grnsight 3.0.0 → 5.1.0

package/web-client/public/gene/PageDesignREADME.md

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+Our Team was Tasked with Designing the Page that Hosts all the Data that is pulled from the various biological databases used. There are not many specific features that are unique to the page design team, but we utilized the bootstrap front-end framework to display all the information in the most easily understandable and aesthetically pleasing fashion.  We used, description lists, tables, and some style tools such as color and "text-muted".

package/web-client/public/gene/api.js

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+"use strict";
+
+// Using "use strict" global
+const serviceRoot = $("#service-root").attr("value");
+const serializer = new XMLSerializer();
+const XMLParser = function (data) {
+    return serializer.serializeToString(data).replace(/\<.*?\>\s?/g, "");
+};
+// console.log("service root: " + serviceRoot)
+
+let defaultJaspar = {
+    jasparID: "Not found",
+    class: "Not found",
+    family: "Not found",
+    sequenceLogo: "Not found",
+    frequencyMatrix: "Not found"
+};
+
+let defaultNCBI  = {
+    ncbiID: "Not found",
+    locusTag: "Not found",
+    genomicSequence: "Not found"
+};
+
+let defaultUniprot = {
+    uniprotID: "Not found",
+    proteinSequence: "Not found",
+    proteinType: "Not found",
+    species: "Species not found"
+};
+
+let defaultGeneOntology = {
+    molecularFunction: "Not found",
+    biologicalProcess: "Not found",
+    cellularComponent: "Not found"
+};
+
+let defaultRegulators = {
+    regulators: "Not found",
+    targets: "Not found"
+};
+
+let defaultYeastmine = {
+    description: "Not found",
+    sgdID: "Not found",
+    geneOntologySummary: "Not found"
+};
+
+
+
+let getUniProtInfo = function (query) {
+    const taxon = query.uniprot;
+    const geneSymbol = query.symbol;
+    // console.log("this is uniprot: " + taxon);
+    return $.get({
+        url: serviceRoot + "/uniprot/uploadlists/",
+        data: {
+            from: "GENENAME",
+            to: "ACC",
+            format: "tab",
+            taxon: taxon,
+            query: geneSymbol,
+        },
+        dataType: "text",
+        timeout: 5000,
+    }).then(function (data) {
+        const regex = new RegExp(geneSymbol + "[ \t\r\n\v\f]*([A-Z0-9]+)", "gm");
+        const id = regex.exec(data)[1];
+        return $.get({
+            url: serviceRoot + "/uniprot/uniprot/" + id + ".xml",
+            timeout: 5000,
+        });
+    });
+};
+
+let getNCBIInfo = function (query) {
+    const geneSymbol = query.symbol;
+    const geneName = query.species.replace(/_/, "+");
+    // console.log("calling ncbi")
+
+    return $.get({
+        url: serviceRoot + "/ncbi/entrez/eutils/esearch.fcgi",
+        data: {
+            db: "gene",
+            term: geneSymbol + "[gene]+" + geneName + "[Organism]",
+        },
+        dataType: "text",
+        timeout: 5000,
+    }).then(function (data) {
+        const regex = /<Id>(\d*)<\/Id>/gm;
+        const id = regex.exec(data)[1];
+        return $.get({
+            url: serviceRoot + "/ncbi/entrez/eutils/esummary.fcgi?db=gene&id=" + id,
+            dataType: "xml",
+            timeout: 5000,
+        });
+    });
+};
+
+let getGeneOntologyInfo = function (query) {
+    const geneSymbol = query.symbol;
+    return $.get({
+        url: serviceRoot + "/yeastmine/backend/locus/" + geneSymbol + "/go_details",
+        dataType: "json",
+        beforeSend: function (xhr) {
+            xhr.setRequestHeader("content-type", "application/json");
+        }
+    }).catch(function () {
+        return defaultGeneOntology;
+    });
+};
+
+let getRegulationInfo = function (query) {
+    const geneSymbol = query.symbol;
+    return $.get({
+        url: serviceRoot + "/yeastmine/backend/locus/" + geneSymbol + "/regulation_details",
+        dataType: "json",
+        beforeSend: function (xhr) {
+            xhr.setRequestHeader("content-type", "application/json");
+        }
+    });
+};
+
+// let getFlyMineInfo = function (query) {
+//     const geneSymbol = query.symbol;
+//     return $.get({
+//         url: serviceRoot + "/flymine/webservice/locus/" + geneSymbol,
+//         dataType: "json",
+//         beforeSend: function (xhr) {
+//             xhr.setRequestHeader("content-type", "application/json");
+//         },
+//     });
+// };
+
+let getYeastMineInfo = function (query) {
+    const geneSymbol = query.symbol;
+    return $.get({
+        url: serviceRoot + "/yeastmine/webservice/locus/" + geneSymbol,
+        dataType: "json",
+        beforeSend: function (xhr) {
+            xhr.setRequestHeader("content-type", "application/json");
+        },
+    });
+};
+
+let getJasparInfo = function (query) {
+    const geneSymbol = query.symbol;
+    const taxon = query.jaspar;
+    // console.log("this is jaspar: " + taxon);
+
+    return $.get({
+        url: serviceRoot + "/jaspar/api/v1/matrix/?tax_id=" + taxon + "&format=json&name=" + geneSymbol.toUpperCase(),
+        dataType: "json",
+        beforeSend: function (xhr) {
+            xhr.setRequestHeader("content-type", "application/json");
+        },
+        timeout: 5000,
+    }).then(function (data) {
+        return (data.results.length === 0 || data.results === undefined) ? {} :
+            $.get({
+                url: serviceRoot + "/jaspar/api/v1/matrix/" + data.results[0].matrix_id,
+                dataType: "json",
+                beforeSend: function (xhr) {
+                    xhr.setRequestHeader("content-type", "application/json");
+                },
+            });
+    });
+};
+
+let defaultValues = {
+    jaspar:  defaultJaspar,
+    ncbi: defaultNCBI,
+    uniprot: defaultUniprot,
+    sgd: defaultYeastmine,
+    geneOntology: defaultGeneOntology,
+    regulators: defaultRegulators
+};
+
+
+let parseRegulators = function (data, symbol) {
+
+    let regs = [];
+    let targs = [];
+
+    data.filter(word => (word.locus1.display_name === symbol.symbol) ? targs[targs.length] = {
+        target:  word.locus2.display_name,
+        regulationOf: word.regulation_of }
+      : regs[regs.length] = {
+          regulator: word.locus1.display_name,
+          regulationOf: word.regulation_of,
+          regulationType: word.regulation_type}) ;
+
+    return {
+        regulators: regs,
+        targets: targs
+    };
+
+};
+
+let parseGeneOntology = function (data) {
+
+
+    let goTemplate = {
+        molecularFunction : [],
+        biologicalProcess : [],
+        cellularComponent : [],
+    };
+
+    for (var k = 0; k < data.length; k++) {
+        let isUnique = true;
+        for (var len = 0; len < k; len++) {
+            if (data[k].go.go_id === data[len].go.go_id) {
+                isUnique = false;
+            }
+        }
+
+        if (isUnique) {
+            switch (data[k].go.go_aspect ) {
+            case "molecular function":
+                goTemplate.molecularFunction[goTemplate.molecularFunction.length] = {
+                    id: data[k].go.go_id,
+                    link: data[k].go.link,
+                    displayName: data[k].go.display_name
+                };
+                break;
+            case "biological process":
+                goTemplate.biologicalProcess[goTemplate.biologicalProcess.length] = {
+                    id: data[k].go.go_id,
+                    link: data[k].go.link,
+                    displayName: data[k].go.display_name
+                };
+                break;
+            case "cellular component":
+                goTemplate.cellularComponent[goTemplate.cellularComponent.length] = {
+                    id: data[k].go.go_id,
+                    link: data[k].go.link,
+                    displayName: data[k].go.display_name
+                };
+                break;
+            }
+        }
+
+    }
+
+    for (var prop in goTemplate) {
+        if (goTemplate[prop].length === 0) {
+            goTemplate[prop] = "Not found";
+        }
+    }
+
+    return goTemplate;
+};
+
+let parseUniprot = function (data) {
+    let uniprotTemplate = {
+        uniprotID: XMLParser(data.getElementsByTagName("name")[0]),
+        proteinSequence: XMLParser(data.getElementsByTagName("sequence")[0]),
+        proteinType: XMLParser(data.getElementsByTagName("protein")[0].childNodes[1].childNodes[1]),
+        species: XMLParser(data.getElementsByTagName("organism")[0].childNodes[1]),
+    };
+
+    for (var prop in uniprotTemplate) {
+        if ((uniprotTemplate[prop] === undefined) || (uniprotTemplate[prop] === null)) {
+            uniprotTemplate[prop] = "Not found";
+        }
+    }
+
+    return uniprotTemplate;
+
+};
+
+let parseNCBI = function (data) {
+    const tagArray = serializer.serializeToString(
+        data.getElementsByTagName("OtherAliases")[0]).split(",");
+    const ncbiTemplate = {
+        ncbiID: data.getElementsByTagName("DocumentSummary")[0].getAttribute("uid"),
+        locusTag: tagArray[0].replace(/\<.*?\>\s?/g, ""),
+        chromosomeSequence: XMLParser(data.getElementsByTagName("ChrAccVer")[0]),
+    };
+
+    for (var prop in ncbiTemplate) {
+        if ((ncbiTemplate[prop] === undefined) || (ncbiTemplate[prop] === null)) {
+            ncbiTemplate[prop] = "Not found";
+        }
+    }
+
+    return ncbiTemplate;
+};
+
+let parseYeastmine = function (data) {
+    const yeastmineTemplate = {
+        description: data.description,
+        sgdID: data.sgdid,
+        geneOntologySummary: data.go_overview.paragraph,
+    };
+
+    for (var prop in yeastmineTemplate) {
+
+        if ((yeastmineTemplate[prop] === undefined) || (yeastmineTemplate[prop] === null)) {
+            yeastmineTemplate[prop] = "Not found";
+        }
+    }
+
+
+
+    return yeastmineTemplate;
+};
+
+// let parseFlymine = function (data) {
+//     const flymineTemplate = {
+//         description: data.description,
+//         sgdID: data.sgdid,
+//         geneOntologySummary: data.go_overview.paragraph,
+//     };
+
+//     for (var prop in flymineTemplate) {
+
+//         if ((flymineTemplate[prop] === undefined) || (flymineTemplate[prop] === null)) {
+//             flymineTemplate[prop] = "Not found";
+//         }
+//     }
+
+
+
+//     return flymineTemplate;
+// };
+
+let parseJaspar = function (data) {
+    // console.log(data)
+    const jasparTemplate = {
+        jasparID : data.matrix_id,
+        class: data.class[0],
+        family: data.family[0],
+        sequenceLogo: data.sequence_logo,
+        frequencyMatrix: data.pfm,
+    };
+
+    for (var prop in jasparTemplate) {
+        if ((jasparTemplate[prop] === undefined) || (jasparTemplate[prop] === null)) {
+            jasparTemplate[prop] = "Not found";
+        }
+    }
+
+    return jasparTemplate;
+};
+
+
+(function ($) {
+    window.api = {
+        getNCBIInfo,
+        getUniProtInfo,
+        getYeastMineInfo,
+        // getFlyMineInfo,
+        getGeneOntologyInfo,
+        getRegulationInfo,
+        getJasparInfo,
+        getGeneInformation: function (symbol) {
+            return $.when(
+             window.api.getNCBIInfo(symbol)
+           ).then(function (ncbiInfo) {
+               defaultValues.ncbi = parseNCBI(ncbiInfo);
+               return window.api.getUniProtInfo(symbol);
+           }).then(function (uniProtInfo) {
+            //    console.log("in uniprot")
+               defaultValues.uniprot = parseUniprot(uniProtInfo);
+               return window.api.getJasparInfo(symbol);
+           }).then(function (jasparInfo) {
+            //    console.log("this is jasparInfo: ")
+            //    console.log(jasparInfo)
+               defaultValues.jaspar = parseJaspar(jasparInfo);
+               return window.api.getYeastMineInfo(symbol);
+           }).then(function (yeastMineInfo) {
+            //    console.log("in yeastmine")
+               defaultValues.sgd = parseYeastmine(yeastMineInfo);
+            //    return window.api.getFlyMineInfo(symbol);
+        //    }).then(function (flyMineInfo) {
+            //    defaultValues.sgd = parseFlymine(flyMineInfo);
+               return window.api.getGeneOntologyInfo(symbol);
+           }).then(function (goInfo) {
+            //    console.log("inside GO call")
+               defaultValues.geneOntology = parseGeneOntology(goInfo);
+               return window.api.getRegulationInfo(symbol);
+           }).then(function (regulationInfo) {
+               // parseRegulators needs both info and symbol
+               defaultValues.regulators = parseRegulators(regulationInfo, symbol);
+               return defaultValues;
+           }).catch(function () {
+            //    window.api.getNCBIInfo(symbol);
+               window.api.getUniProtInfo(symbol);
+               window.api.getYeastMineInfo(symbol);
+            //    window.api.getFlyMineInfo(symbol);
+               window.api.getGeneOntologyInfo(symbol);
+               window.api.getRegulationInfo(symbol);
+               window.api.getJasparInfo(symbol);
+               window.api.getNCBIInfo(symbol);
+
+               if (
+                 defaultValues.ncbi === defaultNCBI &&
+                 defaultValues.uniprot === defaultUniprot &&
+                 defaultValues.sgd === defaultYeastmine &&
+                 defaultValues.geneOntology === defaultGeneOntology &&
+                 defaultValues.regulators === defaultRegulators &&
+                 defaultValues.jaspar === defaultJaspar
+               ) {
+                   const errorString1 = "No gene information was retrieved for " + symbol.symbol + ".";
+
+                   const errorString2 = "This could have happened because:";
+                   const errorString3 = "You can check back later to see if gene information" +
+                   " can be retrieved or submit an issue to https://github.com/dondi/GRNsight.";
+
+                   $("#error2").text(errorString2);
+                   var errorString4 = $("<ul/>").appendTo("#error2");
+                   errorString4.append("<li>The wrong species is selected </li>");
+                   errorString4.append("<li>GRNsight could not access the gene information"
+                   + " from one of the source databases</li>");
+                   errorString4.append("<li>No information exists for the gene in the source databases.</li>");
+
+                   $("#error1").text(errorString1);
+                   $("#error3").text(errorString3);
+
+                   var screenHeight = $(window).height();
+                   var MIN_SCREEN_HEIGHT = 600;
+                   var BORDER = 425;
+                   var setPanel = (screenHeight - BORDER) + "px";
+                   var minPanel = (MIN_SCREEN_HEIGHT - BORDER) + "px";
+                   if (screenHeight > MIN_SCREEN_HEIGHT) {
+                       $("#list-frame").css({ height: setPanel });
+                   } else {
+                       $("#list-frame").css({ height: minPanel });
+                   }
+
+                   $("#errorModal").css({ "font-family": "arial",
+                       "font-size": "14px",
+                       "color": "#333"});
+                   $("#errorModal").modal("show");
+               }
+
+               return defaultValues;
+           });
+        }
+    };
+})($);

package/web-client/public/gene/info.css

@@ -0,0 +1,181 @@
+
+a {
+  color: #16693f;
+}
+
+a:hover {
+  color: #3f1669;
+}
+
+body {
+  font-family: 'Georgia', serif;
+	margin: 0;
+	background-color: #FFFFFF;
+	min-width: 1300px;
+
+}
+
+iframe {
+  border:none;
+}
+
+
+sup {
+  line-height: 2;
+}
+
+
+#gene-name {
+  text-align: left;
+
+}
+#gene-species {
+  font-style: italic;
+  text-align: left;
+}
+
+#iframeHeader {
+  height: 118px;
+  box-sizing: content-box;
+  min-width: 100%;
+}
+
+#iframeMenu {
+  position: absolute;
+  min-height: 450px;
+  min-width: 160px;
+}
+
+#iframeFooter {
+  width: 100%;
+	display: block;
+}
+
+#mainContent {
+  left: 0;
+  right: 0;
+  margin: 20px 0px 0px 209px;
+  padding: 5px 5px 5px 5px;
+}
+
+#pageContent {
+  padding: 0px 5px 5px 10px;
+  margin-right: 8em;
+}
+
+#pageHead {
+  margin-top: 20px;
+  margin-bottom: 25px;
+  font-size: 25px;
+  min-height: 78px;
+}
+
+.btn {
+  color: white;
+  margin-right: 10px;
+}
+
+.btn-green {
+  background-color: #16693f;
+}
+
+.btn-purple {
+  background-color: #3f1669;
+}
+
+.btn-brown {
+  background-color: #693f16;
+}
+
+.btn-turquoise {
+  background-color: #166969;
+}
+
+.btn-violet {
+  background-color: #691640;
+}
+
+.card {
+  margin-bottom: 5px;
+}
+
+.card-header {
+  text-decoration: underline;
+  padding: 7px 15px;
+}
+
+.card-header > h5 {
+  margin-left: -5px;
+  font-size: 16px;
+}
+
+.card-block {
+   margin-left: 10px;
+}
+
+.close {
+  color: black;
+}
+
+.codeSequence {
+  font-family: Courier;
+  color:black;
+}
+
+.container-fluid {
+  padding-left: 0px;
+}
+
+.col {
+  padding: 0px;
+}
+
+.col-12 {
+  padding: 0px;
+}
+
+.database-link {
+  color:  #16693f;
+  font-weight: 700;
+}
+
+.gene-link {
+  color:  #16693f;
+}
+
+.jumbotron {
+  background-color: white;
+  padding-bottom: 0px !important;
+}
+
+.row {
+  margin: 0px;
+}
+
+.sequenceLogo {
+  width: 50%;
+}
+
+.frequencyMatrix {
+  width: 100%;
+}
+
+.green {
+  color: #16693f;
+}
+
+.purple {
+  color: #3f1669;
+}
+
+.brown {
+  color: #693f16;
+}
+
+.turquoise {
+  color: #166969;
+}
+
+.violet {
+  color: #691640;
+}