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.
Files changed (182) hide show
  1. package/README.md +156 -0
  2. package/build.js +196 -0
  3. package/docs/css/imerss-viz-all.css +1227 -0
  4. package/docs/css/imerss-viz-wp-overrides.css +70 -0
  5. package/docs/css/pepiowelh.css +76 -0
  6. package/docs/css/xetthecum-external.css +47 -0
  7. package/docs/css/xetthecum-shared.css +80 -0
  8. package/docs/css/xetthecum.css +526 -0
  9. package/docs/js/imerss-viz-all.js +58 -0
  10. package/docs/js/imerss-viz-all.js.map +1 -0
  11. package/docs/js/jquery.js +10881 -0
  12. package/index.html +81 -0
  13. package/index.js +7 -0
  14. package/indexWithJustMap.html +92 -0
  15. package/indexWithMap.html +79 -0
  16. package/indexWithMapHoweSound.html +91 -0
  17. package/indexWithMapPepiowelh.html +119 -0
  18. package/indexWithMapValdes.html +90 -0
  19. package/indexWithMapXetthecum.html +90 -0
  20. package/package.json +50 -0
  21. package/src/WoRMS/taxonAPI.js +13 -0
  22. package/src/arphify.js +662 -0
  23. package/src/assignNames.js +103 -0
  24. package/src/auxBuild/restoreJQuery.js +1 -0
  25. package/src/buildSource/Comprehensive Lists.html +42 -0
  26. package/src/buildSource/Data Paper Part I Visualisation.html +50 -0
  27. package/src/buildSource/Galiano Life List.html +43 -0
  28. package/src/buildSource/Metchosin/index.html +22 -0
  29. package/src/buildSource/Pe'pi'ow'elh.html +72 -0
  30. package/src/buildSource/Squamish Life List.html +48 -0
  31. package/src/buildSource/Valdes Island Biodiversity.html +64 -0
  32. package/src/buildSource/Xetthecum.html +40 -0
  33. package/src/buildSource/dataPaperSunburstAndMap.html +30 -0
  34. package/src/buildSource/index.html +224 -0
  35. package/src/client/css/imerss-viz-wp-overrides.css +70 -0
  36. package/src/client/css/imerss-viz.css +531 -0
  37. package/src/client/css/pepiowelh.css +76 -0
  38. package/src/client/css/xetthecum-external.css +47 -0
  39. package/src/client/css/xetthecum-shared.css +80 -0
  40. package/src/client/css/xetthecum.css +526 -0
  41. package/src/client/html/imerss-viz-map-only.html +75 -0
  42. package/src/client/html/imerss-viz-map-pepi.html +77 -0
  43. package/src/client/html/imerss-viz-map-xetthecum.html +90 -0
  44. package/src/client/html/imerss-viz-map.html +75 -0
  45. package/src/client/html/imerss-viz.html +58 -0
  46. package/src/client/html/importing Xetthecum patterns.txt +10 -0
  47. package/src/client/html/xetthecum-patterns.html +27 -0
  48. package/src/client/img/Animalia_2.svg +1 -0
  49. package/src/client/img/Animalia_Annelida.svg +655 -0
  50. package/src/client/img/Animalia_Chaetognatha.svg +72 -0
  51. package/src/client/img/Animalia_Cnidaria.svg +173 -0
  52. package/src/client/img/Animalia_Ctenophora.svg +298 -0
  53. package/src/client/img/Animalia_Nemertea.svg +54 -0
  54. package/src/client/img/Animalia_Phoronida.svg +271 -0
  55. package/src/client/img/Animalia_Platyhelminthes.svg +58 -0
  56. package/src/client/img/Animalia_Porifera.svg +220 -0
  57. package/src/client/img/Animalia_Sipuncula.svg +155 -0
  58. package/src/client/img/Arachnoidiscus_schmidtii_web_1-2-scaled.webp +0 -0
  59. package/src/client/img/Arrow-down.svg +11 -0
  60. package/src/client/img/Arrow-up.svg +6 -0
  61. package/src/client/img/Chromista.svg +1 -0
  62. package/src/client/img/Pepiowelh/BlackNoWe2-wb-bb.png +0 -0
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  70. package/src/client/img/Valdes/Valdes Island Conservancy.jpg +0 -0
  71. package/src/client/img/Xetthecum/Agricultural.jpg +0 -0
  72. package/src/client/img/Xetthecum/Anthropogenic_banner.jpg +0 -0
  73. package/src/client/img/Xetthecum/Broad_Leaf.jpg +0 -0
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  76. package/src/client/img/Xetthecum/Conifer_Pole_Sapling.jpg +0 -0
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  80. package/src/client/img/Xetthecum/Forests_banner.jpg +0 -0
  81. package/src/client/img/Xetthecum/Freshwater_banner.jpg +0 -0
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  97. package/src/client/img/Xetthecum/food.svg +38 -0
  98. package/src/client/img/Xetthecum/indicator.svg +52 -0
  99. package/src/client/img/Xetthecum/material.svg +186 -0
  100. package/src/client/img/Xetthecum/medicinal.svg +62 -0
  101. package/src/client/img/Xetthecum/missing-value.svg +3 -0
  102. package/src/client/img/Xetthecum/spiritual.svg +13 -0
  103. package/src/client/img/Xetthecum/trade.svg +74 -0
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  107. package/src/client/img/selected-tick.svg +3 -0
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  109. package/src/client/img/thumbs/Checklist.jpg +0 -0
  110. package/src/client/img/thumbs/Data-Paper-Figma.jpg +0 -0
  111. package/src/client/img/thumbs/Galiano-Data-Paper.jpg +0 -0
  112. package/src/client/img/thumbs/Galiano.jpg +0 -0
  113. package/src/client/img/thumbs/Maxwell.jpg +0 -0
  114. package/src/client/img/thumbs/Squamish.jpg +0 -0
  115. package/src/client/img/thumbs/Valdes.jpg +0 -0
  116. package/src/client/img/thumbs/Xetthecum.jpg +0 -0
  117. package/src/client/img/up-arrow.svg +4 -0
  118. package/src/client/js/autocomplete.js +53 -0
  119. package/src/client/js/checklist.js +179 -0
  120. package/src/client/js/colour.js +139 -0
  121. package/src/client/js/datasetControls.js +212 -0
  122. package/src/client/js/imerss-viz.js +1397 -0
  123. package/src/client/js/leafletMap.js +357 -0
  124. package/src/client/js/leafletMapWithGrid.js +337 -0
  125. package/src/client/js/leafletMapWithRegions.js +381 -0
  126. package/src/client/js/renderSVG.js +108 -0
  127. package/src/client/js/tabs.js +53 -0
  128. package/src/client/js/xetthecum.js +106 -0
  129. package/src/client/json/emptyPhyloMap.json +1 -0
  130. package/src/client/json/kingdomPhyloMap.json +17 -0
  131. package/src/client/json/phyloMap.json +58 -0
  132. package/src/compare.js +97 -0
  133. package/src/compilecsv.js +47 -0
  134. package/src/dataProcessing/LZ4.js +27 -0
  135. package/src/dataProcessing/coordinatePatch.js +151 -0
  136. package/src/dataProcessing/readCSV.js +107 -0
  137. package/src/dataProcessing/readCSVwithMap.js +90 -0
  138. package/src/dataProcessing/readCSVwithoutMap.js +25 -0
  139. package/src/dataProcessing/readJSON.js +23 -0
  140. package/src/dataProcessing/sqlite.js +174 -0
  141. package/src/dataProcessing/summarise.js +122 -0
  142. package/src/dataProcessing/taxonScrape.js +14 -0
  143. package/src/dataProcessing/worker.js +31 -0
  144. package/src/dataProcessing/writeCSV.js +34 -0
  145. package/src/dataProcessing/writeJSON.js +15 -0
  146. package/src/dbtaxa.js +96 -0
  147. package/src/deAuthorise.js +48 -0
  148. package/src/deqgis.js +148 -0
  149. package/src/expressions/expr.js +65 -0
  150. package/src/expressions/jsep.js +925 -0
  151. package/src/filterFirst.js +51 -0
  152. package/src/geom/geoJSON.js +121 -0
  153. package/src/iNaturalist/examples/api.inaturalist.org-v1-taxa!q=Acmispon americanus americanus.json +200 -0
  154. package/src/iNaturalist/examples/api.inaturalist.org-v1-taxa!q=Flabellina japonica.json +61 -0
  155. package/src/iNaturalist/examples/www.inaturalist.org-taxa-877359.json +132 -0
  156. package/src/iNaturalist/iNatUrls.js +17 -0
  157. package/src/iNaturalist/obsAPI.js +150 -0
  158. package/src/iNaturalist/taxonAPI.js +460 -0
  159. package/src/inatObs.js +120 -0
  160. package/src/inattify.js +123 -0
  161. package/src/intersect.js +80 -0
  162. package/src/intersectFilter.js +48 -0
  163. package/src/landlocked.js +137 -0
  164. package/src/lib/jquery.binarytransport.js +51 -0
  165. package/src/lib/lz4-commentary.txt +9 -0
  166. package/src/lib/lz4.js +73 -0
  167. package/src/lib/point-in-polygon.js +36 -0
  168. package/src/lz4.js +40 -0
  169. package/src/marmalise.js +333 -0
  170. package/src/materialise.js +68 -0
  171. package/src/reintegrate.js +71 -0
  172. package/src/taxonomise.js +615 -0
  173. package/src/unscrewGBIF.js +44 -0
  174. package/src/utils/dataSource.js +173 -0
  175. package/src/utils/settleStructure.js +62 -0
  176. package/src/utils/utils.js +92 -0
  177. package/src/viz/plethify.js +39 -0
  178. package/src/wormify.js +154 -0
  179. package/src/xetthecum/xetthecumFilters.js +126 -0
  180. package/test/testDataSource.js +182 -0
  181. package/test/testiNatObsSource.js +38 -0
  182. package/test/testiNatSource.js +50 -0
package/indexWithMapXetthecum.html ADDED
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+ <link rel="stylesheet" href="node_modules/jquery-ui/themes/base/tabs.css" />
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+ <link rel="stylesheet" type="text/css" href="node_modules/infusion/src/framework/core/css/fluid.css" />
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+ <link rel="stylesheet" type="text/css" href="node_modules/accessible-autocomplete/dist/accessible-autocomplete.min.css" />
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+ <script src="node_modules/infusion/src/lib/jquery/core/js/jquery.js"></script>
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+ <script src="node_modules/infusion/src/lib/jquery/ui/js/version.js"></script>
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+ <script src="node_modules/infusion/src/lib/jquery/ui/js/keycode.js"></script>
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+ <script src="node_modules/jquery-ui/ui/widget.js"></script>
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+ <script src="node_modules/jquery-ui/ui/unique-id.js"></script>
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+ <script src="node_modules/jquery-ui/ui/position.js"></script>
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+ <script src="node_modules/jquery-ui/ui/widgets/tabs.js"></script>
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+ <script src="node_modules/jquery-ui/ui/widgets/tooltip.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/jquery.keyboard-a11y.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/DataBinding.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/ModelTransformation.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/ModelTransformationTransforms.js"></script>
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+ <script src="node_modules/infusion/src/framework/enhancement/js/ProgressiveEnhancement.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/FluidView-browser.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/NewViewSupport.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/DataSource.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/ResourceLoader.js"></script>
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+ <script src="node_modules/infusion/src/framework/core/js/ResourceLoader-browser.js"></script>
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+ <script src="node_modules/accessible-autocomplete/dist/accessible-autocomplete.min.js"></script>
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+ <script src="data/Galiano/Galiano_map_0.js"></script>
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+ <script src="https://unpkg.com/leaflet@1.6.0/dist/leaflet.js"></script>
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+ <script src="src/lib/lz4.js"></script>
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+ <script src="src/lib/jquery.binarytransport.js"></script>
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+
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+ <link rel="stylesheet" type="text/css" href="src/client/css/imerss-viz.css"/>
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+ <link rel="stylesheet" type="text/css" href="src/client/css/xetthecum.css"/>
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+
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+ <script src="src/client/js/colour.js"></script>
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+ <script src="src/client/js/renderSVG.js"></script>
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+ <script src="src/client/js/imerss-viz.js"></script>
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+ <script src="src/client/js/leafletMap.js"></script>
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+ <script src="src/client/js/datasetControls.js"></script>
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+ <script src="src/client/js/leafletMapWithGrid.js"></script>
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+ <script src="src/client/js/leafletMapWithRegions.js"></script>
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+ <script src="src/client/js/autocomplete.js"></script>
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+ <script src="src/client/js/tabs.js"></script>
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+ <script src="src/client/js/checklist.js"></script>
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+ <script src="src/client/js/xetthecum.js"></script>
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+
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+ <style>
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+ body {
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+ font-family: Arial, Helvetica, sans-serif;
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+ }
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+ </style>
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+
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+ <title>Xetthecum Map View</title>
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+ </head>
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+
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+ <body>
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+ <h2 class="fl-xetthecum-banner">Xetthecum</h2>
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+ <div class="fl-imerss-container">
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+ </div>
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+ <script>
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+ hortis.sunburstLoaderWithMap(".fl-imerss-container", {
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+ gradeNames: ["hortis.svgPatternLoader", "hortis.xetthecumSunburstLoader"],
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+ markupTemplate: "%resourceBase/html/imerss-viz-map-xetthecum.html",
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+ mapGrades: ["hortis.GBIFTiles"],
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+ mapFlavourGrade: "hortis.leafletMap.withRegions",
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+ renderMarkup: true,
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+ mapBounds: hortis.projectBounds.Xetthecum,
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+ phyloMap: "%resourceBase/json/kingdomPhyloMap.json",
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+ colourCount: "observationCount",
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+ vizFile: "data/Xetthecum/Life.json.lz4"});
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+ </script>
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+ </body>
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+ </html>
package/package.json ADDED
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+ {
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+ "name": "imerss-bioinfo",
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+ "description": "Working data of the IMERSS biodiversity informatics working group, together with algorithms",
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+ "version": "1.0.0",
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+ "author": "Antranig Basman",
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+ "scripts": {
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+ "lint": "fluid-lint-all"
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+ },
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+ "main": "index.js",
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+ "dependencies": {
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+ "infusion": "4.0.0",
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+ "kettle": "2.3.0",
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+ "csv-parser": "3.0.0",
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+ "remove-bom-stream": "2.0.0",
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+ "event-stream": "4.0.1",
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+ "csv-writer": "1.6.0",
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+ "sqlite": "4.1.2",
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+ "sqlite3": "5.1.2",
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+ "exceljs": "4.3.0",
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+ "moment": "2.29.2",
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+ "moment-timezone": "0.5.34",
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+ "jsep": "EricSmekens/jsep#25fcb53",
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+ "glob": "7.2.0",
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+ "minimist": "1.2.6",
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+ "lz4": "0.6.5",
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+ "pako": "2.0.4",
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+ "json5": "2.2.1",
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+ "accessible-autocomplete": "2.0.4",
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+ "jquery-ui": "1.13.1"
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+ },
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+ "devDependencies": {
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+ "terser": "5.12.1",
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+ "fs-extra": "10.0.1",
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+ "eslint": "8.12.0",
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+ "eslint-config-fluid": "2.1.1",
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+ "fluid-lint-all": "1.2.3-dev.20221116T125442Z.fa35dc0.GH-54-1",
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+ "node-jqunit": "1.1.9"
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+ },
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+ "repository": {
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+ "type": "git",
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+ "url": "https://github.com/IMERSS/imerss-bioinfo"
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+ },
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+ "files": [
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+ "/src", "/test", "/index.js", "/build.js", "/index*.html", "/docs/js", "/docs/css"
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+ ],
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+ "engines": {
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+ "node": ">=14.0.0"
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+ },
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+ "license": "BSD-3-Clause"
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+ }
package/src/WoRMS/taxonAPI.js ADDED
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+ /* eslint-env node */
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+
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+ "use strict";
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+
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+ const fluid = require("infusion");
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+ const hortis = fluid.registerNamespace("hortis");
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+
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+ fluid.registerNamespace("hortis.WoRMSTaxa");
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+
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+ hortis.WoRMSTaxa.filenameFromTaxonName = function (taxonAPIFileBase, name) {
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+ return taxonAPIFileBase + "/" + name + ".json";
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+ };
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+