Merge branch '282-accession-apiv1-filter' into 'master'

Resolve "Accession APIv1 /filter"

Closes #282

See merge request genesys-pgr/genesys-server!159

src/main/java/org/genesys2/server/api/v1/AccessionController.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.api.v1;
+
+import java.io.IOException;
+import java.util.UUID;
+
+import javax.servlet.http.HttpServletRequest;
+
+import org.genesys.catalog.api.FilteredPage;
+import org.genesys.catalog.service.ShortFilterService;
+import org.genesys2.server.api.ApiBaseController;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.service.AccessionService;
+import org.genesys2.server.service.filter.AccessionFilter;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Sort;
+import org.springframework.http.MediaType;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.servlet.HandlerMapping;
+
+import io.swagger.annotations.Api;
+
+/**
+ * Accession API v1
+ */
+@RestController("accessionApi1")
+@PreAuthorize("isAuthenticated()")
+@RequestMapping(AccessionController.API_BASE)
+@Api(tags = { "accession" })
+public class AccessionController {
+
+	/** The Constant API_BASE. */
+	public static final String API_BASE =  ApiBaseController.APIv1_BASE + "/acn";
+
+	@Autowired
+	private AccessionService accessionService;
+
+	/** The short filter service. */
+	@Autowired
+	protected ShortFilterService shortFilterService;
+
+
+	/**
+	 * Gets the accession
+	 *
+	 * @param uuid the uuid
+	 * @return the subset
+	 */
+	@GetMapping(value = "/{UUID}", produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Accession getByUuid(@PathVariable("UUID") final UUID uuid) {
+		return accessionService.getByUuid(uuid);
+	}
+
+
+	/**
+	 * Gets the accession
+	 *
+	 * @param uuid the uuid
+	 * @return the subset
+	 */
+	@GetMapping(value = "/10.{dummy:[0-9]+}/**}", produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Accession getByDoi(HttpServletRequest request) {
+		final String fullpath = (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
+		final String doi = fullpath.substring(1);
+
+		return accessionService.getByDoi(doi);
+	}
+
+	
+	/**
+	 * List accessions by filterCode or filter
+	 *
+	 * @param page the page
+	 * @param pageSize the page size
+	 * @param direction the direction
+	 * @param sort the sort
+	 * @param filterCode short filter code
+	 * @param filter the filter
+	 * @return the page
+	 * @throws IOException 
+	 */
+	@PostMapping(value = "/list", produces = { MediaType.APPLICATION_JSON_VALUE })
+	public FilteredPage<Accession> list(@RequestParam(name = "p", required = false, defaultValue = "0") final int page,
+            @RequestParam(name = "l", required = false, defaultValue = "50") final int pageSize,
+            @RequestParam(name = "d", required = false, defaultValue = "ASC") final Sort.Direction direction,
+            @RequestParam(name = "s", required = false, defaultValue = "id") final String[] sort,
+			@RequestParam(name = "f", required = false) String filterCode,
+			@RequestBody(required = false) AccessionFilter filter) throws IOException {
+		
+		if (filterCode != null) {
+			filter = shortFilterService.filterByCode(filterCode, AccessionFilter.class);
+		} else {
+			filterCode = shortFilterService.getCode(filter);
+		}
+		return new FilteredPage<>(filterCode, filter, accessionService.list(filter, new PageRequest(page, Integer.min(pageSize, 100), direction, sort)));
+	}
+
+}

src/main/java/org/genesys2/server/api/v1/PermissionController.java

@@ -28,6 +28,7 @@ import org.genesys.blocks.security.model.AclObjectIdentity;
 import org.genesys.blocks.security.model.AclSid;
 import org.genesys.blocks.security.serialization.SidPermissions;
 import org.genesys.blocks.security.service.CustomAclService;
+import org.genesys2.server.api.ApiBaseController;
 import org.genesys2.server.model.UserRole;
 import org.genesys2.server.model.impl.User;
 import org.genesys2.server.service.UserService;
@@ -55,10 +56,12 @@ import io.swagger.annotations.Api;
  * @author Matija Obreza
  */
 @RestController("permissionApi1")
-@RequestMapping(value = { "/api/v1/permission" })
+@RequestMapping(value =  PermissionController.API_BASE )
 @Api(tags = { "permission" })
 public class PermissionController {
 
+	public static final String API_BASE = ApiBaseController.APIv1_BASE + "/permission";
+
 	private static final Logger LOG = LoggerFactory.getLogger(PermissionController.class);
 
 	/** The acl service. */

src/main/java/org/genesys2/server/api/v1/SubsetController.java

@@ -22,6 +22,7 @@ import java.util.UUID;
 
 import org.genesys.catalog.api.FilteredPage;
 import org.genesys.catalog.service.ShortFilterService;
+import org.genesys2.server.api.ApiBaseController;
 import org.genesys2.server.model.impl.Subset;
 import org.genesys2.server.service.SubsetService;
 import org.genesys2.server.service.filter.SubsetFilter;
@@ -53,7 +54,7 @@ import io.swagger.annotations.Api;
 public class SubsetController {
 
 	/** The Constant API_BASE. */
-	public static final String API_BASE = "/api/v1/subset";
+	public static final String API_BASE = ApiBaseController.APIv1_BASE + "/subset";
 
 	@Autowired
 	private SubsetService subsetService;

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
@@ -124,8 +123,6 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 		return sb.toString();
 	}
 	
-
-	@Transient
 	public String getTaxonNameHtml() {
 		final StringBuilder sb = new StringBuilder();
 		sb.append("<i>").append(genus).append(" ").append(species).append("</i>");

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/persistence/AccessionRepository.java

@@ -33,9 +33,10 @@ import org.springframework.data.domain.Sort;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.querydsl.QueryDslPredicateExecutor;
 import org.springframework.data.repository.query.Param;
 
-public interface AccessionRepository extends JpaRepository<Accession, Long>, AccessionRepositoryCustom {
+public interface AccessionRepository extends JpaRepository<Accession, Long>, AccessionRepositoryCustom, QueryDslPredicateExecutor<Accession> {
 
 	@Query("select a.id from Accession a")
 	public List<Long> listAccessionsIds(Pageable pageable);

src/main/java/org/genesys2/server/api/serialization/FaoInstituteSerializer.java → src/main/java/org/genesys2/server/service/AccessionService.java

-/**
- * Copyright 2014 Global Crop Diversity Trust
+/*
+ * 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.
@@ -12,31 +12,40 @@
  * 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;
 
-package org.genesys2.server.api.serialization;
+import java.util.UUID;
 
-import java.io.IOException;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.service.filter.AccessionFilter;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
 
-import org.genesys2.server.model.impl.FaoInstitute;
+public interface AccessionService {
 
-import com.fasterxml.jackson.core.JsonGenerator;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonSerializer;
-import com.fasterxml.jackson.databind.SerializerProvider;
+	/**
+	 * List accessions by filter
+	 *
+	 * @param filter the filter
+	 * @param page the page
+	 * @return the page
+	 */
+	Page<Accession> list(AccessionFilter filter, Pageable page);
 
-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();
-		}
-	}
+	/**
+	 * Gets accession by uuid
+	 *
+	 * @param uuid the uuid
+	 * @return the accession
+	 */
+	Accession getByUuid(UUID uuid);
 
+	/**
+	 * Gets accession by doi.
+	 *
+	 * @param doi the doi
+	 * @return the by doi
+	 */
+	Accession getByDoi(String doi);
 }

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

+/*
+ * 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.
+ */