 503 ----
.../wqflask/static/packages/TableTools/index.html | 499 ----
.../packages/TableTools/media/as3/ZeroClipboard.as | 221 --
.../TableTools/media/as3/ZeroClipboardPdf.as | 310 ---
.../packages/TableTools/media/as3/lib/AlivePDF.swc | Bin 131230 -> 0 bytes
.../packages/TableTools/media/css/TableTools.css | 326 ---
.../TableTools/media/css/TableTools_JUI.css | 185 --
.../TableTools/media/images/background.png | Bin 944 -> 0 bytes
.../TableTools/media/images/collection.png | Bin 1166 -> 0 bytes
.../TableTools/media/images/collection_hover.png | Bin 1194 -> 0 bytes
.../packages/TableTools/media/images/copy.png | Bin 2184 -> 0 bytes
.../TableTools/media/images/copy_hover.png | Bin 2797 -> 0 bytes
.../packages/TableTools/media/images/csv.png | Bin 1607 -> 0 bytes
.../packages/TableTools/media/images/csv_hover.png | Bin 1854 -> 0 bytes
.../packages/TableTools/media/images/pdf.png | Bin 4325 -> 0 bytes
.../packages/TableTools/media/images/pdf_hover.png | Bin 2786 -> 0 bytes
.../packages/TableTools/media/images/print.png | Bin 2123 -> 0 bytes
.../TableTools/media/images/print_hover.png | Bin 2230 -> 0 bytes
.../TableTools/media/images/psd/collection.psd | Bin 25792 -> 0 bytes
.../TableTools/media/images/psd/copy document.psd | Bin 104729 -> 0 bytes
.../TableTools/media/images/psd/file_types.psd | Bin 1090645 -> 0 bytes
.../TableTools/media/images/psd/printer.psd | Bin 119952 -> 0 bytes
.../packages/TableTools/media/images/xls.png | Bin 1641 -> 0 bytes
.../packages/TableTools/media/images/xls_hover.png | Bin 2061 -> 0 bytes
.../packages/TableTools/media/js/TableTools.js | 2476 --------------------
.../packages/TableTools/media/js/TableTools.min.js | 77 -
.../TableTools/media/js/TableTools.min.js.gz | Bin 8785 -> 0 bytes
.../packages/TableTools/media/js/ZeroClipboard.js | 367 ---
.../packages/TableTools/media/swf/copy_csv_xls.swf | Bin 2165 -> 0 bytes
.../TableTools/media/swf/copy_csv_xls_pdf.swf | Bin 58824 -> 0 bytes
.../static/packages/TableTools/multi_instance.html | 499 ----
.../packages/TableTools/multiple_tables.html | 296 ---
.../static/packages/TableTools/pdf_message.html | 524 -----
.../static/packages/TableTools/plug-in.html | 539 -----
.../static/packages/TableTools/select_multi.html | 507 ----
.../static/packages/TableTools/select_single.html | 505 ----
.../static/packages/TableTools/swf_path.html | 505 ----
.../wqflask/static/packages/TableTools/tabs.html | 348 ---
.../wqflask/static/packages/TableTools/theme.html | 524 -----
wqflask/wqflask/templates/search_error.html | 2 -
46 files changed, 11851 deletions(-)
delete mode 100644 wqflask/wqflask/static/packages/TableTools/alt_init.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/alter_buttons.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/bootstrap.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/button_text.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/collection.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/defaults.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/index.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/as3/ZeroClipboard.as
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/as3/ZeroClipboardPdf.as
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/as3/lib/AlivePDF.swc
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/css/TableTools.css
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/css/TableTools_JUI.css
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/background.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/collection.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/collection_hover.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/copy.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/copy_hover.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/csv.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/csv_hover.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/pdf.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/pdf_hover.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/print.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/print_hover.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/psd/collection.psd
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/psd/copy document.psd
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/psd/file_types.psd
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/psd/printer.psd
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/xls.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/images/xls_hover.png
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/js/TableTools.js
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/js/TableTools.min.js
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/js/TableTools.min.js.gz
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/js/ZeroClipboard.js
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls.swf
delete mode 100644 wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf
delete mode 100644 wqflask/wqflask/static/packages/TableTools/multi_instance.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/multiple_tables.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/pdf_message.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/plug-in.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/select_multi.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/select_single.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/swf_path.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/tabs.html
delete mode 100644 wqflask/wqflask/static/packages/TableTools/theme.html
diff --git a/MANIFEST.in b/MANIFEST.in
index 25beb977..0e0b4bd4 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -52,15 +52,6 @@ include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold
include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/6_delayed_rendering/*
include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/1_dom/*
include wqflask/wqflask/static/packages/*
-include wqflask/wqflask/static/packages/TableTools/*
-include wqflask/wqflask/static/packages/TableTools/media/*
-include wqflask/wqflask/static/packages/TableTools/media/images/*
-include wqflask/wqflask/static/packages/TableTools/media/images/psd/*
-include wqflask/wqflask/static/packages/TableTools/media/swf/*
-include wqflask/wqflask/static/packages/TableTools/media/js/*
-include wqflask/wqflask/static/packages/TableTools/media/css/*
-include wqflask/wqflask/static/packages/TableTools/media/as3/*
-include wqflask/wqflask/static/packages/TableTools/media/as3/lib/*
include wqflask/wqflask/static/packages/underscore/*
include wqflask/wqflask/static/packages/bootstrap/*
include wqflask/wqflask/static/packages/bootstrap/fonts/*
diff --git a/wqflask/wqflask/static/packages/TableTools/alt_init.html b/wqflask/wqflask/static/packages/TableTools/alt_init.html
deleted file mode 100644
index 73853150..00000000
--- a/wqflask/wqflask/static/packages/TableTools/alt_init.html
+++ /dev/null
@@ -1,520 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - initialisation with 'new TableTools()'
-
-
-
Preamble
-
Typically when working with TableTools, the initialisation and insertion into the DOM will be done automatically by DataTables, through the use of the sDom parameter. However, it is also possible to initialise TableTools manually as shown in the example below. Once initialised you can insert the TableTools tool bar node anywhere you wish into the DOM using the instance.dom.container parameter.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/alter_buttons.html b/wqflask/wqflask/static/packages/TableTools/alter_buttons.html
deleted file mode 100644
index 771b0b86..00000000
--- a/wqflask/wqflask/static/packages/TableTools/alter_buttons.html
+++ /dev/null
@@ -1,505 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - button arrangement
-
-
-
Preamble
-
TableTools makes it very simple to arrange the buttons in the toolbar as you see fit. Using the aButtons parameter you can use any of the predefined buttons or customised buttons. The example below shows how TableTools can be initialised to provide only the 'copy-to-clipboard' and 'print view' options (i.e. no save to local file option is available).
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/bootstrap.html b/wqflask/wqflask/static/packages/TableTools/bootstrap.html
deleted file mode 100644
index 664bde3d..00000000
--- a/wqflask/wqflask/static/packages/TableTools/bootstrap.html
+++ /dev/null
@@ -1,551 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
-
-
-
- TableTools with Twitter Bootstrap
-
-
-
Preamble
-
Twitter Bootstrap is a very powerful design framework for allowing you to very quickly create applications with a unified look and feel. DataTables integrates well with Bootstrap, and so does TableTools.
-
This example shows the default Bootstrap theme being used with a Bootstrap styled DataTable. sDom is supplied to the DataTable with a setup suitable for Bootstrap styling, and a TableTools collection is used to show how it can be used in this environment.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/button_text.html b/wqflask/wqflask/static/packages/TableTools/button_text.html
deleted file mode 100644
index 6828eb94..00000000
--- a/wqflask/wqflask/static/packages/TableTools/button_text.html
+++ /dev/null
@@ -1,531 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - customised button text
-
-
-
Preamble
-
You may wish to set your own text for the buttons in the TableTools toolbar, rather than relying on the default built-in text. This is done by overriding the sButtonText parameter of whatever button you wish to alter. The way TableTools allows you to alter a predefined button is by 'extending' it (using the sExtends parameter) and then setting the overriding parameter. A full list of the parameters which can be used is available on the DataTables.net web-site. This example shows how to set the button text as required.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/collection.html b/wqflask/wqflask/static/packages/TableTools/collection.html
deleted file mode 100644
index 4eb3141b..00000000
--- a/wqflask/wqflask/static/packages/TableTools/collection.html
+++ /dev/null
@@ -1,522 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - button collections
-
-
-
Preamble
-
TableTools provides the ability to group buttons into a hidden drop down list, which is activated by clicking on a top-level button. This is achieved by extending the 'collection' predefined button type and setting it's aButtons parameter with the same options as the top level buttons (note that you cannot currently use a collection within a collection).
-
The example below shows the file save buttons grouped into a collection, while the copy and print buttons are left on the top level.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/defaults.html b/wqflask/wqflask/static/packages/TableTools/defaults.html
deleted file mode 100644
index 5ef74a68..00000000
--- a/wqflask/wqflask/static/packages/TableTools/defaults.html
+++ /dev/null
@@ -1,503 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - changing the initialisation defaults
-
-
-
Preamble
-
TableTools provides the ability to override the default initialisation parameters that are used when creating a new instance. This this particularly useful if you have multiple tables which you want to have the same TableTools behaviour - rather than declaring the structure multiple times, you can just set the defaults once. This example shows how to alter the default buttons.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/index.html b/wqflask/wqflask/static/packages/TableTools/index.html
deleted file mode 100644
index 06a2442d..00000000
--- a/wqflask/wqflask/static/packages/TableTools/index.html
+++ /dev/null
@@ -1,499 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example
-
-
-
Preamble
-
This example shows the basic initialisation of TableTools by simply including the 'T' marker in DataTables' sDom parameter. This tell DataTables to insert the TableTools toolbar in that location. Remember to include the Javascript and CSS source files as well!
-
It is worth noting that you might need to set the sSwfPath parameter to tell TableTools where to find the SWF file for copy and file save.
Please use your browser's print function to print this table. Press escape when finished.",sMessage:null,bShowAll:!0,sToolTip:"View print view",sButtonClass:"DTTT_button_print",sButtonText:"Print",fnClick:function(a,b){this.fnPrint(!0,b)}}),text:e.extend({},TableTools.buttonBase),select:e.extend({},TableTools.buttonBase,{sButtonText:"Select button",fnSelect:function(a){0!==this.fnGetSelected().length?e(a).removeClass(this.classes.buttons.disabled):e(a).addClass(this.classes.buttons.disabled)},
-fnInit:function(a){e(a).addClass(this.classes.buttons.disabled)}}),select_single:e.extend({},TableTools.buttonBase,{sButtonText:"Select button",fnSelect:function(a){1==this.fnGetSelected().length?e(a).removeClass(this.classes.buttons.disabled):e(a).addClass(this.classes.buttons.disabled)},fnInit:function(a){e(a).addClass(this.classes.buttons.disabled)}}),select_all:e.extend({},TableTools.buttonBase,{sButtonText:"Select all",fnClick:function(){this.fnSelectAll()},fnSelect:function(a){this.fnGetSelected().length==
-this.s.dt.fnRecordsDisplay()?e(a).addClass(this.classes.buttons.disabled):e(a).removeClass(this.classes.buttons.disabled)}}),select_none:e.extend({},TableTools.buttonBase,{sButtonText:"Deselect all",fnClick:function(){this.fnSelectNone()},fnSelect:function(a){0!==this.fnGetSelected().length?e(a).removeClass(this.classes.buttons.disabled):e(a).addClass(this.classes.buttons.disabled)},fnInit:function(a){e(a).addClass(this.classes.buttons.disabled)}}),ajax:e.extend({},TableTools.buttonBase,{sAjaxUrl:"/xhr.php",
-sButtonText:"Ajax button",fnClick:function(a,b){var c=this.fnGetTableData(b);e.ajax({url:b.sAjaxUrl,data:[{name:"tableData",value:c}],success:b.fnAjaxComplete,dataType:"json",type:"POST",cache:!1,error:function(){alert("Error detected when sending table data to server")}})},fnAjaxComplete:function(){alert("Ajax complete")}}),div:e.extend({},TableTools.buttonBase,{sAction:"div",sTag:"div",sButtonClass:"DTTT_nonbutton",sButtonText:"Text button"}),collection:e.extend({},TableTools.buttonBase,{sAction:"collection",
-sButtonClass:"DTTT_button_collection",sButtonText:"Collection",fnClick:function(a,b){this._fnCollectionShow(a,b)}})};TableTools.classes={container:"DTTT_container",buttons:{normal:"DTTT_button",disabled:"DTTT_disabled"},collection:{container:"DTTT_collection",background:"DTTT_collection_background",buttons:{normal:"DTTT_button",disabled:"DTTT_disabled"}},select:{table:"DTTT_selectable",row:"DTTT_selected"},print:{body:"DTTT_Print",info:"DTTT_print_info",message:"DTTT_PrintMessage"}};TableTools.classes_themeroller=
-{container:"DTTT_container ui-buttonset ui-buttonset-multi",buttons:{normal:"DTTT_button ui-button ui-state-default"},collection:{container:"DTTT_collection ui-buttonset ui-buttonset-multi"}};TableTools.DEFAULTS={sSwfPath:"media/swf/copy_csv_xls_pdf.swf",sRowSelect:"none",sSelectedClass:null,fnPreRowSelect:null,fnRowSelected:null,fnRowDeselected:null,aButtons:["copy","csv","xls","pdf","print"],oTags:{container:"div",button:"a",liner:"span",collection:{container:"div",button:"a",liner:"span"}}};TableTools.prototype.CLASS=
-"TableTools";TableTools.VERSION="2.1.5";TableTools.prototype.VERSION=TableTools.VERSION;"function"==typeof e.fn.dataTable&&"function"==typeof e.fn.dataTableExt.fnVersionCheck&&e.fn.dataTableExt.fnVersionCheck("1.9.0")?e.fn.dataTableExt.aoFeatures.push({fnInit:function(a){a=new TableTools(a.oInstance,"undefined"!=typeof a.oInit.oTableTools?a.oInit.oTableTools:{});TableTools._aInstances.push(a);return a.dom.container},cFeature:"T",sFeature:"TableTools"}):alert("Warning: TableTools 2 requires DataTables 1.9.0 or newer - www.datatables.net/download");
-e.fn.DataTable.TableTools=TableTools})(jQuery,window,document);
diff --git a/wqflask/wqflask/static/packages/TableTools/media/js/TableTools.min.js.gz b/wqflask/wqflask/static/packages/TableTools/media/js/TableTools.min.js.gz
deleted file mode 100644
index 01ce7c04..00000000
Binary files a/wqflask/wqflask/static/packages/TableTools/media/js/TableTools.min.js.gz and /dev/null differ
diff --git a/wqflask/wqflask/static/packages/TableTools/media/js/ZeroClipboard.js b/wqflask/wqflask/static/packages/TableTools/media/js/ZeroClipboard.js
deleted file mode 100644
index ff87ecd8..00000000
--- a/wqflask/wqflask/static/packages/TableTools/media/js/ZeroClipboard.js
+++ /dev/null
@@ -1,367 +0,0 @@
-// Simple Set Clipboard System
-// Author: Joseph Huckaby
-
-var ZeroClipboard_TableTools = {
-
- version: "1.0.4-TableTools2",
- clients: {}, // registered upload clients on page, indexed by id
- moviePath: '', // URL to movie
- nextId: 1, // ID of next movie
-
- $: function(thingy) {
- // simple DOM lookup utility function
- if (typeof(thingy) == 'string') thingy = document.getElementById(thingy);
- if (!thingy.addClass) {
- // extend element with a few useful methods
- thingy.hide = function() { this.style.display = 'none'; };
- thingy.show = function() { this.style.display = ''; };
- thingy.addClass = function(name) { this.removeClass(name); this.className += ' ' + name; };
- thingy.removeClass = function(name) {
- this.className = this.className.replace( new RegExp("\\s*" + name + "\\s*"), " ").replace(/^\s+/, '').replace(/\s+$/, '');
- };
- thingy.hasClass = function(name) {
- return !!this.className.match( new RegExp("\\s*" + name + "\\s*") );
- }
- }
- return thingy;
- },
-
- setMoviePath: function(path) {
- // set path to ZeroClipboard.swf
- this.moviePath = path;
- },
-
- dispatch: function(id, eventName, args) {
- // receive event from flash movie, send to client
- var client = this.clients[id];
- if (client) {
- client.receiveEvent(eventName, args);
- }
- },
-
- register: function(id, client) {
- // register new client to receive events
- this.clients[id] = client;
- },
-
- getDOMObjectPosition: function(obj) {
- // get absolute coordinates for dom element
- var info = {
- left: 0,
- top: 0,
- width: obj.width ? obj.width : obj.offsetWidth,
- height: obj.height ? obj.height : obj.offsetHeight
- };
-
- if ( obj.style.width != "" )
- info.width = obj.style.width.replace("px","");
-
- if ( obj.style.height != "" )
- info.height = obj.style.height.replace("px","");
-
- while (obj) {
- info.left += obj.offsetLeft;
- info.top += obj.offsetTop;
- obj = obj.offsetParent;
- }
-
- return info;
- },
-
- Client: function(elem) {
- // constructor for new simple upload client
- this.handlers = {};
-
- // unique ID
- this.id = ZeroClipboard_TableTools.nextId++;
- this.movieId = 'ZeroClipboard_TableToolsMovie_' + this.id;
-
- // register client with singleton to receive flash events
- ZeroClipboard_TableTools.register(this.id, this);
-
- // create movie
- if (elem) this.glue(elem);
- }
-};
-
-ZeroClipboard_TableTools.Client.prototype = {
-
- id: 0, // unique ID for us
- ready: false, // whether movie is ready to receive events or not
- movie: null, // reference to movie object
- clipText: '', // text to copy to clipboard
- fileName: '', // default file save name
- action: 'copy', // action to perform
- handCursorEnabled: true, // whether to show hand cursor, or default pointer cursor
- cssEffects: true, // enable CSS mouse effects on dom container
- handlers: null, // user event handlers
- sized: false,
-
- glue: function(elem, title) {
- // glue to DOM element
- // elem can be ID or actual DOM element object
- this.domElement = ZeroClipboard_TableTools.$(elem);
-
- // float just above object, or zIndex 99 if dom element isn't set
- var zIndex = 99;
- if (this.domElement.style.zIndex) {
- zIndex = parseInt(this.domElement.style.zIndex) + 1;
- }
-
- // find X/Y position of domElement
- var box = ZeroClipboard_TableTools.getDOMObjectPosition(this.domElement);
-
- // create floating DIV above element
- this.div = document.createElement('div');
- var style = this.div.style;
- style.position = 'absolute';
- style.left = '0px';
- style.top = '0px';
- style.width = (box.width) + 'px';
- style.height = box.height + 'px';
- style.zIndex = zIndex;
-
- if ( typeof title != "undefined" && title != "" ) {
- this.div.title = title;
- }
- if ( box.width != 0 && box.height != 0 ) {
- this.sized = true;
- }
-
- // style.backgroundColor = '#f00'; // debug
- if ( this.domElement ) {
- this.domElement.appendChild(this.div);
- this.div.innerHTML = this.getHTML( box.width, box.height );
- }
- },
-
- positionElement: function() {
- var box = ZeroClipboard_TableTools.getDOMObjectPosition(this.domElement);
- var style = this.div.style;
-
- style.position = 'absolute';
- //style.left = (this.domElement.offsetLeft)+'px';
- //style.top = this.domElement.offsetTop+'px';
- style.width = box.width + 'px';
- style.height = box.height + 'px';
-
- if ( box.width != 0 && box.height != 0 ) {
- this.sized = true;
- } else {
- return;
- }
-
- var flash = this.div.childNodes[0];
- flash.width = box.width;
- flash.height = box.height;
- },
-
- getHTML: function(width, height) {
- // return HTML for movie
- var html = '';
- var flashvars = 'id=' + this.id +
- '&width=' + width +
- '&height=' + height;
-
- if (navigator.userAgent.match(/MSIE/)) {
- // IE gets an OBJECT tag
- var protocol = location.href.match(/^https/i) ? 'https://' : 'http://';
- html += '';
- }
- else {
- // all other browsers get an EMBED tag
- html += '';
- }
- return html;
- },
-
- hide: function() {
- // temporarily hide floater offscreen
- if (this.div) {
- this.div.style.left = '-2000px';
- }
- },
-
- show: function() {
- // show ourselves after a call to hide()
- this.reposition();
- },
-
- destroy: function() {
- // destroy control and floater
- if (this.domElement && this.div) {
- this.hide();
- this.div.innerHTML = '';
-
- var body = document.getElementsByTagName('body')[0];
- try { body.removeChild( this.div ); } catch(e) {;}
-
- this.domElement = null;
- this.div = null;
- }
- },
-
- reposition: function(elem) {
- // reposition our floating div, optionally to new container
- // warning: container CANNOT change size, only position
- if (elem) {
- this.domElement = ZeroClipboard_TableTools.$(elem);
- if (!this.domElement) this.hide();
- }
-
- if (this.domElement && this.div) {
- var box = ZeroClipboard_TableTools.getDOMObjectPosition(this.domElement);
- var style = this.div.style;
- style.left = '' + box.left + 'px';
- style.top = '' + box.top + 'px';
- }
- },
-
- clearText: function() {
- // clear the text to be copy / saved
- this.clipText = '';
- if (this.ready) this.movie.clearText();
- },
-
- appendText: function(newText) {
- // append text to that which is to be copied / saved
- this.clipText += newText;
- if (this.ready) { this.movie.appendText(newText) ;}
- },
-
- setText: function(newText) {
- // set text to be copied to be copied / saved
- this.clipText = newText;
- if (this.ready) { this.movie.setText(newText) ;}
- },
-
- setCharSet: function(charSet) {
- // set the character set (UTF16LE or UTF8)
- this.charSet = charSet;
- if (this.ready) { this.movie.setCharSet(charSet) ;}
- },
-
- setBomInc: function(bomInc) {
- // set if the BOM should be included or not
- this.incBom = bomInc;
- if (this.ready) { this.movie.setBomInc(bomInc) ;}
- },
-
- setFileName: function(newText) {
- // set the file name
- this.fileName = newText;
- if (this.ready) this.movie.setFileName(newText);
- },
-
- setAction: function(newText) {
- // set action (save or copy)
- this.action = newText;
- if (this.ready) this.movie.setAction(newText);
- },
-
- addEventListener: function(eventName, func) {
- // add user event listener for event
- // event types: load, queueStart, fileStart, fileComplete, queueComplete, progress, error, cancel
- eventName = eventName.toString().toLowerCase().replace(/^on/, '');
- if (!this.handlers[eventName]) this.handlers[eventName] = [];
- this.handlers[eventName].push(func);
- },
-
- setHandCursor: function(enabled) {
- // enable hand cursor (true), or default arrow cursor (false)
- this.handCursorEnabled = enabled;
- if (this.ready) this.movie.setHandCursor(enabled);
- },
-
- setCSSEffects: function(enabled) {
- // enable or disable CSS effects on DOM container
- this.cssEffects = !!enabled;
- },
-
- receiveEvent: function(eventName, args) {
- // receive event from flash
- eventName = eventName.toString().toLowerCase().replace(/^on/, '');
-
- // special behavior for certain events
- switch (eventName) {
- case 'load':
- // movie claims it is ready, but in IE this isn't always the case...
- // bug fix: Cannot extend EMBED DOM elements in Firefox, must use traditional function
- this.movie = document.getElementById(this.movieId);
- if (!this.movie) {
- var self = this;
- setTimeout( function() { self.receiveEvent('load', null); }, 1 );
- return;
- }
-
- // firefox on pc needs a "kick" in order to set these in certain cases
- if (!this.ready && navigator.userAgent.match(/Firefox/) && navigator.userAgent.match(/Windows/)) {
- var self = this;
- setTimeout( function() { self.receiveEvent('load', null); }, 100 );
- this.ready = true;
- return;
- }
-
- this.ready = true;
- this.movie.clearText();
- this.movie.appendText( this.clipText );
- this.movie.setFileName( this.fileName );
- this.movie.setAction( this.action );
- this.movie.setCharSet( this.charSet );
- this.movie.setBomInc( this.incBom );
- this.movie.setHandCursor( this.handCursorEnabled );
- break;
-
- case 'mouseover':
- if (this.domElement && this.cssEffects) {
- //this.domElement.addClass('hover');
- if (this.recoverActive) this.domElement.addClass('active');
- }
- break;
-
- case 'mouseout':
- if (this.domElement && this.cssEffects) {
- this.recoverActive = false;
- if (this.domElement.hasClass('active')) {
- this.domElement.removeClass('active');
- this.recoverActive = true;
- }
- //this.domElement.removeClass('hover');
- }
- break;
-
- case 'mousedown':
- if (this.domElement && this.cssEffects) {
- this.domElement.addClass('active');
- }
- break;
-
- case 'mouseup':
- if (this.domElement && this.cssEffects) {
- this.domElement.removeClass('active');
- this.recoverActive = false;
- }
- break;
- } // switch eventName
-
- if (this.handlers[eventName]) {
- for (var idx = 0, len = this.handlers[eventName].length; idx < len; idx++) {
- var func = this.handlers[eventName][idx];
-
- if (typeof(func) == 'function') {
- // actual function reference
- func(this, args);
- }
- else if ((typeof(func) == 'object') && (func.length == 2)) {
- // PHP style object + method, i.e. [myObject, 'myMethod']
- func[0][ func[1] ](this, args);
- }
- else if (typeof(func) == 'string') {
- // name of function
- window[func](this, args);
- }
- } // foreach event handler defined
- } // user defined handler for event
- }
-
-};
diff --git a/wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls.swf b/wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls.swf
deleted file mode 100644
index 082c7acb..00000000
Binary files a/wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls.swf and /dev/null differ
diff --git a/wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf b/wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf
deleted file mode 100644
index 063131df..00000000
Binary files a/wqflask/wqflask/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf and /dev/null differ
diff --git a/wqflask/wqflask/static/packages/TableTools/multi_instance.html b/wqflask/wqflask/static/packages/TableTools/multi_instance.html
deleted file mode 100644
index 14e1e63e..00000000
--- a/wqflask/wqflask/static/packages/TableTools/multi_instance.html
+++ /dev/null
@@ -1,499 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - multiple toolbars
-
-
-
Preamble
-
Like all DataTables control elements, TableTools can have multiple instances specified in the sDom parameter of DataTables. This will create two TableTools toolbars next to the table, providing the same functions. An example of when this might be useful is to show the toolbar both above and below the table - as is done in this example.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/multiple_tables.html b/wqflask/wqflask/static/packages/TableTools/multiple_tables.html
deleted file mode 100644
index 8cd8aef9..00000000
--- a/wqflask/wqflask/static/packages/TableTools/multiple_tables.html
+++ /dev/null
@@ -1,296 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - multiple tables
-
-
-
Preamble
-
This example shows how multiple tables can be initialised with DataTables and TableTools in a single call to the $().dataTable() function. Basically it works as you would expect - no special considerations need be made!
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/pdf_message.html b/wqflask/wqflask/static/packages/TableTools/pdf_message.html
deleted file mode 100644
index e8f66e12..00000000
--- a/wqflask/wqflask/static/packages/TableTools/pdf_message.html
+++ /dev/null
@@ -1,524 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example
-
-
-
Preamble
-
This example shows how you can add a message to the saved PDF using the 'sPdfMessage' parameter. It also shows that the orientation of the output PDF can be changed to landscape which is useful if you have a lot of columns.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/plug-in.html b/wqflask/wqflask/static/packages/TableTools/plug-in.html
deleted file mode 100644
index 08a055bf..00000000
--- a/wqflask/wqflask/static/packages/TableTools/plug-in.html
+++ /dev/null
@@ -1,539 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - plug-ins
-
-
-
Preamble
-
Plug-ins in TableTools take the form of additional buttons types, which provide extra options and flexibility for TableTools. This example shows how a plug-in button type can be defined and then used in the TableTools initialisation. Note that the TableTools.buttonBase object is extended with our required parameters - this base object provides default values for all of the options TableTools can work with, so they don't all have to be defined in our button.
-
Additional plug-ins for TableTools can be found on the DataTables.net site. The example plug-in here shows a button which is used to insert the data from the table into a given element.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/select_multi.html b/wqflask/wqflask/static/packages/TableTools/select_multi.html
deleted file mode 100644
index ee94789c..00000000
--- a/wqflask/wqflask/static/packages/TableTools/select_multi.html
+++ /dev/null
@@ -1,507 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - multi-row select
-
-
-
Preamble
-
As well as providing a button toolbar, TableTools provides everything needed to have selectable rows in the table. Row selection is turned off by default in TableTools, but can be enabled using the sRowSelect parameter, set to either 'multi' or 'single'. When set the end user can select rows by simply clicking on them. TableTools provides a set of API methods and callbacks for controlling and monitoring the row selection in TableTools. There are also a number of pre-defined buttons to provide functions such as select-all and select-none, as shown in this example.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/select_single.html b/wqflask/wqflask/static/packages/TableTools/select_single.html
deleted file mode 100644
index 94a47893..00000000
--- a/wqflask/wqflask/static/packages/TableTools/select_single.html
+++ /dev/null
@@ -1,505 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - single row selection
-
-
-
Preamble
-
As well as providing a button toolbar, TableTools provides everything needed to have selectable rows in the table. Row selection is turned off by default in TableTools, but can be enabled using the sRowSelect parameter, set to either 'multi' or 'single'. When set the end user can select rows by simply clicking on them. TableTools provides a set of API methods and callbacks for controlling and monitoring the row selection in TableTools. This example shows single row selection enabled.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/swf_path.html b/wqflask/wqflask/static/packages/TableTools/swf_path.html
deleted file mode 100644
index c82633b4..00000000
--- a/wqflask/wqflask/static/packages/TableTools/swf_path.html
+++ /dev/null
@@ -1,505 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - setting SWF path
-
-
-
Preamble
-
TableTools uses a Flash SWF file to provide the ability to copy text to the system clipboard and save files locally. TableTools must be able to load the SWF file in order to provide these facilities. If you aren't using the same directory structure as the TableTools package, you will need to set this parameter.
-
Note that TableTools ships with two different SWF files - the only difference between them is that one of them provides the ability to save PDF files while the other doesn't. The trade off is that the PDF capable file is significantly larger in size (56K v 2K).
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/tabs.html b/wqflask/wqflask/static/packages/TableTools/tabs.html
deleted file mode 100644
index 915cc821..00000000
--- a/wqflask/wqflask/static/packages/TableTools/tabs.html
+++ /dev/null
@@ -1,348 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
-
- TableTools example
-
-
-
Preamble
-
This example shows the basic initialisation of TableTools by simply including the 'T' marker in DataTables' sDom parameter. This tell DataTables to insert the TableTools toolbar in that location. Remember to include the Javascript and CSS source files as well!
-
It is worth noting that you might need to set the sSwfPath parameter to tell TableTools where to find the SWF file for copy and file save.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/static/packages/TableTools/theme.html b/wqflask/wqflask/static/packages/TableTools/theme.html
deleted file mode 100644
index fcda07a0..00000000
--- a/wqflask/wqflask/static/packages/TableTools/theme.html
+++ /dev/null
@@ -1,524 +0,0 @@
-
-
-
-
-
-
- TableTools example
-
-
-
-
-
-
-
-
-
-
- TableTools example - jQuery UI theming
-
-
-
Preamble
-
Like DataTables, TableTools can be styled by a jQuery UI theme. The required classes for the theming with TableTools are added automatically when the bJQueryUI option is detected from DataTables. This example shows that in action, and also defines a button collection to show the themeing there.
-
-
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/search_error.html b/wqflask/wqflask/templates/search_error.html
index 22416580..7394c9f9 100644
--- a/wqflask/wqflask/templates/search_error.html
+++ b/wqflask/wqflask/templates/search_error.html
@@ -2,8 +2,6 @@
{% block title %}Search Results{% endblock %}
{% block css %}
-
-
{% endblock %}
{% block content %}
--
cgit v1.2.3
From 518be96a310963a4127a0b569a73c91187c02b64 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 12 Apr 2018 08:20:30 +0000
Subject: README and docs
---
README.md | 13 ++++++++-----
bin/genenetwork2 | 15 ++++++++-------
wqflask/maintenance/gen_select_dataset.py | 3 ---
3 files changed, 16 insertions(+), 15 deletions(-)
diff --git a/README.md b/README.md
index 8221ad65..3e7e64d0 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,11 @@ Once installed GN2 can be run online through a browser interface
./bin/genenetwork2
```
-(default is http://localhost:5003/). We are building up automated
+(default is http://localhost:5003/). For more examples, including running scripts and a Python REPL
+see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
+
+
+We are building up automated
testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with
```sh
@@ -70,16 +74,15 @@ For more information visit http://www.genenetwork.org/
[![JOSS](http://joss.theoj.org/papers/10.21105/joss.00025/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00025)
-GeneNetwork was published in the Journal of Open Source Software as 'GeneNetwork: framework for web-based genetics' by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. WIlliams and Pjotr Prins
+GeneNetwork was published in the Journal of Open Source Software as 'GeneNetwork: framework for web-based genetics' by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. WIlliams and Pjotr Prins
You may also cite the software using
-[![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2).
+[![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2).
## Contact
IRC on #genenetwork on irc.freenode.net.
Code and primary web service managed by Dr. Robert W. Williams and the
-University of Tennessee Health Science Center, Memphis TN, USA.
-
+University of Tennessee Health Science Center, Memphis TN, USA.
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 18e02388..b3a8d8c2 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -15,28 +15,29 @@
# installation path of genenetwork). Say your profile is in
# ~/opt/gn-latest-guix
#
-# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2
+# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2
#
# You can pass in your own settings file, e.g.
#
-# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py
+# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ~/my_settings.py
#
# To run a maintenance python script with settings (instead of the
-# webserver) add that with a -c switch, e.g.
+# webserver) run from the base-dir with settings file and add that
+# script with a -c switch, e.g.
#
-# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 -c ./wqflask/maintenance/gen_select_dataset.py
+# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py
#
# To run any script in the environment
#
-# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD"
+# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD"
#
# To get a python REPL(!)
#
-# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli python
+# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli python
#
# For development you may want to run
#
-# env GN2_PROFILE=~/opt/gn-latest-guix WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2
+# env GN2_PROFILE=~/opt/gn-latest WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2
#
# For staging and production we use gunicorn. Run with something like
# (note you have to provide the server port). Provide a settings file!
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index f62d0cc1..79242661 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -63,9 +63,6 @@ from pprint import pformat as pf
#conn = Engine.connect()
-print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!')
-
-
def parse_db_uri(db_uri):
"""Converts a database URI to the db name, host name, user name, and password"""
--
cgit v1.2.3