imerss-bioinfo 1.3.0 → 1.4.0

package/package.json

@@ -1,7 +1,7 @@
 {
     "name": "imerss-bioinfo",
     "description": "Working data of the IMERSS biodiversity informatics working group, together with algorithms",
-    "version": "1.3.0",
+    "version": "1.4.0",
     "author": "Antranig Basman",
     "scripts": {
         "lint": "fluid-lint-all"

package/src/client/js/checklist.js

@@ -24,7 +24,7 @@ hortis.checklistItem = function (entry, selectedId) {
     const selectedClass = rank === "species" && record.id === selectedId ? " class=\"fl-checklist-selected\"" : "";
     const header = "<li " + selectedClass + ">";
     let name = "<p " + styleprop + rowid + " class=\"flc-checklist-rank-" +
-        rank + "\">" + hortis.encodeHTML(record.iNaturalistTaxonName) + "</p>";
+        rank + "\">" + hortis.encodeHTML(record.taxonName || record.iNaturalistTaxonName) + "</p>";
     if (record.commonName) {
         name += " - <p " + styleprop + rowid + " class=\"flc-checklist-common-name\">" + record.commonName + "</p>";
     }

package/src/client/js/datasetControls.js

@@ -1,5 +1,6 @@
 "use strict";
 
+// noinspection ES6ConvertVarToLetConst // otherwise this is a duplicate on minifying
 var hortis = fluid.registerNamespace("hortis");
 
 // Weird, non-general purpose intersect which modifies target by excluding source
@@ -12,14 +13,14 @@ hortis.intersect = function (target, source) {
 };
 
 hortis.combineDatasets = function (enabledList, quantiserDatasets) {
-    var intersect;
-    var union = {
+    let intersect;
+    const union = {
         obsCount: 0,
         buckets: {},
         byTaxonId: {}
     };
     enabledList.forEach(function (enabled) {
-        var dataset = quantiserDatasets[enabled];
+        const dataset = quantiserDatasets[enabled];
         if (!intersect) {
             intersect = {
                 buckets: fluid.extend({}, dataset.buckets),
@@ -41,7 +42,7 @@ hortis.combineDatasets = function (enabledList, quantiserDatasets) {
 
 hortis.renderDatasetControls = function (datasetEnabled, squareSide, datasets, quantiser, indexVersion) {
     console.log("renderDatasetControls executing for indexVersion " + indexVersion);
-    var togo = [{
+    const togo = [{
         type: "hortis.datasetControlHeader"
     }];
 
@@ -53,9 +54,9 @@ hortis.renderDatasetControls = function (datasetEnabled, squareSide, datasets, q
             quantiserDataset: quantiser.datasets[datasetId]
         });
     });
-    var enabledList = fluid.transforms.setMembershipToArray(datasetEnabled);
+    const enabledList = fluid.transforms.setMembershipToArray(datasetEnabled);
 
-    var createFooter = function (prefix, dataset) {
+    const createFooter = function (prefix, dataset) {
         if (prefix) {
             hortis.quantiser.datasetToSummary(dataset, squareSide);
             dataset.obsCount = (prefix === "Union" ? dataset.obsCount : "");
@@ -68,7 +69,7 @@ hortis.renderDatasetControls = function (datasetEnabled, squareSide, datasets, q
         }, dataset));
     };
     if (enabledList.length > 1 && Object.keys(quantiser.datasets).length > 0) { // TODO: Ensure that relay pulls quantiser on startup!
-        var combinedDatasets = hortis.combineDatasets(enabledList, quantiser.datasets);
+        const combinedDatasets = hortis.combineDatasets(enabledList, quantiser.datasets);
         createFooter("Intersection", combinedDatasets.intersect);
         createFooter("Union", combinedDatasets.union);
     } else {
@@ -193,7 +194,7 @@ hortis.datasetControl.columnNames = {
 };
 
 hortis.datasetControl.renderExtraColumns = function (markup, isHeader, dataset, quantiserDataset) {
-    var extraColumns = fluid.transform(hortis.datasetControl.columnNames, function (columnInfo, key) {
+    const extraColumns = fluid.transform(hortis.datasetControl.columnNames, function (columnInfo, key) {
         return fluid.stringTemplate(markup, {
             columnClass: columnInfo.clazz,
             text: isHeader ? columnInfo.name : quantiserDataset[key]
@@ -204,8 +205,8 @@ hortis.datasetControl.renderExtraColumns = function (markup, isHeader, dataset,
 
 hortis.datasetControl.renderMarkup = function (markup, isHeader, dataset, quantiserDatasets, datasetId) {
     // Whilst we believe we have stuck this into the "source" model, it never actually arrives in the parent relay before rendering starts
-    var quantiserDataset = quantiserDatasets && quantiserDatasets[datasetId];
-    var extraColumns = hortis.datasetControl.renderExtraColumns(markup.cell, isHeader, dataset, quantiserDataset);
+    const quantiserDataset = quantiserDatasets && quantiserDatasets[datasetId];
+    const extraColumns = hortis.datasetControl.renderExtraColumns(markup.cell, isHeader, dataset, quantiserDataset);
     return fluid.stringTemplate(markup.container, {
         extraColumns: extraColumns
     });

package/src/client/js/imerss-viz.js

@@ -695,7 +695,7 @@ hortis.renderTaxonDisplay = function (row, markup, options) {
         if (row.phyloPicUrl) {
             dumpPhyloPic("phyloPic", row.phyloPicUrl);
         }
-        dumpRow(row.rank, row.iNaturalistTaxonName, "fl-taxonDisplay-rank");
+        dumpRow(row.rank, row.taxonName || row.iNaturalistTaxonName, "fl-taxonDisplay-rank");
         hortis.commonFields.forEach(function (field) {
             dumpRow(field, row[field]);
         });
@@ -709,9 +709,9 @@ hortis.renderTaxonDisplay = function (row, markup, options) {
         if (row.species) {
             // Used to read:
             // dumpRow("Species:", row.species + (row.authority ? (" " + row.authority) : ""), "fl-taxonDisplay-rank");
-            // "species" now just holdes raw species name. In the long term we should support our own normalised species name
+            // "species" now just holds raw species name. In the long term we should support our own normalised species name
             // composed of taxon and infrataxon name but this is at least now complete and agrees with what is shown in the tooltip
-            dumpRow("iNaturalistTaxonName", row.iNaturalistTaxonName + (row.authority ? (" " + row.authority) : ""), "fl-taxonDisplay-rank", options);
+            dumpRow("iNaturalistTaxonName", (row.taxonName || row.iNaturalistTaxonName) + (row.authority ? (" " + row.authority) : ""), "fl-taxonDisplay-rank", options);
         }
         if (row.hulqName) { // wot no polymorphism?
             togo += hortis.dumpHulqName(row, markup);
@@ -793,7 +793,7 @@ hortis.renderTooltip = function (row) {
     } else {
         terms.taxonRank = "Species";
     }
-    const names = [row.iNaturalistTaxonName, row.commonName, row.hulqName].filter(name => name);
+    const names = [(row.taxonName || row.iNaturalistTaxonName), row.commonName, row.hulqName].filter(name => name);
     terms.taxonNames = names.join(" / ");
     return fluid.stringTemplate(hortis.tooltipTemplate, terms);
 };

package/src/client/js/leafletMap.js

@@ -62,7 +62,8 @@ fluid.defaults("hortis.leafletMap", {
         "buildMap.addTiles": "hortis.leafletMap.addTileLayer({that}.map, {that}.options.tileOptions)",
         "clearMapSelection.mapBlock": {
             changePath: "mapBlockTooltipId",
-            value: null
+            value: null,
+            source: "{arguments}.0"
         }
     },
     invokers: {

package/src/client/js/leafletMapWithBareRegions.js

@@ -31,9 +31,9 @@ fluid.defaults("hortis.leafletMap.withRegionsBase", {
         regions: "{sunburst}.viz.classes"
     },
     listeners: {
-        "clearMapSelection.regions": "hortis.clearSelectedRegions({that})",
-        //                                                                          class,       community
-        "selectRegion.regionSelection": "hortis.leafletMap.regionSelection({that}, {arguments}.0, {arguments}.1)",
+        "clearMapSelection.regions": "hortis.clearSelectedRegions({that}, {arguments}.0)",
+        //                                                                          class,       community,      source
+        "selectRegion.regionSelection": "hortis.leafletMap.regionSelection({that}, {arguments}.0, {arguments}.1, {arguments}.2)"
     }
 });
 
@@ -93,14 +93,15 @@ hortis.leafletMap.selectedRegions = function (selectedRegion, regions) {
 };
 
 // TODO: This gets preserved but we need to split off the outerPanel update
-hortis.leafletMap.regionSelection = function (map, className, community) {
-    map.applier.change("mapBlockTooltipId", community);
-    map.applier.change("selectedRegions", hortis.leafletMap.selectedRegions(className, map.classes));
-    map.applier.change("selectedCommunities", hortis.leafletMap.selectedRegions(community, map.communities));
+hortis.leafletMap.regionSelection = function (map, className, community, source) {
+    map.applier.change("mapBlockTooltipId", community, "ADD", source);
+    map.applier.change("selectedRegions", hortis.leafletMap.selectedRegions(className, map.classes), "ADD", source);
+    map.applier.change("selectedCommunities", hortis.leafletMap.selectedRegions(community, map.communities), "ADD", source);
 
 };
 
-hortis.clearSelectedRegions = function (map) {
-    map.applier.change("selectedRegions", hortis.leafletMap.selectedRegions(null, map.classes));
-    map.applier.change("selectedCommunities", hortis.leafletMap.selectedRegions(null, map.communities));
+hortis.clearSelectedRegions = function (map, source) {
+    // mapBlockTooltipId is cleared in LeafletMap
+    map.applier.change("selectedRegions", hortis.leafletMap.selectedRegions(null, map.classes), "ADD", source);
+    map.applier.change("selectedCommunities", hortis.leafletMap.selectedRegions(null, map.communities), "ADD", source);
 };

package/src/descrolly.js

@@ -11,6 +11,7 @@ require("./dataProcessing/readJSON.js");
 require("./dataProcessing/writeJSON.js");
 require("./dataProcessing/readCSV.js");
 require("./dataProcessing/readCSVWithMap.js");
+require("./client/js/colour.js");
 
 require("./iNaturalist/taxonAPI.js");
 
@@ -48,8 +49,10 @@ hortis.descrolly = async function (config) {
         classes: {}
     };
 
-    await hortis.asyncForEach(scrollyInput.MAP_LABEL, async function (label, index) {
-        const taxaString = scrollyInput.taxa[index];
+    const scrollyInputTaxa = scrollyInput.taxa;
+
+    await hortis.asyncForEach(scrollyInputTaxa.MAP_LABEL, async function (label, index) {
+        const taxaString = scrollyInputTaxa.taxa[index];
         const taxa = taxaString.split(",").map(fluid.trim);
         console.log("Found " + taxa.length + " taxa for key " + label);
         const byTaxonId = {};
@@ -67,10 +70,13 @@ hortis.descrolly = async function (config) {
             } else {
                 console.log("Failed to look up taxon " + san);
             }
-            scrollyFeatures.classes[label] = {byTaxonId};
+            const fillColor = fluid.colour.hexToArray(scrollyInput.palette.col[index]);
+            scrollyFeatures.classes[label] = {byTaxonId, fillColor};
         });
     });
 
+
+
     hortis.writeJSONSync(fluid.module.resolvePath(config.scrollyFeatures), scrollyFeatures);
 };
 

package/src/marmalise.js

@@ -281,7 +281,7 @@ hortis.indexScrollyRegions = function (treeBuilder) {
             const row = summaryById[key];
             byTaxonId[row.id] = true;
         });
-        return {byTaxonId};
+        return {byTaxonId, fillColor: clazz.fillColor};
     });
     return {
         communities: newClasses,

package/src/taxonomise.js

@@ -62,7 +62,8 @@ hortis.baseCommonOutMap = fluid.freezeRecursive({
     "columns": {
         "iNaturalistTaxonName": "iNaturalist taxon name",
         "iNaturalistTaxonId": "iNaturalist taxon ID",
-        "taxonName": "Taxon name"
+        "taxonName": "Taxon name",
+        "authority": "Author" // TODO: Make this conditional on whether it is present in input?
     }
 });