Add DOI field

src/main/java/org/genesys2/server/model/elastic/AccessionDetails.java

@@ -60,6 +60,8 @@ public class AccessionDetails {
 	private Boolean art15;
 	private Integer sampStat;
 	private List<Integer> storage;
+	@Field(type = FieldType.String)
+	private String doi;
 
 	@Field(type = FieldType.Object)
 	private Institute institute;
@@ -132,6 +134,7 @@ public class AccessionDetails {
 		ad.cropName=accession.getCropName();
 		ad.inSgsv = accession.getInSvalbard() != null && accession.getInSvalbard() == true ? true : false;
 		ad.cropName = accession.getCropName();
+		ad.doi = accession.getDoi();
 
 		if (accession.getAccessionId().getPdci() != null) {
 			ad.pdciScore = accession.getAccessionId().getPdci().getScore();
@@ -538,4 +541,12 @@ public class AccessionDetails {
 	public void setAcceName(String acceName) {
 		this.acceName = acceName;
 	}
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
 }

src/main/java/org/genesys2/server/model/genesys/Accession.java

@@ -40,7 +40,7 @@ import javax.persistence.UniqueConstraint;
 @Entity
 @Table(name = "accession",
 	// Unique constraints
-	uniqueConstraints = { @UniqueConstraint(name = "UQ_accession_genus_inst", columnNames = { "instituteId", "taxGenus", "acceNumb" }) },
+	uniqueConstraints = { @UniqueConstraint(name = "UQ_accession_genus_inst", columnNames = { "instituteId", "taxGenus", "acceNumb" }),	@UniqueConstraint(name = "UQ_accession_doi", columnNames = {"doi"})},
 	// Indexes
 	indexes = { @Index(name = "IX_seqNo", columnList = "seqNo"), @Index(name = "IX_accession_lastModifiedDate", columnList = "lastModifiedDate") })
 public class Accession extends AccessionData {

src/main/java/org/genesys2/server/model/genesys/AccessionData.java

@@ -81,6 +81,9 @@ public abstract class AccessionData implements IdUUID, Serializable {
 	@JoinColumn(name = "id")
 	private AccessionId accessionId;
 
+	@Column(name = "doi")
+	private String doi;
+
 	@Column(name = "instCode", length = 10, nullable = false)
 	private String instituteCode;
 
@@ -414,4 +417,12 @@ public abstract class AccessionData implements IdUUID, Serializable {
 	public void setCrop(Crop crop) {
 		this.crop = crop;
 	}
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
 }

src/main/java/org/genesys2/server/model/json/AccessionJson.java

@@ -78,6 +78,8 @@ public class AccessionJson {
 	private boolean historic;
 	@JsonProperty(value = Accession.ACCEURL)
 	private String acceUrl;
+	@JsonProperty(value = Accession.DOI)
+	private String doi;
 
 	public long getVersion() {
 		return version;
@@ -302,4 +304,12 @@ public class AccessionJson {
 	public void setAcceUrl(String acceUrl) {
 		this.acceUrl = acceUrl;
 	}
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
 }

src/main/java/org/genesys2/server/model/json/Api1Constants.java

@@ -191,6 +191,11 @@ public interface Api1Constants {
 		 */
 		public static final String CROPNAME = "cropName";
 
+		/**
+		 * Accession DOI (Digital Object Identifier)
+		 */
+		public static final String DOI = "doi";
+
 	}
 
 	public static interface Institute {

src/main/java/org/genesys2/server/service/FilterConstants.java

@@ -91,4 +91,6 @@ public interface FilterConstants {
 
 	public static final String LAST_MODIFIED_DATE = "lastModifiedDate";
 
+	public static final String DOI = "doi";
+
 }

src/main/java/org/genesys2/server/service/impl/DirectMysqlQuery.java

@@ -208,6 +208,7 @@ public class DirectMysqlQuery {
 		createQuery(whereBuffer, "col.collMissId", filters.get(FilterConstants.COLLMISSID), params);
 		createQuery(whereBuffer, "storage.storage", filters.get(FilterConstants.STORAGE), params);
 		createQuery(whereBuffer, "pdci.score", filters.get(FilterConstants.PDCI), params);
+		createQuery(whereBuffer, "doi", filters.get(FilterConstants.DOI), params);
 
 		for (final AppliedFilter methodFilter : filters.methodFilters()) {
 			// Handle Genesys Method!

src/main/java/org/genesys2/server/service/impl/FilterHandler.java

@@ -83,6 +83,7 @@ public class FilterHandler {
 		this.availableFilters.add(new BasicFilter(FilterConstants.CROPS, DataType.STRING));
 		this.availableFilters.add(new BasicFilter(FilterConstants.CROPNAME, DataType.STRING));
 		this.availableFilters.add(new BasicFilter(FilterConstants.LISTS, DataType.STRING));
+		this.availableFilters.add(new BasicFilter(FilterConstants.DOI, DataType.STRING));
 
 		this.availableFilters.add(new BasicFilter(FilterConstants.REGION_ORIGIN, DataType.STRING));
 		this.availableFilters.add(new BasicFilter(FilterConstants.REGION_HOLD_INSTITUTE, DataType.STRING));

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -220,6 +220,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		columnList.add("geo." + Api1Constants.Geo.LATITUDE_LONGITUDE);
 		columnList.add("coll." + Api1Constants.Collecting.COLLMISSID);
 		columnList.add("pdci." + Api1Constants.Pdci.SCORE);
+		columnList.add(Api1Constants.Accession.DOI);
 		availableDisplayColumns = Collections.unmodifiableList(columnList);
 
 		List<String> displayList = new ArrayList<String>();

src/main/resources/content/language.properties

@@ -431,6 +431,7 @@ filter.lastModifiedDate=Last Modified Date
 filter.alias=Accession name
 filter.crops=Crop name
 filter.cropName=Provided crop name
+filter.doi=DOI
 filter.regionOfOrigin=Region of Origin
 filter.regionOfHoldingInstitute=Region of Holding Institute
 filter.orgCty.iso3=Country of Origin
@@ -753,6 +754,7 @@ resolver.resolve=Resolve
 
 resolver.page.reverse.title=Resolution results
 accession.purl=Permanent URL
+accession.doi=DOI
 
 menu.admin.kpi=KPI
 admin.kpi.index.page=KPI

src/main/resources/liquibase/liquibase-changeLog.yml

@@ -178,3 +178,38 @@ databaseChangeLog:
     - sql:
         comment:         accountType#SYSTEM to user#sys==1
         sql:             update user set sys = 1 where accountType = 'SYSTEM';
+
+- changeSet:
+    id:                  1497558768000-2
+    author:              maxymborodenko (generated)
+    changes:
+    - addColumn:
+        tableName:       accession
+        columns:
+        - column:
+            name:        doi
+            type:        varchar(255)
+
+- changeSet:
+    id:                     1497558768000-3
+    author:                 maxymborodenko (generated)
+    changes:
+    - addUniqueConstraint:
+        columnNames:        doi
+        constraintName:     UQ_accession_doi
+        deferrable:         true
+        disabled:           true
+        initiallyDeferred:  true
+        tableName:          accession
+        tablespace:         A String
+
+- changeSet:
+    id:                  1497558768000-4
+    author:              maxymborodenko (generated)
+    changes:
+    - addColumn:
+        tableName:       accessionhistoric
+        columns:
+        - column:
+            name:        doi
+            type:        varchar(255)
\ No newline at end of file

src/main/webapp/WEB-INF/jsp/accession/details.jsp

@@ -341,6 +341,20 @@
 							</p>
 						</div>
 					</div>
+					<div class="row">
+						<div class="col-lg-6 col-md-6 col-sm-6 col-xs-12">
+							<p>
+								<spring:message code="accession.doi" />
+							</p>
+						</div>
+						<div class="col-lg-6 col-md-6 col-sm-6 col-xs-12">
+							<p property="dc:identifier">
+								<c:if test="${(accession.doi ne null) && (accession.doi ne '')}">
+									<a href="<c:url value="https://www.genesys-pgr.org/${accession.doi}" />"><c:out value="https://www.genesys-pgr.org/${accession.doi}" /></a>
+								</c:if>
+							</p>
+						</div>
+					</div>
 				</c:if>
 
 

src/main/webapp/WEB-INF/jsp/accession/explore2.jsp

@@ -239,6 +239,18 @@
                                     <c:when test="${col eq 'pdci.score'}">
                                         <td class="notimportant <c:if test='${i.count ge 2}'>hidden-xs</c:if> <c:if test='${i.count gt 2}'>hidden-sm</c:if>"><p><fmt:formatNumber value="${accession.pdciScore}"/></p></td>
                                     </c:when>
+                                    <c:when test="${col eq 'doi'}">
+                                        <td class="notimportant <c:if test='${i.count ge 2}'>hidden-xs</c:if> <c:if test='${i.count gt 2}'>hidden-sm</c:if>">
+                                        <c:choose>
+                                            <c:when test="${accession.doi ne null}">
+                                                <p>${accession.doi}</p>
+                                            </c:when>
+                                            <c:otherwise>
+                                                <p></p>
+                                            </c:otherwise>
+                                        </c:choose>
+                                        </td>
+                                    </c:when>
                                     <c:otherwise>
                                         <c:set var="elVal" value="${accession}" />
                                         <c:forTokens items="${col}" delims="." var="item">
@@ -880,6 +892,15 @@
                                 'class': "notimportant <c:if test='${i.count ge 2}'>hidden-xs</c:if> <c:if test='${i.count gt 2}'>hidden-sm</c:if>"
                             }).appendTo(row))));
                         </c:when>
+                        <c:when test="${col eq 'doi'}">
+	                        $("<i/>", { text: pagedData.content[i].doi })
+	                        .appendTo($("<span/>", {
+	                            dir: "ltr",
+	                            'class': "sci-name"
+	                        }).appendTo($("<p></p>").appendTo($("<td/>", {
+                                'class': "notimportant <c:if test='${i.count ge 2}'>hidden-xs</c:if> <c:if test='${i.count gt 2}'>hidden-sm</c:if>"
+                            }).appendTo(row))));
+                        </c:when>
                         <c:when test="${col eq 'crops'}">
                             var cropNamesTd = $("<td/>", {
                                 'class': "notimportant <c:if test='${i.count ge 2}'>hidden-xs</c:if> <c:if test='${i.count gt 2}'>hidden-sm</c:if>"

src/main/webapp/WEB-INF/tags/filters/filter-list.tag

@@ -173,4 +173,9 @@
                         appliedFilters="${appliedFilters}" type="range"/>
     </filters:panel>
 
+    <filters:panel id="doi" title="filter.doi">
+        <filters:filter availableFilters="${availableFilters}" filterMap="${filters}" filterKey="doi"
+                        appliedFilters="${appliedFilters}" type="exact"/>
+    </filters:panel>
+
 </filters:group>
\ No newline at end of file

src/main/webapp/WEB-INF/tags/filters/filter.tag

@@ -123,6 +123,16 @@
 			</span>
                 </div>
             </c:when>
+            <c:when test="${type eq 'exact'}">
+                <div class="input-group">
+                    <input id="<c:out value="${normalizedKey}" />_input" class="span2 form-control string-type" />
+                    <span class="input-group-btn">
+                        <button class="btn btn-secondary notimportant filter-auto" type="button" norm-key="<c:out value="${normalizedKey}" />" i-key="<c:out value="${filter.key}" />">
+                            <span class="glyphicon glyphicon-plus"></span>
+                        </button>
+                    </span>
+                </div>
+            </c:when>
             <c:when test="${type eq 'range'}">
                 <c:choose>
                     <c:when test="${filterKey eq 'geo.latitude'}">