Improved JSON serialization and filtering

- No  custom JsonSerializers, use annotations instead
- Added AccessionFilter#coll <- AccessionCollectFilter

src/main/java/org/genesys2/server/api/serialization/CountrySerializer.java

-/**
- * Copyright 2014 Global Crop Diversity Trust
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *   http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- **/
-
-package org.genesys2.server.api.serialization;
-
-import java.io.IOException;
-
-import org.genesys2.server.model.impl.Country;
-
-import com.fasterxml.jackson.core.JsonGenerator;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonSerializer;
-import com.fasterxml.jackson.databind.SerializerProvider;
-
-public class CountrySerializer extends JsonSerializer<Country> {
-
-	@Override
-	public void serialize(Country country, JsonGenerator jgen, SerializerProvider sp) throws IOException, JsonProcessingException {
-		if (country == null) {
-			jgen.writeNull();
-		} else {
-			jgen.writeStartObject();
-			jgen.writeObjectField("code", country.getCode3());
-			jgen.writeObjectField("name", country.getName());
-			jgen.writeObjectField("refnameId", country.getRefnameId());
-			jgen.writeObjectField("current", country.isCurrent());
-			jgen.writeEndObject();
-		}
-	}
-
-}

src/main/java/org/genesys2/server/api/serialization/FaoInstituteSerializer.java

-/**
- * Copyright 2014 Global Crop Diversity Trust
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- **/
-
-package org.genesys2.server.api.serialization;
-
-import java.io.IOException;
-
-import org.genesys2.server.model.impl.FaoInstitute;
-
-import com.fasterxml.jackson.core.JsonGenerator;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonSerializer;
-import com.fasterxml.jackson.databind.SerializerProvider;
-
-public class FaoInstituteSerializer extends JsonSerializer<FaoInstitute> {
-
-	@Override
-	public void serialize(FaoInstitute institute, JsonGenerator jgen, SerializerProvider sp) throws IOException, JsonProcessingException {
-		if (institute == null) {
-			jgen.writeNull();
-		} else {
-			jgen.writeStartObject();
-			jgen.writeObjectField("instCode", institute.getCode());
-			jgen.writeObjectField("name", institute.getFullName());
-			jgen.writeEndObject();
-		}
-	}
-
-}

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

@@ -36,6 +36,7 @@ import javax.persistence.Transient;
 
 import org.genesys.blocks.model.AuditedVersionedModel;
 import org.genesys.blocks.model.IdUUID;
+import org.genesys.blocks.model.JsonViews;
 import org.genesys.blocks.model.SelfCleaning;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.Crop;
@@ -45,8 +46,8 @@ import org.genesys2.util.NumberUtils;
 import org.hibernate.annotations.Type;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonUnwrapped;
+import com.fasterxml.jackson.annotation.JsonView;
 
 @MappedSuperclass
 public abstract class AccessionData extends AuditedVersionedModel implements IdUUID, Serializable, SelfCleaning {
@@ -70,6 +71,7 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 	
 	@ManyToOne(cascade = {}, optional = false)
 	@JoinColumn(name = "instituteId")
+	@JsonView({ JsonViews.Minimal.class })
 	private FaoInstitute institute;
 
 	@Column(name = "acceNumb", nullable = false, length = 128)
@@ -87,7 +89,7 @@ public abstract class AccessionData extends AuditedVersionedModel implements IdU
 
 	@ManyToOne(cascade = {}, optional = false)
 	@JoinColumn(name = "taxonomyId2")
-	@JsonIgnoreProperties(value = { "id", "version" })
+	@JsonView({ JsonViews.Minimal.class })
 	private Taxonomy2 taxonomy;
 
 	// FIXME: Remove?

src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java

@@ -27,17 +27,16 @@ import javax.persistence.Lob;
 import javax.persistence.OneToMany;
 import javax.persistence.PrePersist;
 import javax.persistence.Table;
-import javax.persistence.Transient;
 import javax.persistence.UniqueConstraint;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-
 import org.apache.commons.lang3.StringUtils;
 import org.genesys2.server.model.GlobalVersionedAuditedModel;
 import org.genesys2.server.model.impl.CropTaxonomy;
 import org.hibernate.annotations.Type;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
 @Cacheable
 @Entity
 // Add index on all fields

src/main/java/org/genesys2/server/model/impl/Country.java

@@ -23,20 +23,27 @@ import java.util.Comparator;
 import java.util.List;
 import java.util.Locale;
 
-import javax.persistence.*;
+import javax.persistence.Cacheable;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.Lob;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.persistence.Transient;
 
 import org.genesys.blocks.model.BasicModel;
-import org.genesys2.server.api.serialization.CountrySerializer;
+import org.genesys.blocks.model.JsonViews;
 import org.hibernate.annotations.Type;
 
+import com.fasterxml.jackson.annotation.JsonView;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 
 @Cacheable
 @Entity
 @Table(name = "country")
-@JsonSerialize(using = CountrySerializer.class)
 public class Country extends BasicModel {
 
 	private static final long serialVersionUID = -1688723909298769804L;
@@ -45,6 +52,7 @@ public class Country extends BasicModel {
 	private String code3;
 
 	@Column(unique = false, length = 2)
+	@JsonView({ JsonViews.Public.class } )
 	private String code2;
 	private boolean current;
 
@@ -52,23 +60,31 @@ public class Country extends BasicModel {
 	private String name;
 
 	@Column(length = 3)
+	@JsonView({ JsonViews.Public.class } )
 	private String codeNum;
+
+	@JsonView({ JsonViews.Public.class } )
 	private Long refnameId;
 
 	@ManyToOne(fetch = FetchType.LAZY, optional = true)
 	@JoinColumn(name = "regionId")
+	@JsonView({ JsonViews.Public.class } )
 	private GeoRegion region;
 
 	@Column(name = "minLongitude")
+	@JsonView({ JsonViews.Public.class } )
 	private Double minLongitude;
 
 	@Column(name = "minLatitude")
+	@JsonView({ JsonViews.Public.class } )
 	private Double minLatitude;
 
 	@Column(name = "maxLongitude")
+	@JsonView({ JsonViews.Public.class } )
 	private Double maxLongitude;
 
 	@Column(name = "maxLatitude")
+	@JsonView({ JsonViews.Public.class } )
 	private Double maxLatitude;
 
 	/**
@@ -76,17 +92,21 @@ public class Country extends BasicModel {
 	 */
 	@Lob
 	@Type(type = "org.hibernate.type.TextType")
+	@JsonView({ JsonViews.Public.class })
 	private String nameL;
 
 	@Lob
 	@Type(type = "org.hibernate.type.TextType")
+	@JsonView({ JsonViews.Public.class } )
 	private String wikiLink;
 
 	@Transient
+	@JsonView({ JsonViews.Protected.class })
 	private JsonNode nameJ;
 
 	@ManyToOne(cascade = {}, optional = true)
 	@JoinColumn(name = "replacedBy")
+	@JsonView({ JsonViews.Public.class })
 	private Country replacedBy;
 
 	public Country() {

src/main/java/org/genesys2/server/model/impl/FaoInstitute.java

@@ -35,19 +35,17 @@ import javax.persistence.OneToMany;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.databind.annotation.JsonSerialize;
-
 import org.apache.commons.lang3.StringUtils;
 import org.genesys.blocks.model.BasicModel;
 import org.genesys.blocks.model.EntityId;
+import org.genesys.blocks.model.JsonViews;
 import org.genesys.blocks.security.model.AclAwareModel;
-import org.genesys2.server.api.serialization.FaoInstituteSerializer;
+
+import com.fasterxml.jackson.annotation.JsonView;
 
 @Cacheable
 @Entity
 @Table(name = "faoinstitute", uniqueConstraints = @UniqueConstraint(columnNames = { "code" }), indexes = { @Index(columnList = "code", name = "code_FAOINSTITUTE") })
-@JsonSerialize(using = FaoInstituteSerializer.class)
 public class FaoInstitute extends BasicModel implements GeoReferencedEntity, AclAwareModel, EntityId {
 
 	private static final long serialVersionUID = -8773002513838748431L;
@@ -61,12 +59,15 @@ public class FaoInstitute extends BasicModel implements GeoReferencedEntity, Acl
 	private String fullName;
 
 	@Column(length = 100)
+	@JsonView({ JsonViews.Public.class })
 	private String type;
 
 	@Column(length = 300)
+	@JsonView({ JsonViews.Public.class })
 	private String url;
 
 	@Column(length = 300)
+	@JsonView({ JsonViews.Public.class })
 	private String email;
 
 	@Column(length = LEN_ACRONYM)
@@ -76,16 +77,17 @@ public class FaoInstitute extends BasicModel implements GeoReferencedEntity, Acl
 	private String vCode;
 
 	@Column(name = "codeSGSV")
+	@JsonView({ JsonViews.Public.class })
 	private String codeSGSV;
 
 	private boolean current;
 
-	@JsonIgnore
 	@ManyToOne(cascade = {}, optional = true)
 	@JoinColumn(name = "countryId")
+	@JsonView({ JsonViews.Minimal.class })
 	private Country country;
 
-	@JsonIgnore
+	@JsonView({ JsonViews.Protected.class })
 	@OneToMany(cascade = {})
 	@JoinColumn(referencedColumnName = "code", name = "instCode")
 	@MapKey(name = "setting")

src/main/java/org/genesys2/server/model/impl/GeoRegion.java

@@ -17,9 +17,12 @@ import javax.persistence.OneToMany;
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
+import org.genesys.blocks.model.JsonViews;
 import org.genesys.blocks.model.VersionedModel;
 import org.hibernate.annotations.Type;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonView;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
@@ -38,16 +41,20 @@ public class GeoRegion extends VersionedModel {
 
 	@ManyToOne()
 	@JoinColumn(name = "parentId")
+	@JsonView({ JsonViews.Public.class })
 	private GeoRegion parentRegion;
 
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "region")
+	@JsonView({ JsonViews.Public.class })
 	private List<Country> countries;
 
 	@Lob
 	@Type(type = "org.hibernate.type.TextType")
+	@JsonIgnore
 	private String nameL;
 
 	@Transient
+	@JsonIgnore
 	private JsonNode nameJ;
 
 	public String getIsoCode() {

src/main/java/org/genesys2/server/service/filter/AccessionCollectFilter.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.genesys2.server.service.filter;
+
+import static org.genesys2.server.model.genesys.QAccessionCollect.accessionCollect;
+
+import java.util.Set;
+
+import org.genesys.blocks.model.filters.BasicModelFilter;
+import org.genesys.blocks.model.filters.StringFilter;
+import org.genesys2.server.model.genesys.AccessionCollect;
+import org.genesys2.server.model.genesys.QAccessionCollect;
+
+import com.querydsl.core.BooleanBuilder;
+import com.querydsl.core.types.Predicate;
+
+/**
+ * Filters for {@link AccessionCollect}
+ */
+public class AccessionCollectFilter extends BasicModelFilter {
+
+	/** The date. */
+	public StringFilter date;
+	
+	/** The numb. */
+	public StringFilter numb;
+	
+	/** The mission. */
+	public Set<String> mission;
+	
+	/** The site. */
+	public StringFilter site;
+	
+	/**
+	 * Builds the query.
+	 *
+	 * @return the predicate
+	 */
+	public Predicate buildQuery() {
+		return buildQuery(accessionCollect);
+	}
+
+	/**
+	 * Builds the query.
+	 *
+	 * @param collect the country
+	 * @return the predicate
+	 */
+	public Predicate buildQuery(QAccessionCollect collect) {
+		final BooleanBuilder and = new BooleanBuilder();
+		super.buildQuery(collect._super, and);
+
+		if (date != null) {
+			and.and(date.buildQuery(collect.collDate));
+		}
+		if (numb != null) {
+			and.and(numb.buildQuery(collect.collNumb));
+		}
+		if (site != null) {
+			and.and(site.buildQuery(collect.collSite));
+		}
+		if (mission != null && !mission.isEmpty()) {
+			and.and(collect.collMissId.in(mission));
+		}
+		return and;
+	}
+
+}

src/main/java/org/genesys2/server/service/filter/AccessionFilter.java

@@ -22,15 +22,13 @@ import java.util.Set;
 import org.genesys.blocks.model.filters.NumberFilter;
 import org.genesys.blocks.model.filters.StringFilter;
 import org.genesys.blocks.model.filters.UuidModelFilter;
+import org.genesys2.server.model.genesys.Accession;
 
 import com.querydsl.core.BooleanBuilder;
 import com.querydsl.core.types.Predicate;
 
-// TODO: Auto-generated Javadoc
 /**
- * The Class SubsetFilter.
- *
- * @author Maxym Borodenko
+ * Filters for {@link Accession}
  */
 public class AccessionFilter extends UuidModelFilter {
 
@@ -73,6 +71,8 @@ public class AccessionFilter extends UuidModelFilter {
 
 	public AccessionGeoFilter geo;
 
+	public AccessionCollectFilter coll;
+
 	/**
 	 * Builds the query.
 	 *
@@ -112,15 +112,18 @@ public class AccessionFilter extends UuidModelFilter {
 		if (origin != null) {
 			and.and(origin.buildQuery(accession.countryOfOrigin));
 		}
-		if (geo != null) {
-			and.and(geo.buildQuery(accession.accessionId.geo));
-		}		
 		if (mlsStatus != null) {
 			and.and(accession.mlsStatus.eq(mlsStatus));
 		}
 		if (available != null) {
 			and.and(accession.available.eq(available));
 		}
+		if (geo != null) {
+			and.and(geo.buildQuery(accession.accessionId.geo));
+		}
+		if (coll != null) {
+			and.and(coll.buildQuery(accession.accessionId.coll));
+		}
 
 		return and;
 	}