Final commit before release 1.8.0.

CHANGELOG.md

@@ -4,6 +4,27 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/) 
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [1.8.0] - 2018-10-24
+### Added
+ - Added PWA capability including app manifest ('manifest.json') and service worker ('sw.js') to enable depolyment of Identikit resources as mobile apps capable of being used away from the internet.
+ - Added a new visualisation ('vis6') which is a mobile-first multi-access key capable of using the PWA features to download resources for offline use.
+ - Updated documentation, especially 'Deploying your visualisations' and 'Getting started', to explain how to deploy PWA Identikit apps with vis6.
+ - Added a configuration option (tbv.opts.ignoreNegativeScoring) to instruct Identikit to ignore negative scores (issue 26). Documented in 'Deploying your visualisations'.
+ - Added a facility for knowledge-base developers to provide a downloadable PDF to describe their resource. If a file called 'info.pdf' is found in the knowledge-base folder, a download link is added to the main tool interface (issue #21).
+ - Added a mechanism for checking APIs of objects against template interfaces.
+### Fixed
+ - Addressed typo is KB checking (issue #22).
+ - Addressed issue whereby clearing value in spin control (character input) with keyboard, but software treated value as zero rather than null (issue #24).
+### Changed
+ - Implemented architectural changes to separate three levels of interface: overarching GUI, visualisations and user-input GUIs.
+ - Moved visualisation-specific CSS out of general CSS file (tombio.css) and into separate CSS files for individual tools.
+ - Multiple spaces in kb values (or translated values) caused problem. These are now removed as the KB is loaded (issue #25).
+ - Improved layout of images and their captions on help dialogs (issue #31).
+ - Updated D3 to version 5 (issue #32).
+ - Changed and added a number of top-level configuration options (documented in 'Deploying your visualisations').
+### Removed
+ - Citation of individual tools removed (issue #29).
+
 ## [1.7.1] - 2018-06-11
 ### Fixed
  - Addressed problem with 'close' and 'full-size' image controls not working in the side-by-side comparison tool when galleria image small.
@@ -84,7 +105,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 ### Fixed
  - Vertical orientation of character names in the two-column visualisation updated to make it work with Safari and IE.
  - Added better handling of the image control in mobile devices - especially iPad - by adding pinch zoom and explicit display/hiding of image controls with a press gesture.
- ### Changed
+### Changed
  - Individual character scores on the single-column key visualisation are now rounded *down* to the nearest 0.1 to avoid confusion of non-perfect matches apparently scoring a perfect match.
  - (Developers note) Moved definition of matching score colour ramp out of individual visualisations and into prototype visualisation module (visP). 
  - (Developers note) Moved knowledge-base integrity checks to a separate javascript module to promote code clarity.

ReleaseNotes.md

@@ -1,5 +1,18 @@
 # Release notes for existing knoweldge-base developers
 These notes are intended to help existing knowledge-base developers move from one version of the FSC Identikit to another. These notes were first released with version 1.7.0 of the Identikit and will be updated on each succeeding release.
+
+## Release 1.8.0
+The main feature of release 1.8.0 is a new visualisation ('vis6') which is a 'mobile-first' multi-access key that is suitable for using on small-format devices such as smartphones. Using this visualisation and the new Progressive Web App (PWA) features of Identikit 1.8.0, you can build mobile-first multi-access keys which can be deployed as apps on smartphones and even used away from an internet connection.
+
+### Updating to release 1.8.0
+The procedure for updating to a new release of the Identikit is the same as demonstrated in this video: http://www.fscbiodiversity.uk/fullscreen/tombiovis-upgrade. (The video was made when version 1.4.1 was released and was still referred to then as *the Framework*.)
+
+### Changes to *vis.html*
+Once again, we've made a number of changes to the way Identikit initialisation options are handled. These are described in the document *Deploying your visualisations*. For the most part, the old ways of initialising things are still supported, but not recommended (i.e. they are *deprecated*). So the chances are that the copy if *vis.html* that you use to run the Identikit whilst developing and testing your knowlege-base will still work. But we nevertheless recommend that you update your vis.html (or whatever you use) to reflect the new configuration options.
+
+### Addition of *vism.html*
+This new template high-level page is a version of *vis.html* which is configured specifically  to demonstrate the new mobile-first multi-access key on the provided *biscuits* knowledge-base. You can use this template to make a mobile-first multi-access key based on your own knowledge-base.
+
 ## Release 1.7.1
 This was a minor update to address a couple of small bugs with 1.7.0. Knowledge-base developers moving to version 1.7.1 from earlier versions should consult the notes below for version 1.7.0.
 ## Release 1.7.0

kb/biscuits/config.csv

@@ -12,8 +12,9 @@ authors,metadata,yes,"Bell, C.",,
 publisher,metadata,no,Field Studies Council,,
 location,metadata,no,"Preston Montford, Shrewsbury",,
 contact,metadata,no,,,
-version,metadata,yes,1.7.1,,
+version,metadata,yes,1.8.0,,
 #Releases - keep track of the release history below this line. Most recent releases at the top. The version code in the 'value' column below this line should match that of the current release above it.,,,,,
+release,history,no,1.8.0,10/24/2018,Minor changes.
 release,history,no,1.7.1,6/1/2018,Minor fix to add new media fields.
 release,history,no,1.7,6/1/2018,Modified by RB to complement version 1.7.0 release of Identikit.
 release,history,no,1.0,11/22/2016,Modified by RB to illustrate some of the different features of knowledge representation.

manifest.json

@@ -28,7 +28,7 @@
             "type": "image/png"
         }
     ],
-    "start_url": "/vis.html",
+    "start_url": "vis.html",
     "display": "standalone",
     "background_color": "#3E4EB8",
     "theme_color": "#2F3BA2"

sw.js

@@ -1,11 +1,12 @@
 //See comments at the end of description of caching strategy
 
-var kbCacheName = "tombio-kb-cache-1";
-var kbImgStdCacheName = "tombio-kb-img-std-cache-1";
-var kbImgSmlCacheName = "tombio-kb-img-sml-cache-1";
-var kbImgLrgCacheName = "tombio-kb-img-lrg-cache-1";
-var kbTxtCacheName = "tombio-kb-txt-cache-1";
-var genCacheName = "tombio-gen-cache-1";
+var cacheno = 8;
+var kbCacheName = "tombio-kb-cache-" + cacheno;
+var kbImgStdCacheName = "tombio-kb-img-std-cache-" + cacheno;
+var kbImgSmlCacheName = "tombio-kb-img-sml-cache-" + cacheno;
+var kbImgLrgCacheName = "tombio-kb-img-lrg-cache-" + cacheno;
+var kbTxtCacheName = "tombio-kb-txt-cache-" + cacheno;
+var genCacheName = "tombio-gen-cache-" + cacheno;
 var allCacheNames = [genCacheName, kbCacheName, kbImgStdCacheName, kbImgSmlCacheName, kbImgLrgCacheName, kbTxtCacheName]
 var url = new URL(location);
 var tombiokbpath = url.searchParams.get('tombiokbpath');

tombio/guiLargeJqueryUi.js

@@ -159,8 +159,29 @@
         //An area for tools to add info
         $("<div>").attr("id", "tombioGuiLargeJqueryUiFlashDisplay").css("display", "none").appendTo("#tombioGuiLargeJqueryUi");
 
-        //Tool drop-down
-        $("<select>").attr("id", "tombioGuiLargeJqueryUiVisualisation").appendTo("#tombioGuiLargeJqueryUi");
+        //Tool drop-down and PDF info button
+        var table = $("<table>").appendTo("#tombioGuiLargeJqueryUi");
+        var tr = $("<tr>").appendTo(table);
+        var td1 = $("<td>").appendTo(tr);
+        var td2 = $("<td>").appendTo(tr);
+        $("<select>").attr("id", "tombioGuiLargeJqueryUiVisualisation").appendTo(td1);
+
+        //Add Info PDF button if info.pdf file is found
+        $.ajax({
+            //https://forums.asp.net/t/1640966.aspx?Check+file+exist+on+server+using+Javascript
+            type: "HEAD",
+            url: tbv.opts.tombiokbpath + "info.pdf",
+            success: function (data) {
+                var img = $("<img>").attr("src", tbv.opts.tombiopath + "resources/pdf.png");
+                img.css("height", "25px");
+                img.css("position", "relative");
+                img.css("top", "-3px");
+                var a = $("<a>").attr("href", tbv.opts.tombiokbpath + "info.pdf");
+                a.append(img);
+                td2.append(a);
+            }
+        });
+
 
         //Divs for taxa and controls
         $("<div>").addClass("tombioNoSelect").attr("id", "tombioGuiLargeJqueryUiControlsAndTaxa").appendTo("#tombioGuiLargeJqueryUi");

tombio/guiOnsenUi.js

@@ -121,12 +121,12 @@
         html += '<ons-toolbar>';
 
         var tb = "";
-        tb += '<ons-toolbar-button id="tombioUiFullscreenMenuButton" onclick="tombiovis.gui.main.fn.requestFullscreen()">';
-        tb += '<ons-icon icon="md-fullscreen"></ons-icon>';
-        tb += '</ons-toolbar-button>';
-        tb += '<ons-toolbar-button id="tombioUiExitFullscreenMenuButton" onclick="tombiovis.gui.main.fn.exitFullscreen()" style="display: none">';
-        tb += '<ons-icon icon="md-fullscreen-exit"></ons-icon>';
-        tb += '</ons-toolbar-button>';
+        //tb += '<ons-toolbar-button id="tombioUiFullscreenMenuButton" onclick="tombiovis.gui.main.fn.requestFullscreen()">';
+        //tb += '<ons-icon icon="md-fullscreen"></ons-icon>';
+        //tb += '</ons-toolbar-button>';
+        //tb += '<ons-toolbar-button id="tombioUiExitFullscreenMenuButton" onclick="tombiovis.gui.main.fn.exitFullscreen()" style="display: none">';
+        //tb += '<ons-icon icon="md-fullscreen-exit"></ons-icon>';
+        //tb += '</ons-toolbar-button>';
         tb += '<ons-toolbar-button id="tombioUiContextMenuButton" onclick="tombiovis.gui.main.openContext()">';
         tb += '<ons-icon icon="md-more-vert"></ons-icon>';
         tb += '</ons-toolbar-button>';
@@ -274,10 +274,15 @@
 
         //Add handler for orientation change
         ons.orientation.on('change', function () {
+            console.log("Orientation changed")
             splitterSideHideShow();
             resizeElements();
             //Refresh the selected tool
-            tbv.f.refreshVisualisation();
+            //The timeout delay seems to be required otherwise the refresh method fires before divs have resized
+            setTimeout(function () {
+                tbv.f.refreshVisualisation();
+                mainMenuPos();
+            }, 1000);
         });    
 
         //Check interface
@@ -331,10 +336,22 @@
 
         //The option *values* currentVisInfo, kbInfo, visInfo & tombioCitation have software-wide meaning, not just this gui
         icon = '<div class="left"><ons-icon icon="md-info" class="list-item__icon"></ons-icon></div>'
+
         toolOptions.push($('<ons-list-item id="optCurrentVisInfo" value="currentVisInfo" class="html" data-class="info">' + icon + 'Using the...</ons-list-item>'));
         toolOptions.push($('<ons-list-item value="kbInfo" class="html" data-class="info">' + icon + 'About the Knowledge-base</ons-list-item>'));
         toolOptions.push($('<ons-list-item value="visInfo" class="html" data-class="info">' + icon + 'About FSC Identikit</ons-list-item>'));
         toolOptions.push($('<ons-list-item value="tombioCitation" class="html" data-class="info">' + icon + 'Get citation text</ons-list-item>'));
+        toolOptions.push($('<ons-list-item id="optPdfInfo" style="display: none">' + icon + '<a href="' + tbv.opts.tombiokbpath + "info.pdf" + '">About this resource PDF</a></ons-list-item>'));
+
+        //Show the PDF Info option if info.pdf file is found
+        $.ajax({
+            //https://forums.asp.net/t/1640966.aspx?Check+file+exist+on+server+using+Javascript
+            type: "HEAD",
+            url: tbv.opts.tombiokbpath + "info.pdf",
+            success: function (data) {
+                $('#optPdfInfo').show();
+            }
+        });
 
         //If developer's section added above, then add a header for standard reload and download
         toolOptions.push($('<ons-list-header>Other</ons-list-header>'));
@@ -489,6 +506,21 @@
                 //Set initialised flag
                 tbv.v.initialised = true;
             }
+
+            //Show/hide context menu button
+            var contextMenuNeeded;
+            console.log(selectedToolName);
+            Object.keys(tbv.gui.main.contextMenu.items).forEach(function (contextItem) {
+                console.log(tbv.gui.main.contextMenu.visContexts[contextItem])
+                if (tbv.gui.main.contextMenu.visContexts[contextItem].indexOf(selectedToolName) != -1) {
+                    contextMenuNeeded = true;
+                }
+            })
+            if (contextMenuNeeded) {
+                $('ons-toolbar-button#tombioUiContextMenuButton.toolbar-button').show();
+            } else {
+                $('ons-toolbar-button#tombioUiContextMenuButton.toolbar-button').hide();
+            }
         }
     }
 
@@ -653,21 +685,13 @@
             $('#tombioOnsMenu').attr('collapse', '');
         }
 
-        //
-        console.log("vis width", $('#tombioOnsVisDisplay').width());
-        if ($('#tombioOnsVisDisplay').width() < 208) {
-            $('#tombioOnsToolsRight').hide();
-            $('#tombioOnsToolsLeft').show();
-        } else {
-            $('#tombioOnsToolsRight').show();
-            $('#tombioOnsToolsLeft').hide();
-        }  
+        mainMenuPos();
 
         splitterSideHideShow();
 
         tbv.f.refreshVisualisation();
     }
- 
+
     tbv.gui.main.contextMenu = {
         //Create the context menu object
         items: {}, //Links to each item in the menu
@@ -745,6 +769,16 @@
         $('#tombioUiExitFullscreenMenuButton').hide();
     }
 
+    function mainMenuPos() {
+        if ($('#tombioOnsVisDisplay').width() < 208) {
+            $('#tombioOnsToolsRight').hide();
+            $('#tombioOnsToolsLeft').show();
+        } else {
+            $('#tombioOnsToolsRight').show();
+            $('#tombioOnsToolsLeft').hide();
+        }  
+    }
+
     function splitterSideHideShow() {
 
         //This function has several purposes.
@@ -813,13 +847,13 @@
         html.append($("<p>").html(t));
         html.append($("<b>").html(tbv.f.getCitation(tbv.d.softwareMetadata, "Software")));
 
-        //Generate the citation for the current tool
-        html.append($("<h3>").text("Citation for last selected visualisation tool"))
-        t = "This is the reference you can use for the last selected visualisation tool.";
-        t += " The tool version number is updated whenever there is a new release of the tool.";
-        t += " If you cite a tool, there's no need to cite the core software separately since it is implicit.";
-        html.append($("<p>").html(t));
-        html.append($("<b>").html(tbv.f.getCitation(tbv.v.visualisations[tbv.v.lastVis].metadata, "Software", tbv.d.softwareMetadata.title)));
+        ////Generate the citation for the current tool
+        //html.append($("<h3>").text("Citation for last selected visualisation tool"))
+        //t = "This is the reference you can use for the last selected visualisation tool.";
+        //t += " The tool version number is updated whenever there is a new release of the tool.";
+        //t += " If you cite a tool, there's no need to cite the core software separately since it is implicit.";
+        //html.append($("<p>").html(t));
+        //html.append($("<b>").html(tbv.f.getCitation(tbv.v.visualisations[tbv.v.lastVis].metadata, "Software", tbv.d.softwareMetadata.title)));
 
         //Generate the citation for the knowledge-base
         html.append($("<h3>").text("Citation for knowledge-base"))

tombio/kbchecks.js

@@ -306,7 +306,7 @@
         //Check that all characters (column headers) on the taxa tab have corresponding values in the characters tab.
         charactersFromTaxaTab.forEach(function (character, iCol) {
             if (charactersFromCharactersTab.indexOf(character) == -1) {
-                errors.append($('<li class="tombioValid3">').html("There is no row on the <i>characters</i> worksheet for the character <b>'" + character + "'</b> represented by a column (column " + (iCol + 1) + ") on the <i>taxa</i> worksheet. All columns on the <i>taxa</i> tab must be represented by a row in the <i>characters</i> worksheet regardless of whether or not they are used. Names are case sensitive. Note that rows will not be seen unless the <b>Group</b> column has a value."));
+                errors.append($('<li class="tombioValid3">').html("There is no row on the <i>characters</i> worksheet for the character <b>'" + character + "'</b> represented by a column (column " + (iCol + 1) + ") on the <i>taxa</i> worksheet. All columns on the <i>taxa</i> tab must be represented by a row in the <i>characters</i> worksheet regardless of whether or not they are used. Names are case sensitive. Note that rows will not be seen unless the <b>Status</b> column has a value."));
                 characters = false;
             }
         })