Merge pull request #59 from Jollyfant/dev

Version 2.0.1
Jollyfant · Feb 25, 2020 · 9d06570 · 9d06570
2 parents 1618a3c + 24aad39
commit 9d06570
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Showing 20 changed files with 772 additions and 122 deletions.
diff --git a/changelog/index.html b/changelog/index.html
@@ -77,6 +77,47 @@ <h5> Paleomagnetism.org 2 - Changelog </h5>
         </div>
 
         <div id="accordion">
+
+          <div class="card">
+            <div class="card-header" id="headingTwo">
+              <button class="btn btn-link" data-toggle="collapse" data-target="#collapseTwo" aria-expanded="true" aria-controls="collapseTwo">
+                Paleomagnetism.org 2.1.0 - Release <small class="text-muted">&nbsp; 2020-02-25</small>
+              </button>
+            </div>
+            <div id="collapseTwo" class="collapse show" aria-labelledby="headingTwo" data-parent="#accordion">
+              <div class="card-body">
+              <b> Change Summary </b>
+              <p> Some new features were added for user convenience. Minor bugs were fixed.
+              <ul>
+                <p> <b> Features </b>
+                <li> Added window to add some metadata to collections in the statistics portal. This can be used when exporting .pub files for sharing for literature data that cannot be submitted to the data library.
+                <li> Added satellite imagery to the geography portal (#53).
+              </ul>
+              <ul>
+                <p> <b> Fixes </b>
+                <li> Added new paper (Koymans et al., 2020) to the references page.
+                <li> Fixed JSON exporting in statistics portal mean directions tab.
+                <li> Fixed reading of input files in reversed order. The order is now as expected.
+                <li> Intensity plot in the interpretation portal now uses categories instead of numeric values.
+                <li> Size of charts in the interpretation portal has been increased.
+                <li> The PalPole description on the miscellaneous portal has been updated.
+                <li> A warning is now shown when the application is run in to beta mode.
+                <li> Map width in the geography portal has been reduced and bounds were removed (#51, #52).
+                <li> Fixed GPlates rotation files for plate ID "0" which is the same as "000" (#54)
+                <li> Fixed accidental swap of latitude, longitude in publication preview map.
+                <li> Fixed CTMD test not working for reversed directions.
+                <li> Added Remasoft (RS3) file format.
+                <li> Data library author information is now taken from DOI by default.
+                <li> Added age and generated country based on lat, lng to data library.
+                <li> Prevent linking to statistics/geography portal when no interpreted components are available.
+              </ul>
+
+              </div>
+            </div>
+          </div>
+
+          <p>
+
           <div class="card">
             <div class="card-header" id="headingOne">
               <button class="btn btn-link" data-toggle="collapse" data-target="#collapseOne" aria-expanded="true" aria-controls="collapseOne">
@@ -85,7 +126,7 @@ <h5> Paleomagnetism.org 2 - Changelog </h5>
             </div>
     <div id="collapseOne" class="collapse show" aria-labelledby="headingOne" data-parent="#accordion">
           <div class="card-body">
-            <b> Change Summary <20>
+            <b> Change Summary </b>
             <p> The release of Paleomagnetism 2.0.0 exists in parallel with the <a href="http://old.paleomagnetism.org">old application</a>. The old version may have some additional features in the statistics portal that were removed in this version. This version of Paleomagnetism.org focuses on raw demagnetization data and its provenance, and may therefore be more limited in what it allows.
             <ul>
               <p> <b> Features </b>

diff --git a/collection/js/index.js b/collection/js/index.js
@@ -18,8 +18,6 @@ function addMap(specimens) {
   var mapOptions = {
     "minZoom": 1,
     "maxZoom": 13,
-    "maxBounds": new L.latLngBounds(new L.latLng(-90, -180), new L.latLng(90, 180)),
-    "maxBoundsViscosity": 0.5,
     "attributionControl": true
   }
 

diff --git a/css/style.css b/css/style.css
@@ -31,7 +31,10 @@ p {
 
 #wrapper {
   position: relative;
+  width: 80%;
+  margin: auto;
 }
+
 .popover {
   min-width: 25%;
 }

diff --git a/geography/index.html b/geography/index.html
@@ -192,14 +192,24 @@ <h5 class="mb-0">
                               </h5>
                            </div>
                            <div id="collapseOne" class="collapse" aria-labelledby="headingOne" data-parent="#accordion">
-                              <div class="card-body" style='text-align: left;'>
-                                 <div class="form-check text-center">
+                              <div class="card-body" style='text-align: center;'>
+                                 <div class="form-check form-check-inline">
                                     <input class="form-check-input" type="checkbox" value="" id="defaultCheck1" checked>
                                     <label class="form-check-label" for="defaultCheck1">
-                                      Enable grid
+                                      Grid
                                     </label>
                                  </div>
+
+                                 <div class="form-check form-check-inline">
+                                    <input class="form-check-input" type="checkbox" value="" id="enable-satellite">
+                                    <label class="form-check-label" for="enable-satellite">
+                                      Satellite
+                                    </label>
+                                 </div>
+
+                                 <br>
                                  <br>
+
                                  <div class="form-group">
                                     <div class="row">
                                        <div class="col">

diff --git a/geography/js/gplates.js b/geography/js/gplates.js
@@ -99,12 +99,12 @@ function readGPlatesRotation(ID, age) {
   }
 
   // Continue when we are referencing the fixed plate ID
-  while(ID !== "000") {
+  while(parseInt(ID) !== 0) {
 
     var plateData = GPlatesData[ID];
 
     // Search input for matching plateID & age
-    for(var i = 0; i < plateData.length; i++) {
+    for(var i = 1; i < plateData.length; i++) {
 
       if(plateData[i].age < age) {
 

diff --git a/geography/js/index.js b/geography/js/index.js
@@ -18,20 +18,22 @@ function addMap() {
    */
 
   const MAP_CONTAINER = "map";
-  const TILE_LAYER = "https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png";
+  const TILE_LAYER_DEFAULT = "https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png";
+  const TILE_LAYER_ARCGIS = "https://server.arcgisonline.com/ArcGIS/rest/services/World_Imagery/MapServer/tile/{z}/{y}/{x}";
   const VIEWPORT = new L.latLng(35, 0);
 
   // Set map options (bounds)
   var mapOptions = {
     "minZoom": 2,
-    "maxBounds": new L.latLngBounds(new L.latLng(-90, -180), new L.latLng(90, 180)),
-    "maxBoundsViscosity": 0.5,
     "attributionControl": true
   }
 
   // Create the map and tile layer
   map = L.map(MAP_CONTAINER, mapOptions).setView(VIEWPORT, 1);
-  L.tileLayer(TILE_LAYER).addTo(map);
+
+  window.defaultLayer = L.tileLayer(TILE_LAYER_DEFAULT);
+  window.arcgisLayer = L.tileLayer(TILE_LAYER_ARCGIS);
+  toggleSatelliteLayer();
 
   // Reload the map when the tab is focussed on
   $("#nav-apwp-tab").on("shown.bs.tab", map.invalidateSize.bind(map));
@@ -65,10 +67,10 @@ function createGridLayer(map) {
    */
 
   return L.latlngGraticule({
-    "opacity": 0.5,
+    "opacity": 1,
     "color": HIGHCHARTS_WHITE,
-    "fontColor": HIGHCHARTS_BLACK,
-    "font": "12px Helvetica",
+    "fontColor": HIGHCHARTS_WHITE,
+    "font": "12px Sans-Serif",
     "showLabel": true,
     "zoomInterval": [
       {"start": 2, "end": 3, "interval": 30},
@@ -81,6 +83,18 @@ function createGridLayer(map) {
 
 }
 
+function toggleSatelliteLayer() {
+
+  if(document.getElementById("enable-satellite").checked) {
+    map.removeLayer(window.defaultLayer);
+    map.addLayer(window.arcgisLayer);
+  } else {
+    map.removeLayer(window.arcgisLayer);
+    map.addLayer(window.defaultLayer);
+  }
+
+}
+
 function toggleGridLayer() {
 
   /*
@@ -244,6 +258,7 @@ function registerEventHandlers() {
   document.getElementById("cutoff-selection").addEventListener("change", redrawCharts);
   document.addEventListener("keydown", keyboardHandler);
   document.getElementById("defaultCheck1").addEventListener("change", toggleGridLayer);
+  document.getElementById("enable-satellite").addEventListener("change", toggleSatelliteLayer);
   document.getElementById("calculate-reference").addEventListener("click", plotPredictedDirections);
 
   document.getElementById("defer-input").addEventListener("click", inputFileWrapper);

diff --git a/interpretation/index.html b/interpretation/index.html
@@ -125,6 +125,7 @@ <h5> Paleomagnetism.org 2 - Interpretation </h5>
                         <option value="CJONES">PaleoMag (orientation error: don't use)</option>
                         <option value="PALEOMAC">PaleoMac</option>
                         <option value="BCN2G">BCN2G</option>
+                        <option value="RS3">Remasoft</option>
                         <option value="JR5">JR5 (experimental)</option>
                         <option value="JR6">JR6 (experimental)</option>
                      </optgroup>
@@ -190,7 +191,7 @@ <h5> Paleomagnetism.org 2 - Interpretation </h5>
                   <div class="row">
 
                      <!-- Step Controller -->
-                     <div class="col-md-2">
+                     <div class="col-md-12 col-lg-2">
 
                         <!-- Demagnetization Type Selector -->
                         <div style="border: 1px solid lightgrey;" class="btn-group d-flex btn-group-toggle" data-toggle="buttons">
@@ -215,10 +216,10 @@ <h5> Paleomagnetism.org 2 - Interpretation </h5>
                      </div>
 
                      <!-- Zijderveld & Equal Area Plot -->
-                     <div class="col-md-5">
+                     <div class="col-md-12 col-lg-5">
                         <div id="zijderveld-container"></div>
                      </div>
-                     <div class="col-md-5">
+                     <div class="col-md-12 col-lg-5">
                         <div id="hemisphere-container"></div>
                      </div>
 

diff --git a/interpretation/js/graphs.js b/interpretation/js/graphs.js
@@ -108,6 +108,7 @@ function plotIntensityDiagram(hover) {
   var specimen = getSelectedSpecimen();
 
   var intensities = new Array();
+  var categories = new Array();
   var hoverIndex = null;
 
   specimen.steps.forEach(function(step, i) {
@@ -122,11 +123,11 @@ function plotIntensityDiagram(hover) {
       hoverIndex = intensities.length;
     }
 
-    // Get the treatment step as a number
-    var treatmentStep = extractNumbers(step.step);
+    // Use categories to stop mixing AF / TH
+    categories.push(step.step)
 
     intensities.push({
-      "x": treatmentStep,
+      "x": i,
       "y": new Coordinates(step.x, step.y, step.z).length,
       "stepIndex": i
     });
@@ -217,7 +218,7 @@ function plotIntensityDiagram(hover) {
     "zIndex": 0
   });
 
-  createIntensityDiagram(hover, plotSeries);
+  createIntensityDiagram(hover, plotSeries, categories);
 
 }
 
@@ -447,6 +448,7 @@ function plotZijderveldDiagram(hover) {
     "chart": {
     "animation": false,
     "id": "zijderveld-container",
+    "height": 500,
     "zoomType": "xy",
       "events": {
         "load": resetMarkerSize
@@ -833,7 +835,7 @@ function resetMarkerSize() {
 
 }
 
-function createIntensityDiagram(hover, series) {
+function createIntensityDiagram(hover, series, categories) {
 
   /*
    * Function createIntensityDiagram
@@ -894,6 +896,7 @@ function createIntensityDiagram(hover, series) {
       "formatter": intensityTooltip
     },
     "xAxis": {
+      "categories": categories,
       "title": {
         "text": "Demagnetization steps"
       }
@@ -1099,6 +1102,7 @@ function eqAreaProjection(hover) {
   Highcharts.chart(CHART_CONTAINER, {
     "chart": {
       "polar": true,
+      "height": 500,
       "events": {
         "load": resetMarkerSize
       },