imerss-bioinfo 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +156 -0
- package/build.js +196 -0
- package/docs/css/imerss-viz-all.css +1227 -0
- package/docs/css/imerss-viz-wp-overrides.css +70 -0
- package/docs/css/pepiowelh.css +76 -0
- package/docs/css/xetthecum-external.css +47 -0
- package/docs/css/xetthecum-shared.css +80 -0
- package/docs/css/xetthecum.css +526 -0
- package/docs/js/imerss-viz-all.js +58 -0
- package/docs/js/imerss-viz-all.js.map +1 -0
- package/docs/js/jquery.js +10881 -0
- package/index.html +81 -0
- package/index.js +7 -0
- package/indexWithJustMap.html +92 -0
- package/indexWithMap.html +79 -0
- package/indexWithMapHoweSound.html +91 -0
- package/indexWithMapPepiowelh.html +119 -0
- package/indexWithMapValdes.html +90 -0
- package/indexWithMapXetthecum.html +90 -0
- package/package.json +50 -0
- package/src/WoRMS/taxonAPI.js +13 -0
- package/src/arphify.js +662 -0
- package/src/assignNames.js +103 -0
- package/src/auxBuild/restoreJQuery.js +1 -0
- package/src/buildSource/Comprehensive Lists.html +42 -0
- package/src/buildSource/Data Paper Part I Visualisation.html +50 -0
- package/src/buildSource/Galiano Life List.html +43 -0
- package/src/buildSource/Metchosin/index.html +22 -0
- package/src/buildSource/Pe'pi'ow'elh.html +72 -0
- package/src/buildSource/Squamish Life List.html +48 -0
- package/src/buildSource/Valdes Island Biodiversity.html +64 -0
- package/src/buildSource/Xetthecum.html +40 -0
- package/src/buildSource/dataPaperSunburstAndMap.html +30 -0
- package/src/buildSource/index.html +224 -0
- package/src/client/css/imerss-viz-wp-overrides.css +70 -0
- package/src/client/css/imerss-viz.css +531 -0
- package/src/client/css/pepiowelh.css +76 -0
- package/src/client/css/xetthecum-external.css +47 -0
- package/src/client/css/xetthecum-shared.css +80 -0
- package/src/client/css/xetthecum.css +526 -0
- package/src/client/html/imerss-viz-map-only.html +75 -0
- package/src/client/html/imerss-viz-map-pepi.html +77 -0
- package/src/client/html/imerss-viz-map-xetthecum.html +90 -0
- package/src/client/html/imerss-viz-map.html +75 -0
- package/src/client/html/imerss-viz.html +58 -0
- package/src/client/html/importing Xetthecum patterns.txt +10 -0
- package/src/client/html/xetthecum-patterns.html +27 -0
- package/src/client/img/Animalia_2.svg +1 -0
- package/src/client/img/Animalia_Annelida.svg +655 -0
- package/src/client/img/Animalia_Chaetognatha.svg +72 -0
- package/src/client/img/Animalia_Cnidaria.svg +173 -0
- package/src/client/img/Animalia_Ctenophora.svg +298 -0
- package/src/client/img/Animalia_Nemertea.svg +54 -0
- package/src/client/img/Animalia_Phoronida.svg +271 -0
- package/src/client/img/Animalia_Platyhelminthes.svg +58 -0
- package/src/client/img/Animalia_Porifera.svg +220 -0
- package/src/client/img/Animalia_Sipuncula.svg +155 -0
- package/src/client/img/Arachnoidiscus_schmidtii_web_1-2-scaled.webp +0 -0
- package/src/client/img/Arrow-down.svg +11 -0
- package/src/client/img/Arrow-up.svg +6 -0
- package/src/client/img/Chromista.svg +1 -0
- package/src/client/img/Pepiowelh/BlackNoWe2-wb-bb.png +0 -0
- package/src/client/img/Pepiowelh/BlackNoWe2-wb.png +0 -0
- package/src/client/img/Pepiowelh/BlackNoWe2.png +0 -0
- package/src/client/img/Pepiowelh/Ecocultural Mapping Banner.svg +1 -0
- package/src/client/img/Plankton.jpg +0 -0
- package/src/client/img/Plantae.svg +1 -0
- package/src/client/img/Plantae_2.svg +1 -0
- package/src/client/img/Protista.svg +1 -0
- package/src/client/img/Valdes/Valdes Island Conservancy.jpg +0 -0
- package/src/client/img/Xetthecum/Agricultural.jpg +0 -0
- package/src/client/img/Xetthecum/Anthropogenic_banner.jpg +0 -0
- package/src/client/img/Xetthecum/Broad_Leaf.jpg +0 -0
- package/src/client/img/Xetthecum/Caves.jpg +0 -0
- package/src/client/img/Xetthecum/Coastal_Bluffs.jpg +0 -0
- package/src/client/img/Xetthecum/Conifer_Pole_Sapling.jpg +0 -0
- package/src/client/img/Xetthecum/Developed.jpg +0 -0
- package/src/client/img/Xetthecum/Dock.jpg +0 -0
- package/src/client/img/Xetthecum/Eelgrass.jpg +0 -0
- package/src/client/img/Xetthecum/Forests_banner.jpg +0 -0
- package/src/client/img/Xetthecum/Freshwater_banner.jpg +0 -0
- package/src/client/img/Xetthecum/Greig_Creek.jpg +0 -0
- package/src/client/img/Xetthecum/Intertidal.jpg +0 -0
- package/src/client/img/Xetthecum/Laughlin_Lake.jpg +0 -0
- package/src/client/img/Xetthecum/Marine_banner.jpg +0 -0
- package/src/client/img/Xetthecum/Mature_Conifer_Forest.jpg +0 -0
- package/src/client/img/Xetthecum/Porlier_Pass_Road.jpg +0 -0
- package/src/client/img/Xetthecum/Riparian.jpg +0 -0
- package/src/client/img/Xetthecum/Rural.jpg +0 -0
- package/src/client/img/Xetthecum/Subtidal.jpg +0 -0
- package/src/client/img/Xetthecum/Wetland.jpg +0 -0
- package/src/client/img/Xetthecum/Woodland.jpg +0 -0
- package/src/client/img/Xetthecum/Woodland_banner.jpg +0 -0
- package/src/client/img/Xetthecum/Xetthecum.jpg +0 -0
- package/src/client/img/Xetthecum/Young_Conifer_Forest.jpg +0 -0
- package/src/client/img/Xetthecum/Young_Mixed_Forest.jpg +0 -0
- package/src/client/img/Xetthecum/food.svg +38 -0
- package/src/client/img/Xetthecum/indicator.svg +52 -0
- package/src/client/img/Xetthecum/material.svg +186 -0
- package/src/client/img/Xetthecum/medicinal.svg +62 -0
- package/src/client/img/Xetthecum/missing-value.svg +3 -0
- package/src/client/img/Xetthecum/spiritual.svg +13 -0
- package/src/client/img/Xetthecum/trade.svg +74 -0
- package/src/client/img/audio.svg +5 -0
- package/src/client/img/external-link.svg +3 -0
- package/src/client/img/selected-eye.svg +4 -0
- package/src/client/img/selected-tick.svg +3 -0
- package/src/client/img/thumbs/BCLeps.jpg +0 -0
- package/src/client/img/thumbs/Checklist.jpg +0 -0
- package/src/client/img/thumbs/Data-Paper-Figma.jpg +0 -0
- package/src/client/img/thumbs/Galiano-Data-Paper.jpg +0 -0
- package/src/client/img/thumbs/Galiano.jpg +0 -0
- package/src/client/img/thumbs/Maxwell.jpg +0 -0
- package/src/client/img/thumbs/Squamish.jpg +0 -0
- package/src/client/img/thumbs/Valdes.jpg +0 -0
- package/src/client/img/thumbs/Xetthecum.jpg +0 -0
- package/src/client/img/up-arrow.svg +4 -0
- package/src/client/js/autocomplete.js +53 -0
- package/src/client/js/checklist.js +179 -0
- package/src/client/js/colour.js +139 -0
- package/src/client/js/datasetControls.js +212 -0
- package/src/client/js/imerss-viz.js +1397 -0
- package/src/client/js/leafletMap.js +357 -0
- package/src/client/js/leafletMapWithGrid.js +337 -0
- package/src/client/js/leafletMapWithRegions.js +381 -0
- package/src/client/js/renderSVG.js +108 -0
- package/src/client/js/tabs.js +53 -0
- package/src/client/js/xetthecum.js +106 -0
- package/src/client/json/emptyPhyloMap.json +1 -0
- package/src/client/json/kingdomPhyloMap.json +17 -0
- package/src/client/json/phyloMap.json +58 -0
- package/src/compare.js +97 -0
- package/src/compilecsv.js +47 -0
- package/src/dataProcessing/LZ4.js +27 -0
- package/src/dataProcessing/coordinatePatch.js +151 -0
- package/src/dataProcessing/readCSV.js +107 -0
- package/src/dataProcessing/readCSVwithMap.js +90 -0
- package/src/dataProcessing/readCSVwithoutMap.js +25 -0
- package/src/dataProcessing/readJSON.js +23 -0
- package/src/dataProcessing/sqlite.js +174 -0
- package/src/dataProcessing/summarise.js +122 -0
- package/src/dataProcessing/taxonScrape.js +14 -0
- package/src/dataProcessing/worker.js +31 -0
- package/src/dataProcessing/writeCSV.js +34 -0
- package/src/dataProcessing/writeJSON.js +15 -0
- package/src/dbtaxa.js +96 -0
- package/src/deAuthorise.js +48 -0
- package/src/deqgis.js +148 -0
- package/src/expressions/expr.js +65 -0
- package/src/expressions/jsep.js +925 -0
- package/src/filterFirst.js +51 -0
- package/src/geom/geoJSON.js +121 -0
- package/src/iNaturalist/examples/api.inaturalist.org-v1-taxa!q=Acmispon americanus americanus.json +200 -0
- package/src/iNaturalist/examples/api.inaturalist.org-v1-taxa!q=Flabellina japonica.json +61 -0
- package/src/iNaturalist/examples/www.inaturalist.org-taxa-877359.json +132 -0
- package/src/iNaturalist/iNatUrls.js +17 -0
- package/src/iNaturalist/obsAPI.js +150 -0
- package/src/iNaturalist/taxonAPI.js +460 -0
- package/src/inatObs.js +120 -0
- package/src/inattify.js +123 -0
- package/src/intersect.js +80 -0
- package/src/intersectFilter.js +48 -0
- package/src/landlocked.js +137 -0
- package/src/lib/jquery.binarytransport.js +51 -0
- package/src/lib/lz4-commentary.txt +9 -0
- package/src/lib/lz4.js +73 -0
- package/src/lib/point-in-polygon.js +36 -0
- package/src/lz4.js +40 -0
- package/src/marmalise.js +333 -0
- package/src/materialise.js +68 -0
- package/src/reintegrate.js +71 -0
- package/src/taxonomise.js +615 -0
- package/src/unscrewGBIF.js +44 -0
- package/src/utils/dataSource.js +173 -0
- package/src/utils/settleStructure.js +62 -0
- package/src/utils/utils.js +92 -0
- package/src/viz/plethify.js +39 -0
- package/src/wormify.js +154 -0
- package/src/xetthecum/xetthecumFilters.js +126 -0
- package/test/testDataSource.js +182 -0
- package/test/testiNatObsSource.js +38 -0
- package/test/testiNatSource.js +50 -0
|
@@ -0,0 +1,65 @@
|
|
|
1
|
+
/* eslint-env node */
|
|
2
|
+
|
|
3
|
+
"use strict";
|
|
4
|
+
|
|
5
|
+
const fluid = require("infusion");
|
|
6
|
+
|
|
7
|
+
const Jsep = require("./jsep.js");
|
|
8
|
+
|
|
9
|
+
const hortis = fluid.registerNamespace("hortis");
|
|
10
|
+
|
|
11
|
+
fluid.registerNamespace("hortis.expr");
|
|
12
|
+
|
|
13
|
+
hortis.expr.binops = {
|
|
14
|
+
"+" : function (a, b) { return a + b; },
|
|
15
|
+
"-" : function (a, b) { return a - b; },
|
|
16
|
+
"*" : function (a, b) { return a * b; },
|
|
17
|
+
"/" : function (a, b) { return a / b; },
|
|
18
|
+
"==" : function (a, b) { return a === b; },
|
|
19
|
+
"===" : function (a, b) { return a === b; },
|
|
20
|
+
"!=" : function (a, b) { return a !== b; },
|
|
21
|
+
"!==" : function (a, b) { return a !== b; },
|
|
22
|
+
"||" : function (a, b) { return a || b; },
|
|
23
|
+
"&&" : function (a, b) { return a && b; },
|
|
24
|
+
"%" : function (a, b) { return a % b; }
|
|
25
|
+
};
|
|
26
|
+
|
|
27
|
+
hortis.expr.evaluate = function (node, scope) {
|
|
28
|
+
if (node.type === "Literal") {
|
|
29
|
+
return node.value;
|
|
30
|
+
} else if (node.type === "Identifier") {
|
|
31
|
+
if (node.name in scope) {
|
|
32
|
+
return scope[node.name];
|
|
33
|
+
} else {
|
|
34
|
+
fluid.fail("Name " + node.name + " is not found in scope - possible values are " + Object.keys(scope).join(", "));
|
|
35
|
+
}
|
|
36
|
+
} else if (node.type === "BinaryExpression") {
|
|
37
|
+
const opfunc = hortis.expr.binops[node.operator];
|
|
38
|
+
if (!opfunc) {
|
|
39
|
+
fluid.fail("Unknown binary operator " + node.operator + " - possible values are " + Object.keys(hortis.expr.binops).join(", "));
|
|
40
|
+
}
|
|
41
|
+
const left = hortis.expr.evaluate(node.left, scope);
|
|
42
|
+
const right = hortis.expr.evaluate(node.right, scope);
|
|
43
|
+
return opfunc(left, right);
|
|
44
|
+
} else {
|
|
45
|
+
fluid.fail("Unknown node type " + node.type);
|
|
46
|
+
}
|
|
47
|
+
};
|
|
48
|
+
|
|
49
|
+
hortis.expr.parse = function (expr) {
|
|
50
|
+
return new Jsep(expr).parse();
|
|
51
|
+
};
|
|
52
|
+
|
|
53
|
+
/*
|
|
54
|
+
var expr = "genus === \"Rabeleria\"";
|
|
55
|
+
|
|
56
|
+
var parsed = jsep(expr);
|
|
57
|
+
|
|
58
|
+
console.log(parsed);
|
|
59
|
+
|
|
60
|
+
var evaluated = hortis.expr.evaluate(parsed, {
|
|
61
|
+
genus: "Rabeleria"
|
|
62
|
+
});
|
|
63
|
+
|
|
64
|
+
console.log("Evaluted to " + evaluated);
|
|
65
|
+
*/
|