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redesign the gene disease pair displayer
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@chenyian-nibio
chenyian-nibio committed Sep 7, 2018
1 parent dbd3726 commit fc7408e
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Showing 3 changed files with 275 additions and 2 deletions.
4 changes: 2 additions & 2 deletions targetmine/webapp/resources/webapp/WEB-INF/webconfig-model.xml
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replacesFields="parent, alternateForms"
types="ChemblCompound"/>

<reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneDiseasePairDisplayer"
jspName="model/geneDiseasePairDisplayer.jsp"
<reportdisplayer javaClass="org.intermine.bio.web.displayer.AltGeneDiseasePairDisplayer"
jspName="model/altGeneDiseasePairDisplayer.jsp"
replacesFields="diseases, geneDiseasePairs"
placement="Disease"
types="Gene"/>
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158 changes: 158 additions & 0 deletions targetmine/webapp/resources/webapp/model/altGeneDiseasePairDisplayer.jsp
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<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
<%@ taglib tagdir="/WEB-INF/tags" prefix="im"%>
<%@ taglib uri="/WEB-INF/struts-html.tld" prefix="html" %>

<div class="collection-table">

<c:choose>
<c:when test="${empty geneticDiseaseList}">
<h3>No genetic disease association.</h3>
</c:when>
<c:otherwise>
<h3>
${numOfAssociations} Genetic disease association<c:if test="${numOfAssociations > 1}">s</c:if>
</h3>
<table>
<thead>
<tr>
<th style="min-width: 390px;"><b>GWAS catalog</b></th>
<th style="min-width: 150px;">
<c:if test="${!empty geneticDiseaseList['gwas']}">p-value</c:if> &nbsp;
</th>
<th style="min-width: 82px;">Number of publications</th>
<th style="min-width: 82px;">Number of SNPs</th>
</tr>
</thead>
<tbody>
<c:choose>
<c:when test="${empty geneticDiseaseList['gwas']}">
<tr>
<td class="smallnote" colspan="4"><i>No items in this category.</i></td>
</tr>
</c:when>
<c:otherwise>
<c:forEach var="entryInfo" items="${geneticDiseaseList['gwas']}">
<tr>
<td>${entryInfo['diseaseColumn']}</td>
<td>${entryInfo['gwasColumn']}</td>
<td>${entryInfo['pubCountColumn']}</td>
<td>${entryInfo['snpCountColumn']}</td>
</tr>
</c:forEach>
</c:otherwise>
</c:choose>
</tbody>
<thead>
<tr>
<th><b>ClinVar</b></th>
<th colspan="3">
<c:if test="${!empty geneticDiseaseList['clinvar']}">Clinical significant</c:if> &nbsp;
</th>
</tr>
</thead>
<tbody>
<c:choose>
<c:when test="${empty geneticDiseaseList['clinvar']}">
<tr>
<td class="smallnote" colspan="4"><i>No items in this category.</i></td>
</tr>
</c:when>
<c:otherwise>
<c:forEach var="entryInfo" items="${geneticDiseaseList['clinvar']}">
<tr>
<td>${entryInfo['diseaseColumn']}</td>
<td>${entryInfo['clinvarColumn']}</td>
<td>${entryInfo['pubCountColumn']}</td>
<td>${entryInfo['snpCountColumn']}</td>
</tr>
</c:forEach>
</c:otherwise>
</c:choose>
</tbody>
<thead>
<tr><th colspan="4"><b>dbSNP-PubMed-MeSH</b></th></tr>
</thead>
<tbody>
<c:choose>
<c:when test="${empty geneticDiseaseList['dbsnpMesh']}">
<tr>
<td class="smallnote" colspan="4"><i>No items in this category.</i></td>
</tr>
</c:when>
<c:otherwise>
<c:forEach var="entryInfo" items="${geneticDiseaseList['dbsnpMesh']}">
<tr>
<td>${entryInfo['diseaseColumn']}</td>
<td>&nbsp;</td>
<td>${entryInfo['pubCountColumn']}</td>
<td>${entryInfo['snpCountColumn']}</td>
</tr>
</c:forEach>
</c:otherwise>
</c:choose>
</tbody>
</table>

</c:otherwise>
</c:choose>
</div>

<c:choose>
<c:when test="${empty disgenet}">
<!-- show nothing?-->
</c:when>
<c:otherwise>
<div class="collection-table">
<h3>
${fn:length(disgenet)} Disease association<c:if test="${fn:length(disgenet) > 1}">s</c:if> from DisGeNet
</h3>
<table>
<thead>
<tr>
<th>Disease</th>
<th>Number of publications</th>
</tr>
</thead>
<tbody>
<c:forEach var="disease" items="${disgenet}">
<tr>
<td><a href="report.do?id=${disease.id}">${disease.diseaseTerm.name}</a></td>
<td><a href="report.do?id=${disease.id}">${fn:length(disease.publications)}</a></td>
</tr>
</c:forEach>
</tbody>
</table>
</div>
</c:otherwise>
</c:choose>

<c:choose>
<c:when test="${empty others}">
<!-- show nothing?-->
</c:when>
<c:otherwise>
<div class="collection-table">
<h3>
${fn:length(others)} Other disease association<c:if test="${fn:length(others) > 1}">s</c:if>
</h3>
<table>
<thead>
<tr>
<th>Disease</th>
<th>Source</th>
</tr>
</thead>
<tbody>
<c:forEach var="disease" items="${others}">
<tr>
<td><a href="report.do?id=${disease.id}">${disease.diseaseTerm.name}</a></td>
<td>${disease.dataSet.name}</td>
</tr>
</c:forEach>
</tbody>
</table>
</div>
</c:otherwise>
</c:choose>
115 changes: 115 additions & 0 deletions targetmine/webapp/src/org/intermine/bio/web/displayer/AltGeneDiseasePairDisplayer.java
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package org.intermine.bio.web.displayer;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import javax.servlet.http.HttpServletRequest;

import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.intermine.api.InterMineAPI;
import org.intermine.model.InterMineObject;
import org.intermine.web.displayer.ReportDisplayer;
import org.intermine.web.logic.config.ReportDisplayerConfig;
import org.intermine.web.logic.results.ReportObject;

/**
* An alternative GeneDiseasePair displayer
*
* @author chenyian
*
*/
public class AltGeneDiseasePairDisplayer extends ReportDisplayer {
protected static final Logger LOG = Logger.getLogger(AltGeneDiseasePairDisplayer.class);

public AltGeneDiseasePairDisplayer(ReportDisplayerConfig config, InterMineAPI im) {
super(config, im);
// TODO Auto-generated constructor stub
}

@SuppressWarnings("unchecked")
@Override
public void display(HttpServletRequest request, ReportObject reportObject) {
InterMineObject gene = (InterMineObject) reportObject.getObject();

Map<String, List<Map<String, String>>> ret = new HashMap<String, List<Map<String,String>>>();
ret.put("gwas", new ArrayList<Map<String, String>>());
ret.put("clinvar", new ArrayList<Map<String, String>>());
ret.put("dbsnpMesh", new ArrayList<Map<String, String>>());
List<InterMineObject> disgenet = new ArrayList<InterMineObject>();
List<InterMineObject> others = new ArrayList<InterMineObject>(); // so far only OMIM?

try {
String geneSymbol = (String) gene.getFieldValue("symbol");

Set<InterMineObject> geneDiseasePairs = (Set<InterMineObject>) gene.getFieldValue("geneDiseasePairs");
for (InterMineObject gdItem : geneDiseasePairs) {
Map<String,String> entryInfo = new HashMap<String, String>();
InterMineObject diseaseTerm = (InterMineObject) gdItem.getFieldValue("diseaseTerm");
String name = (String) diseaseTerm.getFieldValue("name");
entryInfo.put("diseaseColumn", String.format("<a href=\"report.do?id=%s\">%s - %s</a>", gdItem.getId().toString(), name, geneSymbol));

Set<InterMineObject> publications = (Set<InterMineObject>) gdItem.getFieldValue("publications");
if (publications != null) {
entryInfo.put("pubCountColumn", String.valueOf(publications.size()));
} else {
entryInfo.put("pubCountColumn", "0");
}

Set<InterMineObject> snps = (Set<InterMineObject>) gdItem.getFieldValue("snps");
entryInfo.put("snpCountColumn", String.valueOf(snps.size()));

Set<InterMineObject> gwasItems = (Set<InterMineObject>) gdItem.getFieldValue("gwas");
Set<InterMineObject> alleles = (Set<InterMineObject>) gdItem.getFieldValue("alleles");
if (gwasItems != null && !gwasItems.isEmpty()) {
List<String> list = new ArrayList<String>();
for (InterMineObject gwas : gwasItems) {
Double pvalue = (Double) gwas.getFieldValue("pvalue");
list.add(String.format("<a href=\"report.do?id=%s\">%s</a>", gwas.getId().toString(), pvalue.toString()));
}
entryInfo.put("gwasColumn", StringUtils.join(list, ", "));
ret.get("gwas").add(entryInfo);
} else if (alleles != null && !alleles.isEmpty()) {
Set<String> csSet = new HashSet<String>();
for (InterMineObject allele : alleles) {
csSet.add((String) allele.getFieldValue("clinicalSignificance"));
}
List<String> list = new ArrayList<String>(csSet);
Collections.sort(list);
entryInfo.put("clinvarColumn", StringUtils.join(list, ", "));
ret.get("clinvar").add(entryInfo);
} else {
ret.get("dbsnpMesh").add(entryInfo);
}
}

// process diseases
Set<InterMineObject> diseases = (Set<InterMineObject>) gene.getFieldValue("diseases");
for (InterMineObject disease : diseases) {
InterMineObject dataSet = (InterMineObject) disease.getFieldValue("dataSet");
String dataSetName = (String) dataSet.getFieldValue("name");
if (dataSetName.equals("DisGeNET")) {
disgenet.add(disease);
} else {
others.add(disease);
}
}

} catch (IllegalAccessException e) {
LOG.error(e.getMessage());
}

request.setAttribute("geneticDiseaseList", ret);
request.setAttribute("numOfAssociations", Integer.valueOf(
ret.get("gwas").size() + ret.get("clinvar").size() + ret.get("dbsnpMesh").size()));
request.setAttribute("disgenet", disgenet);
request.setAttribute("others", others);

}

}

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