diff options
Diffstat (limited to 'bh20simplewebuploader/static')
| -rw-r--r-- | bh20simplewebuploader/static/blog.css | 17 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/image/CWL.png | bin | 0 -> 11066 bytes | |||
| -rw-r--r-- | bh20simplewebuploader/static/image/ESR.png | bin | 0 -> 67869 bytes | |||
| -rw-r--r-- | bh20simplewebuploader/static/image/curii.logo.ai.png | bin | 0 -> 16739 bytes | |||
| -rw-r--r-- | bh20simplewebuploader/static/image/curii.logo.ai.svg | 3 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/image/edit.png | bin | 0 -> 2452 bytes | |||
| -rw-r--r-- | bh20simplewebuploader/static/main.css | 38 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.js | 151 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/map.js | 50 |
9 files changed, 140 insertions, 119 deletions
diff --git a/bh20simplewebuploader/static/blog.css b/bh20simplewebuploader/static/blog.css index 82a7c51..3ee8c44 100644 --- a/bh20simplewebuploader/static/blog.css +++ b/bh20simplewebuploader/static/blog.css @@ -4,12 +4,13 @@ .timestamp { font-family: monospace; color: darkgreen; } h1,h2 { font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,monospace; color:black;background-color:#F0F8FF; } -h2 { color: darkblue; } -h3,h4 { color: black; } +h2 { color: black; } +h3,h4 { color: black; margin:0; } code { color: darkblue; } -body {font-family: Palatino, 'Palatino Linotype', serif; color:black;background-color:#e5d8f0; font-size: large } +body {font-family: Palatino, 'Palatino Linotype', serif; color:black; background-color:white; font-size: large } -div.verbatim { margin: 30px; color: black; background-color: white; border-style:outset; font-family: palatino font, monospace; font-size:80%; font-weight:bold; } +div.verbatim { margin: 30px; color: black; background-color: white; border-style:outset; + font-family: palatino font, monospace; font-size:80%; font-weight:bold; } div.quote { font-family: palatino font, monospace; font-size:80%; } div.quotation { font-family: palatino font, monospace; font-size:80%; } pre.example { margin: 30px; font-family: prestige, monospace; color:black; font-size:70%; background-color: lightyellow; } @@ -23,10 +24,10 @@ div[id="text-table-of-contents"]{ } div[class^="outline-text"] { margin: 10px; - background-color:#ebe6f0; - border-style: dotted; - border-color: #98bf21; - border-width: 1px; + // background-color:white; + // border-style: dotted; + // border-color: #98bf21; + // border-width: 1px; font-family: Palatino, 'Palatino Linotype', serif; color:black; font-size: large } span[class="todo TESTING"] { diff --git a/bh20simplewebuploader/static/image/CWL.png b/bh20simplewebuploader/static/image/CWL.png Binary files differnew file mode 100644 index 0000000..81d1807 --- /dev/null +++ b/bh20simplewebuploader/static/image/CWL.png diff --git a/bh20simplewebuploader/static/image/ESR.png b/bh20simplewebuploader/static/image/ESR.png Binary files differnew file mode 100644 index 0000000..557c798 --- /dev/null +++ b/bh20simplewebuploader/static/image/ESR.png diff --git a/bh20simplewebuploader/static/image/curii.logo.ai.png b/bh20simplewebuploader/static/image/curii.logo.ai.png Binary files differnew file mode 100644 index 0000000..401afad --- /dev/null +++ b/bh20simplewebuploader/static/image/curii.logo.ai.png diff --git a/bh20simplewebuploader/static/image/curii.logo.ai.svg b/bh20simplewebuploader/static/image/curii.logo.ai.svg new file mode 100644 index 0000000..e87ea05 --- /dev/null +++ b/bh20simplewebuploader/static/image/curii.logo.ai.svg @@ -0,0 +1,3 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!-- Created with Inkscape (http://www.inkscape.org/) --> +<svg width="1333.3" height="1333.3" version="1.1" viewBox="0 0 1333.3 1333.3" xml:space="preserve" 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\ No newline at end of file diff --git a/bh20simplewebuploader/static/image/edit.png b/bh20simplewebuploader/static/image/edit.png Binary files differnew file mode 100644 index 0000000..571b08c --- /dev/null +++ b/bh20simplewebuploader/static/image/edit.png diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index b9b27f4..6e651a4 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -47,7 +47,7 @@ h2 > svg { float: right; } -#map { +#mapid { width: 800px; height: 440px; border: 1px solid #AAA; @@ -178,7 +178,7 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } .about { display: grid; - grid-template-columns: repeat(2, 1fr); + grid-template-columns: 1fr 1fr; grid-auto-flow: row; } @@ -229,7 +229,7 @@ a { #metadata_fill_form { column-count: 4; margin-top: 0.5em; - column-width: 250px; + column-width: 15em; } .record, .record .field-group, .record .field-group .field { @@ -238,6 +238,8 @@ a { -webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */ page-break-inside: avoid; /* Firefox */ break-inside: avoid; + display: block; + width: 90%; } .record { @@ -258,6 +260,10 @@ a { width: max-content; } +.control { + width: 100%; +} + .filter-options { width: 100%; } @@ -304,9 +310,10 @@ footer { } .sponsors img { - width: 80%; - display:block; - margin:auto; + width: auto; + display: block; + margin: auto; + height: 4em; } .loader { @@ -377,3 +384,22 @@ div.status { vertical-align: top; border-bottom: 1px solid #ddd; } + +.map { + padding: 20px 32px; + // display: inline-block; +} + +.editbutton { + float: right; + text-align: right; + background-color: lightgrey; + border: 2px solid #4CAF50; + border-radius: 12px; + color: black; + padding: 5px 32px; + // text-decoration: none; + display: inline-block; + font-size: 16px; + box-shadow: 0 8px 16px 0 rgba(0,0,0,0.2), 0 6px 20px 0 rgba(0,0,0,0.19); +} diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js index 751e478..1633c25 100644 --- a/bh20simplewebuploader/static/main.js +++ b/bh20simplewebuploader/static/main.js @@ -13,70 +13,41 @@ function myFunction() { } } -let map = L.map( 'map', { - center: [37.0902, -95.7129], // Default to U.S.A - minZoom: 3, - zoom: 0 -}); -L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', { - attribution: '© <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a>', - subdomains: ['a','b','c'] -}).addTo( map ); - -let markers = L.markerClusterGroup().addTo(map) - - function fetchAPI(apiEndPoint) { - fetch(scriptRoot + apiEndPoint) - .then(response => { - return response.json(); - }) - .then(data => { - console.log(data); - markers.clearLayers(); - document.getElementById("results").classList.remove("invisible"); - document.getElementById("loader").classList.add("invisible"); - if (!(apiEndPoint === "/api/getAllaccessions")) { - for (let i = 0; i < data.length; i++) { - let {"count": fastaCount, GPS, LocationLabel: label } = data[i]; - let coordinates = GPS.split(" "); - if (!(coordinates == null)) { - let lat, lon; - [lon, lat] = coordinates.map(parseFloat); - let point = L.point() - let marker = L.marker([lat, lon]); - marker.bindPopup("<b>" + label + "</b><br/>" + "FastaCount: " +fastaCount); - markers.addLayer(marker) - }} - } - // Reload the map - map.invalidateSize(); - }); - document.getElementById("results").classList.add("invisible"); - document.getElementById("loader").classList.remove("invisible"); - -} - -// Copy from function above but now added as table instead of plain json -function fetchAPIV2(apiEndPoint) { - fetch(scriptRoot + apiEndPoint) - .then(response => { - return response.json(); - }) - .then(data => { - console.log(data) - htmlString="<table>" - - // Depending on what we want to explore we'd have to call a different function ....? But how to Include that? - for (var i=0; i<data.length;i++) { - htmlString=htmlString+"<tr><td><a href='#' onclick='fetchSEQByLocation(\""+data[i]["key"]+"\");'>"+data[i]["label"]+"</a></td><td>"+data[i]["count"]+"<td></tr>" - } - htmlString=htmlString+"</table>" - - document.getElementById("table").innerHTML = htmlString - }); - - document.getElementById("results").classList.add("invisible"); + fetch(scriptRoot + apiEndPoint) + .then(response => { + return response.json(); + }) + .then(data => { + console.log(data); + }); + document.getElementById("map_view").classList.add("invisible"); + document.getElementById("loader").classList.remove("invisible"); +} + +// Copy from function above but now output HTML table instead of plain json +function fetchHTMLTable(apiEndPoint) { + fetch(scriptRoot + apiEndPoint) + .then(response => { + return response.json(); + }) + .then(data => { + console.log(data) + htmlString="<table>" + + // Depending on what we want to explore we'd have to call a different function ....? But how to Include that? + /* + for (var i=0; i<data.length;i++) { + htmlString=htmlString+"<tr><td><a href='#' onclick='fetchSEQByLocation(\""+data[i]["key"]+"\");'>"+data[i]["label"]+"</a></td><td>"+data[i]["count"]+"<td></tr>" + } +*/ + for (var i=0; i<data.length;i++) { + htmlString=htmlString+"<tr><td>"+data[i]["label"]+"</td><td>"+data[i]["count"]+"<td></tr>" + } + htmlString=htmlString+"</table>" + + document.getElementById("table").innerHTML = htmlString + }); } @@ -85,36 +56,39 @@ let search = () => { fetchAPI(scriptRoot + "/api/getDetailsForSeq?seq=" + encodeURIComponent(m)); } +// Get count from Arvados let fetchCount = () => { fetchAPI("/api/getCount"); } +// Get count from Virtuoso let fetchCountDB = () => { fetchAPI("/api/getCountDB"); } let fetchSEQCountBySpecimen = () => { - fetchAPIV2("/api/getSEQCountbySpecimenSource"); + fetchHTMLTable("/api/getSEQCountbySpecimenSource"); } let fetchSEQCountByLocation = () => { - fetchAPIV2("/api/getSEQCountbyLocation"); + fetchHTMLTable("/api/getSEQCountbyLocation"); } let fetchSEQCountByTech = () => { - fetchAPIV2("/api/getSEQCountbytech"); + fetchHTMLTable("/api/getSEQCountbytech"); } let fetchAllaccessions = () => { - fetchAPI("/api/getAllaccessions"); + fetchHTMLTable("/api/getAllaccessions"); }; -let fetchCountByGPS = () => { - fetchAPI("/api/getCountByGPS"); +let fetchMap = () => { + fetchAPI("/api/getCountByGPS"); + updateMapMarkers(); }; let fetchSEQCountbyLocation = () => { - fetchAPIV2("/api/getSEQCountbyLocation"); + fetchHTMLTable("/api/getSEQCountbyLocation"); }; let fetchSEQByLocation = () => { @@ -122,7 +96,7 @@ let fetchSEQByLocation = () => { }; let fetchSEQCountbyContinent = () => { - fetchAPIV2("/api/getSEQCountbyContinent"); + fetchHTMLTable("/api/getSEQCountbyContinent"); } @@ -195,7 +169,7 @@ function addField(e) { // Increment the number and use the keypath and number to set IDs and cross // references. // TODO: Heavily dependent on the form field HTML. Maybe we want custom - // elements for the labeled controlsd that know how to be list items? + // elements for the labeled controls that know how to be list items? fieldNumber++ newField.dataset.number = fieldNumber let newID = keypath + '[' + fieldNumber + ']' @@ -252,36 +226,3 @@ function on_submit_button() { return false; } } - - - -// - -function drawMap(){ - -// initialize the map on the "map" div with a given center and zoom -var mymap = L.map('mapid').setView([51.505, -0.09], 1); - -L.tileLayer('https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', { - attribution: '© <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> contributors' -}).addTo(mymap); - -fetch(scriptRoot + "api/getCountByGPS") - .then(response => { - console.log(response) - return response.json(); - }) - .then(data => { - - for (var i=0; i<data.length;i++) { - gps=data[i]["GPS"].split(" ") - var circle = L.circle([gps[1], gps[0]], { - color: 'red', - fillColor: '#f03', - fillOpacity: 0.5, - radius: parseInt(data[i]["count"]) //not working for whatever reason - }).addTo(mymap); - } - - }); -} diff --git a/bh20simplewebuploader/static/map.js b/bh20simplewebuploader/static/map.js new file mode 100644 index 0000000..1003f7d --- /dev/null +++ b/bh20simplewebuploader/static/map.js @@ -0,0 +1,50 @@ + +var map = L.map( 'mapid', { + center: [51.505, -0.09], // Default to U.S.A + minZoom: 2, + zoom: 0 +}); + +L.tileLayer( 'http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png', { + attribution: '© <a href="https://www.openstreetmap.org/copyright">OpenStreetMap</a> | <a href="http://covid19.genenetwork.org/">COVID-19 PubSeq</a>', + subdomains: ['a','b','c'] +}).addTo(map); + + +function drawMap(){ + var mymap = map; + + fetch(scriptRoot + "api/getCountByGPS") + .then(response => { + console.log(response) + return response.json(); + }) + .then(data => { + updateMapMarkers(data); + + }); + document.getElementById("map_view").classList.remove("invisible"); + map.invalidateSize(); +} + + + +/* This function updates the map with markers + * +*/ +function updateMapMarkers(data) { + let markers = L.markerClusterGroup(); + for (let i = 0; i < data.length; i++) { + let {"count": fastaCount, GPS, LocationLabel: label } = data[i]; + let coordinates = GPS.split(" "); + if (!(coordinates == null)) { + let lat, lon; + [lon, lat] = coordinates.map(parseFloat); + let point = L.point() + marker = (L.marker([lat, lon])); + marker.bindPopup("<b>" + label + "</b><br/>" + "SARS-CoV-2<br/>sequences: " +fastaCount); + markers.addLayer(marker); + } + } + map.addLayer(markers); +} |
