<commit_before><%@ taglib uri="http://struts.apache.org/tags-html" prefix="html"%>
<%@ taglib uri="http://struts.apache.org/tags-bean" prefix="bean"%>
<%@ taglib uri="http://struts.apache.org/tags-logic" prefix="logic"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
<jsp:include page="/bodyMessage.jsp?bundle=particle" />
<div class="animatedtabs" id="summaryTabALL">
	<ul>
		<li class="selected">
			<a	href="javascript:showSummary('ALL', ${fn:length(publicationCategories)})"
				title="All"><span>All</span> </a>
			<c:url var="printUrl" value="${actionName}">
				<c:param name="dispatch" value="summaryPrint" />
				<c:param name="sampleId" value="${sampleId}" />
				<c:param name="location" value="${location}" />
			</c:url>
			<c:url var="exportUrl" value="${actionName}">
				<c:param name="dispatch" value="summaryExport" />
				<c:param name="sampleId" value="${sampleId}" />
				<c:param name="location" value="${location}" />
			</c:url>
			<a href="javascript:printPage('${printUrl}')" id="printUrlAll" style="display: none;"></a>
			<a href="${exportUrl}" id="exportUrlAll" style="display: none;"></a>
		</li>
		<li>
			<c:forEach var="type" items="${publicationCategories}" varStatus="ind">
				<a	href="javascript:showSummary('${ind.count}', ${fn:length(publicationCategories)})"
					title="${type}"><span>${type}</span> </a>
				<a href="javascript:printPage('${printUrl}&type=${type}')" id="printUrl${ind.count}" style="display: none;"></a>
				<a href="${exportUrl}&type=${type}" id="exportUrl${ind.count}" style="display: none;"></a>
			</c:forEach>
		</li>
		<li>
			<a href="publication.do?dispatch=setupNew&sampleId=${sampleId}"><span>Other</span>
			</a>
		</li>
	</ul>
</div>
<c:forEach var="type" items="${publicationCategories}" varStatus="ind">
	<div class="animatedtabs" id="summaryTab${ind.count}"
		style="display: none;">
		<ul>
			<li>
				<a href="javascript:showSummary('ALL', ${fn:length(publicationCategories)})" title="All"><span>All</span>
				</a>
			</li>
			<c:forEach var="type" items="${publicationCategories}"
				varStatus="ind2">
				<c:choose>
					<c:when test="${ind.count eq ind2.count }">
						<c:set var="selectedClass" value="selected" />
					</c:when>
					<c:otherwise>
						<c:set var="selectedClass" value="" />
					</c:otherwise>
				</c:choose>
				<li class="${selectedClass}">
					<a href="javascript:showSummary('${ind2.count}', ${fn:length(publicationCategories)})" title="${type}"><span>${type}</span>
					</a>
				</li>
			</c:forEach>
			<li>
				<a href="publication.do?dispatch=setupNew&sampleId=${sampleId}"><span>Other</span>
				</a>
			</li>
		</ul>
	</div>
</c:forEach>
<table class="summaryViewLayer1" width="100%">
	<c:if test="${! empty publicationCategories && empty printView}">
		<tr>
			<td>
				<a href="javascript:printPage('${printUrl}')" id="printLink">Print</a>&nbsp;&nbsp;
				<a href="${exportUrl}" id="exportLink">Export</a>
			</td>
		</tr>
	</c:if>
	<tr>
		<td>
			<c:forEach var="type" items="${publicationCategories}" varStatus="ind">
				<table id="summarySection${ind.count}" class="smalltable3"
					cellpadding="0" cellspacing="0" border="0" width="100%">
					<tr>
						<th align="left">
							<a name="${type}" id="${type}">${type}</a>
							&nbsp;&nbsp;&nbsp;
							<a href="#" class="addlink"><img align="middle"
									src="images/btn_add.gif" border="0" /></a>&nbsp;&nbsp;
							<a><img align="middle" src="images/btn_delete.gif" border="0" />
							</a>
						</th>
					</tr>
					<tr>
						<td>
							<c:choose>
								<c:when
									test="${! empty publicationSummaryView.category2Publications[type]}">
									<div class="indented4">
										<table class="summarytable" width="90%" border="0"
											cellpadding="0" cellspacing="0" summary="">
											<tr>
												<th width="20%">
													Title
												</th>
												<th width="20%">
													Author(s)
												</th>
												<th width="20%">
													Bibliography Info
												</th>
												<th width="15%">
													Abstract/Download Link
												</th>
												<th>
													Research Category
												</th>
												<th>
													Created Date
												</th>
												<th width="5%">
													&nbsp;
												</th>
											</tr>
											<c:forEach var="pubBean"
												items="${publicationSummaryView.category2Publications[type]}">
												<c:set var="pubObj" value="${pubBean.domainFile}" />
												<tr>
													<td valign="top">
														${pubObj.title}&nbsp;
													</td>
													<td valign="top">
														<c:if test="${!empty pubBean.authors}">
															<c:forEach var="author" items="${pubBean.authors}">
												${author.lastName}, ${author.firstName} ${author.initial}<br>
															</c:forEach>
														</c:if>
														&nbsp;
													</td>
													<td valign="top">
														${pubBean.bibliographyInfo} &nbsp;
													</td>
													<td valign="top">
														<c:choose>
															<c:when test="${! empty pubObj.pubMedId}">
																<a target="_abstract"
																	href="http://www.ncbi.nlm.nih.gov/pubmed/${pubObj.pubMedId}">PMID:
																	${pubObj.pubMedId }</a>&nbsp;
															</c:when>
															<c:otherwise>
																<c:choose>
																	<c:when test="${! empty pubObj.digitalObjectId}">
																		<a target="_abstract"
																			href="http://dx.doi.org/${pubObj.digitalObjectId}">PMID:
																			${pubObj.digitalObjectId }</a>&nbsp;
																	</c:when>
																	<c:otherwise>
																		<a
																			href="searchPublication.do?dispatch=download&amp;publicationId=${pubObj.id}&amp;location=${param.location}"
																			target="${pubBean.urlTarget}">${pubOjb.uri}</a>&nbsp;
																	</c:otherwise>
																</c:choose>
															</c:otherwise>
														</c:choose>
														&nbsp;
													</td>
													<td valign="top">
														<c:out value="${fn:replace(pubObj.researchArea, ';', '<br>')}" escapeXml="false"/>&nbsp;
													</td>
													<td valign="top">
														${pubBean.createdDateStr}&nbsp;
													</td>
													<td valign="top">
														<c:url var="pubUrl" value="publication.do">
															<c:param name="sampleId" value="${sampleId}" />
															<c:param name="dispatch" value="setupUpdate" />
															<c:param name="publicationId" value="${pubObj.id}" />
															<c:param name="location" value="${location}" />
														</c:url>
														<a href="${pubUrl}">Edit</a>
													</td>
												</tr>
											</c:forEach>
										</table>
									</div><commit_msg>updated add button url<commit_after><%@ taglib uri="http://struts.apache.org/tags-html" prefix="html"%>
<%@ taglib uri="http://struts.apache.org/tags-bean" prefix="bean"%>
<%@ taglib uri="http://struts.apache.org/tags-logic" prefix="logic"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
<jsp:include page="/bodyMessage.jsp?bundle=particle" />
<div class="animatedtabs" id="summaryTabALL">
	<ul>
		<li class="selected">
			<a
				href="javascript:showSummary('ALL', ${fn:length(publicationCategories)})"
				title="All"><span>All</span> </a>
			<c:url var="printUrl" value="${actionName}">
				<c:param name="dispatch" value="summaryPrint" />
				<c:param name="sampleId" value="${sampleId}" />
				<c:param name="location" value="${location}" />
			</c:url>
			<c:url var="exportUrl" value="${actionName}">
				<c:param name="dispatch" value="summaryExport" />
				<c:param name="sampleId" value="${sampleId}" />
				<c:param name="location" value="${location}" />
			</c:url>
			<a href="javascript:printPage('${printUrl}')" id="printUrlAll"
				style="display: none;"></a>
			<a href="${exportUrl}" id="exportUrlAll" style="display: none;"></a>
		</li>
		<li>
			<c:forEach var="type" items="${publicationCategories}"
				varStatus="ind">
				<a
					href="javascript:showSummary('${ind.count}', ${fn:length(publicationCategories)})"
					title="${type}"><span>${type}</span> </a>
				<a href="javascript:printPage('${printUrl}&type=${type}')"
					id="printUrl${ind.count}" style="display: none;"></a>
				<a href="${exportUrl}&type=${type}" id="exportUrl${ind.count}"
					style="display: none;"></a>
			</c:forEach>
		</li>
		<li>
			<a href="publication.do?dispatch=setupNew&sampleId=${sampleId}"><span>Other</span>
			</a>
		</li>
	</ul>
</div>
<c:forEach var="type" items="${publicationCategories}" varStatus="ind">
	<div class="animatedtabs" id="summaryTab${ind.count}"
		style="display: none;">
		<ul>
			<li>
				<a
					href="javascript:showSummary('ALL', ${fn:length(publicationCategories)})"
					title="All"><span>All</span> </a>
			</li>
			<c:forEach var="type" items="${publicationCategories}"
				varStatus="ind2">
				<c:choose>
					<c:when test="${ind.count eq ind2.count }">
						<c:set var="selectedClass" value="selected" />
					</c:when>
					<c:otherwise>
						<c:set var="selectedClass" value="" />
					</c:otherwise>
				</c:choose>
				<li class="${selectedClass}">
					<a
						href="javascript:showSummary('${ind2.count}', ${fn:length(publicationCategories)})"
						title="${type}"><span>${type}</span> </a>
				</li>
			</c:forEach>
			<li>
				<a href="publication.do?dispatch=setupNew&sampleId=${sampleId}"><span>Other</span>
				</a>
			</li>
		</ul>
	</div>
</c:forEach>
<table class="summaryViewLayer1" width="100%">
	<c:if test="${! empty publicationCategories && empty printView}">
		<tr>
			<td>
				<a href="javascript:printPage('${printUrl}')" id="printLink">Print</a>&nbsp;&nbsp;
				<a href="${exportUrl}" id="exportLink">Export</a>
			</td>
		</tr>
	</c:if>
	<tr>
		<td>
			<c:forEach var="type" items="${publicationCategories}"
				varStatus="ind">
				<table id="summarySection${ind.count}" class="smalltable3"
					cellpadding="0" cellspacing="0" border="0" width="100%">
					<tr>
						<th align="left">
							<a name="${type}" id="${type}">${type}</a> &nbsp;&nbsp;&nbsp;
							<a
								href="publication.do?dispatch=setupNew&sampleId=${sampleId}&type=${type}"
								class="addlink"><img align="middle" src="images/btn_add.gif"
									border="0" /></a>&nbsp;&nbsp;
							<c:if test="${! empty publicationSummaryView.category2Publications[type]}">
								<a><img align="middle" src="images/btn_delete.gif"
										border="0" /> </a>
							</c:if>
						</th>
					</tr>
					<tr>
						<td>
							<c:choose>
								<c:when
									test="${! empty publicationSummaryView.category2Publications[type]}">
									<div class="indented4">
										<table class="summarytable" width="90%" border="0"
											cellpadding="0" cellspacing="0" summary="">
											<tr>
												<th width="20%">
													Title
												</th>
												<th width="20%">
													Author(s)
												</th>
												<th width="20%">
													Bibliography Info
												</th>
												<th width="15%">
													Abstract/Download Link
												</th>
												<th>
													Research Category
												</th>
												<th>
													Created Date
												</th>
												<th width="5%">
													&nbsp;
												</th>
											</tr>
											<c:forEach var="pubBean"
												items="${publicationSummaryView.category2Publications[type]}">
												<c:set var="pubObj" value="${pubBean.domainFile}" />
												<tr>
													<td valign="top">
														${pubObj.title}&nbsp;
													</td>
													<td valign="top">
														<c:if test="${!empty pubBean.authors}">
															<c:forEach var="author" items="${pubBean.authors}">
												${author.lastName}, ${author.firstName} ${author.initial}<br>
															</c:forEach>
														</c:if>
														&nbsp;
													</td>
													<td valign="top">
														${pubBean.bibliographyInfo} &nbsp;
													</td>
													<td valign="top">
														<c:choose>
															<c:when test="${! empty pubObj.pubMedId}">
																<a target="_abstract"
																	href="http://www.ncbi.nlm.nih.gov/pubmed/${pubObj.pubMedId}">PMID:
																	${pubObj.pubMedId }</a>&nbsp;
															</c:when>
															<c:otherwise>
																<c:choose>
																	<c:when test="${! empty pubObj.digitalObjectId}">
																		<a target="_abstract"
																			href="http://dx.doi.org/${pubObj.digitalObjectId}">PMID:
																			${pubObj.digitalObjectId }</a>&nbsp;
																	</c:when>
																	<c:otherwise>
																		<a
																			href="searchPublication.do?dispatch=download&amp;publicationId=${pubObj.id}&amp;location=${param.location}"
																			target="${pubBean.urlTarget}">${pubOjb.uri}</a>&nbsp;
																	</c:otherwise>
																</c:choose>
															</c:otherwise>
														</c:choose>
														&nbsp;
													</td>
													<td valign="top">
														<c:out
															value="${fn:replace(pubObj.researchArea, ';', '<br>')}"
															escapeXml="false" />
														&nbsp;
													</td>
													<td valign="top">
														${pubBean.createdDateStr}&nbsp;
													</td>
													<td valign="top">
														<c:url var="pubUrl" value="publication.do">
															<c:param name="sampleId" value="${sampleId}" />
															<c:param name="dispatch" value="setupUpdate" />
															<c:param name="publicationId" value="${pubObj.id}" />
															<c:param name="location" value="${location}" />
														</c:url>
														<a href="${pubUrl}">Edit</a>
													</td>
												</tr>
											</c:forEach>
										</table>
									</div>
{'fraction_non_alphanumeric': 0.20344165540780773, 'fraction_numerical': 0.004764275047998294, 'mean_word_length': 2.289824561403509, 'pattern_counts': {'":': 0, '<': 375, '<?xml version=': 0, '>': 375, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1884146', 'n_tokens_mistral': 7338, 'n_tokens_neox': 4604, 'n_words': 712}