Crops API v1

- annex1 to crop
- crop service to create/update by crop
- overview data
- simple tests
- added cachable to accessionCount

src/main/java/org/genesys2/server/api/v1/CropsController.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.v1;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import io.swagger.annotations.Api;
+import net.sf.oval.ConstraintViolation;
+import net.sf.oval.Validator;
+import org.genesys.blocks.model.JsonViews;
+import org.genesys.filerepository.InvalidRepositoryPathException;
+import org.genesys2.server.api.ApiBaseController;
+import org.genesys2.server.api.ModelValidationException;
+import org.genesys2.server.api.OAuth2Cleanup;
+import org.genesys2.server.exception.AuthorizationException;
+import org.genesys2.server.model.genesys.Parameter;
+import org.genesys2.server.model.impl.Crop;
+import org.genesys2.server.model.impl.CropRule;
+import org.genesys2.server.model.impl.CropTaxonomy;
+import org.genesys2.server.service.CropService;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.TraitService;
+import org.genesys2.spring.ResourceNotFoundException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.i18n.LocaleContextHolder;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.http.MediaType;
+import org.springframework.security.access.AccessDeniedException;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.web.bind.annotation.*;
+
+import javax.xml.bind.ValidationException;
+import java.util.List;
+
+@RestController("cropApi1")
+@RequestMapping(value = { CropsController.CONTROLLER_URL, "/json/v1/crops" })
+@Api(tags = { "crop" })
+public class CropsController extends ApiBaseController {
+
+	public static final String CONTROLLER_URL = ApiBaseController.APIv1_BASE + "/crops";
+
+	@Autowired
+	GenesysService genesysService;
+
+	@Autowired
+	TraitService traitService;
+
+	@Autowired
+	CropService cropService;
+
+	/**
+	 * List all crops
+	 * @return 
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@RequestMapping(value = "", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public List<Crop> listCrops() {
+		LOG.info("Listing crops");
+		final List<Crop> crops = cropService.list(LocaleContextHolder.getLocale());
+		return crops;
+	}
+
+	/**
+	 * Add a crop
+	 * @return 
+	 * 
+	 * @return
+	 * @throws ValidationException
+	 */
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@RequestMapping(value = { "/save" }, method = { RequestMethod.PUT, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Crop saveCrop(@RequestBody Crop cropJson) throws ValidationException {
+		LOG.info("Creating crop");
+		final Validator validator = new Validator();
+		final List<ConstraintViolation> violations = validator.validate(cropJson);
+		if (violations.size() > 0) {
+			throw new ModelValidationException("Crop does not validate", violations);
+		}
+		Crop crop = cropService.getCrop(cropJson.getShortName());
+
+		if (crop == null) {
+			crop = cropService.addCrop(cropJson);
+		} else {
+			crop = cropService.updateCrop(cropJson);
+		}
+
+		return crop;
+	}
+
+	/**
+	 * Get crop /crops/{shortName}
+	 * @return 
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@RequestMapping(value = "/{shortName}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Crop getCrop(@PathVariable("shortName") String shortName) throws AuthorizationException {
+		LOG.info("Getting crop {}", shortName);
+		return cropService.getCrop(shortName);
+	}
+
+
+	/**
+	 * Get crop details /crops/{shortName}/details
+	 * @return
+	 *
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@JsonView(JsonViews.Public.class)
+	@RequestMapping(value = "/{shortName}/details/{lang}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public CropService.CropDetails getCropDetails(@PathVariable("shortName") String shortName, @PathVariable("lang") String lang) throws InvalidRepositoryPathException {
+		LOG.info("Getting crop details {}", shortName);
+		return cropService.getDetails(shortName, lang);
+	}
+
+	/**
+	 * Delete crop /crops/{shortName}
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@RequestMapping(value = "/{shortName}", method = RequestMethod.DELETE, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody Crop deleteCrop(@PathVariable("shortName") String shortName) throws AuthorizationException {
+		LOG.info("Getting crop {}", shortName);
+		return cropService.delete(cropService.getCrop(shortName));
+	}
+
+	/**
+	 * Get crop descriptors /crops/{shortName}/descriptors
+	 * @return 
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@RequestMapping(value = "/{shortName}/descriptors", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Page<Parameter> getCropDescriptors(@PathVariable("shortName") String shortName) throws AuthorizationException {
+		LOG.info("Getting crop descriptors {}", shortName);
+		final Crop crop = cropService.getCrop(shortName);
+		final Page<Parameter> descriptors = traitService.listTraits(crop, new PageRequest(0, 50));
+		return OAuth2Cleanup.clean(descriptors);
+	}
+
+	/**
+	 * Get crop taxonomy rules /crops/{shortName}/rules
+	 * @return 
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@RequestMapping(value = "/{shortName}/rules", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public List<CropRule> getCropRules(@PathVariable("shortName") String shortName) throws AuthorizationException {
+		LOG.info("Getting crop rules {}", shortName);
+		final Crop crop = cropService.getCrop(shortName);
+		final List<CropRule> cropRules = cropService.getCropRules(crop);
+		return cropRules;
+	}
+
+	/**
+	 * Get crop taxonomy rules /crops/{shortName}/rules
+	 * 
+	 * @return
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@RequestMapping(value = "/{shortName}/rules", method = { RequestMethod.PUT, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody List<CropRule> updateCropRules(@PathVariable("shortName") String shortName, @RequestBody List<CropRule> rules) throws AuthorizationException {
+		LOG.info("Updating crop rules for {}", shortName);
+		final Crop crop = cropService.getCrop(shortName);
+		if (crop == null)
+			throw new ResourceNotFoundException("No crop " + shortName);
+
+		cropService.setCropRules(crop, rules);
+
+		return cropService.getCropRules(crop);
+	}
+
+	/**
+	 * Get crop taxonomies /crops/{shortName}/taxa
+	 * @return 
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@RequestMapping(value = "/{shortName}/taxa", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Page<CropTaxonomy> getCropTaxa(@PathVariable("shortName") String shortName) throws AuthorizationException {
+		LOG.info("Getting crop taxa {}", shortName);
+		final Crop crop = cropService.getCrop(shortName);
+		final Page<CropTaxonomy> cropTaxa = cropService.getCropTaxonomies(crop, new PageRequest(0, 50));
+		return OAuth2Cleanup.clean(cropTaxa);
+	}
+
+	/**
+	 * Rebuild taxonomy-crop lists
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@RequestMapping(value = "/rebuild", method = RequestMethod.POST, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public void rebuild() {
+		cropService.rebuildTaxonomies();
+	}
+
+	/**
+	 * Rebuild taxonomy-crop lists
+	 * 
+	 * @return
+	 * @throws AuthorizationException
+	 */
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@RequestMapping(value = "{shortName}/rebuild", method = RequestMethod.POST, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public void rebuildCrop(@PathVariable("shortName") String shortName) {
+		LOG.info("Updating crop rules for {}", shortName);
+		final Crop crop = cropService.getCrop(shortName);
+		if (crop == null)
+			throw new ResourceNotFoundException("No crop " + shortName);
+
+		cropService.rebuildTaxonomies(crop);
+	}
+
+}

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

@@ -80,6 +80,9 @@ public class Crop extends GlobalVersionedAuditedModel implements AclAwareModel {
 	@Column(nullable = false, length = 200)
 	private String name;
 
+	@Column(name = "annex1")
+	private boolean annex1 = false;
+
 	@Lob
 	@Type(type = "org.hibernate.type.TextType")
 	private String description;
@@ -255,4 +258,12 @@ public class Crop extends GlobalVersionedAuditedModel implements AclAwareModel {
 	public void setOtherNames(List<String> otherNames) {
 		this.otherNames = otherNames;
 	}
+
+	public boolean isAnnex1() {
+		return annex1;
+	}
+
+	public void setAnnex1(boolean annex1) {
+		this.annex1 = annex1;
+	}
 }

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

@@ -18,8 +18,12 @@ package org.genesys2.server.service;
 
 import java.util.List;
 import java.util.Locale;
+import java.util.Map;
 
+import org.genesys.filerepository.InvalidRepositoryPathException;
+import org.genesys.filerepository.model.RepositoryImage;
 import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.Article;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.CropRule;
 import org.genesys2.server.model.impl.CropTaxonomy;
@@ -30,6 +34,8 @@ public interface CropService {
 
 	Crop getCrop(String shortName);
 
+	CropDetails getDetails(String shortName, String lang) throws InvalidRepositoryPathException;
+
 	List<Crop> listCrops();
 
 	Page<Crop> listCrops(Pageable pageable);
@@ -57,6 +63,7 @@ public interface CropService {
 	 */
 	Crop addCrop(String shortName, String name, String description, String i18n);
 
+	Crop addCrop(Crop crop);
 	/**
 	 * Updates a crop record
 	 * 
@@ -68,6 +75,8 @@ public interface CropService {
 	 */
 	Crop updateCrop(Crop crop, String name, String description, String i18n);
 
+	Crop updateCrop(Crop crop);
+
 	CropRule addCropRule(Crop crop, String genus, String species, boolean included);
 
 	List<CropRule> getCropRules(Crop crop);
@@ -110,4 +119,23 @@ public interface CropService {
 	Crop updateAliases(Crop crop, List<String> otherNames);
 
 
+	class CropDetails {
+		public Crop crop;
+		public Article blurb;
+		public long accessionCount;
+		public List<RepositoryImage> covers;
+		public Map<String, ElasticsearchService.TermResult> overview;
+
+
+		public static CropDetails from(Crop crop, Article blurb, long accessionCount, List<RepositoryImage> covers, Map<String, ElasticsearchService.TermResult> overview){
+			CropDetails cropDetails = new CropDetails();
+			cropDetails.crop = crop;
+			cropDetails.blurb = blurb;
+			cropDetails.accessionCount = accessionCount;
+			cropDetails.covers = covers;
+			cropDetails.overview = overview;
+
+			return cropDetails;
+		}
+	}
 }

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

@@ -15,6 +15,7 @@
  */
 package org.genesys2.server.service.filter;
 
+import java.io.Serializable;
 import java.util.Set;
 import java.util.UUID;
 
@@ -32,7 +33,7 @@ import com.querydsl.core.types.Predicate;
 /**
  * Filters for {@link Accession}.
  */
-public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession> {
+public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession> implements Serializable {
 
 	/** The historic. */
 	public Boolean historic;

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

@@ -150,6 +150,7 @@ public class AccessionServiceImpl implements AccessionService {
     }
 
     @Override
+	@Cacheable(value = "accessionCount")
 	public long countAccessions(AccessionFilter filter) {
 		long total = elasticsearchService.count(Accession.class, filter);
 

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

@@ -16,19 +16,20 @@
 
 package org.genesys2.server.service.impl;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Locale;
-import java.util.Set;
+import java.nio.file.Paths;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.Predicate;
 import org.apache.commons.lang3.StringUtils;
+import org.genesys.filerepository.InvalidRepositoryPathException;
+import org.genesys.filerepository.model.ImageGallery;
+import org.genesys.filerepository.model.RepositoryImage;
+import org.genesys.filerepository.service.ImageGalleryService;
+import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.Article;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.CropRule;
 import org.genesys2.server.model.impl.CropTaxonomy;
@@ -36,10 +37,8 @@ import org.genesys2.server.persistence.CropRepository;
 import org.genesys2.server.persistence.CropRuleRepository;
 import org.genesys2.server.persistence.CropTaxonomyRepository;
 import org.genesys2.server.persistence.Taxonomy2Repository;
-import org.genesys2.server.service.CRMException;
-import org.genesys2.server.service.ContentService;
-import org.genesys2.server.service.CropService;
-import org.genesys2.server.service.HtmlSanitizer;
+import org.genesys2.server.service.*;
+import org.genesys2.server.service.filter.AccessionFilter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -47,7 +46,9 @@ import org.springframework.cache.annotation.CacheEvict;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.springframework.security.access.AccessDeniedException;
 import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.security.oauth2.common.exceptions.UnauthorizedUserException;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
@@ -76,6 +77,15 @@ public class CropServiceImpl implements CropService {
 	@Autowired
 	private ContentService contentService;
 
+	@Autowired
+	private AccessionService accessionService;
+
+	@Autowired
+	private ElasticsearchService elasticsearchService;
+
+	@Autowired
+	private ImageGalleryService imageGalleryService;
+
 	@Autowired
 	private Taxonomy2Repository taxonomy2Repository;
 
@@ -100,6 +110,27 @@ public class CropServiceImpl implements CropService {
 		return crop;
 	}
 
+	@Override
+	@Transactional(readOnly = true, noRollbackFor = AccessDeniedException.class)
+	public CropDetails getDetails(String shortName, String lang) throws AccessDeniedException, InvalidRepositoryPathException {
+
+		Locale locale = lang == null ? Locale.getDefault() : Locale.forLanguageTag(lang);
+
+		Crop crop = getCrop(shortName);
+
+		Article article = contentService.getArticle(crop, "blurp", locale);
+		AccessionFilter byCrop = new AccessionFilter();
+		byCrop.cropName = crop.getName();
+		long accessionCount = accessionService.countAccessions(byCrop);
+
+		ImageGallery imageGallery = imageGalleryService.loadImageGallery(Paths.get("/crop/"+ crop.getShortName() +"/cover"));
+		List<RepositoryImage> covers = imageGallery == null ? Collections.emptyList() : imageGallery.getImages();
+
+		Map<String, ElasticsearchService.TermResult> overview = getOverviewData(byCrop);
+
+		return CropDetails.from(crop, article, accessionCount, covers, overview);
+	}
+
 	@PreAuthorize("hasRole('ADMINISTRATOR')")
 	@Override
 	@Transactional
@@ -346,6 +377,24 @@ public class CropServiceImpl implements CropService {
 		return crop;
 	}
 
+	@Override
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#crop, 'ADMINISTRATION')")
+	@Transactional(readOnly = false)
+	@CacheEvict(allEntries = true, value = CACHE_CROPS)
+	public Crop updateCrop(Crop crop) {
+		final Crop toUpdate = getCrop(crop.getShortName());
+		copyValues(toUpdate, crop);
+		return cropRepository.save(toUpdate);
+	}
+
+	@Override
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	@Transactional(readOnly = false)
+	@CacheEvict(allEntries = true, value = CACHE_CROPS)
+	public Crop addCrop(Crop crop) {
+		return cropRepository.save(crop);
+	}
+
 	@Override
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#crop, 'ADMINISTRATION')")
 	@Transactional(readOnly = false)
@@ -445,4 +494,30 @@ public class CropServiceImpl implements CropService {
 			cropTaxonomyRepository.save(toAdd);
 		}
 	}
+
+	private Map<String, ElasticsearchService.TermResult> getOverviewData(AccessionFilter byCropFilter) {
+		String[] terms = new String[] {"taxonomy.genus", "taxonomy.genusSpecies", "institute.code",
+				"institute.country.code3", "mlsStatus", "available"};
+
+		try {
+			return elasticsearchService.termStatisticsAuto(Accession.class, byCropFilter, 10, terms);
+		} catch (SearchException e) {
+			LOG.error("Error occurred during search", e);
+			return null;
+		}
+	}
+
+
+	private void copyValues(Crop target, Crop source) {
+
+		target.setDescription(source.getDescription());
+		target.setI18n(source.getI18n());
+		target.setName(source.getName());
+
+		if (source.getOtherNames() != null) {
+			target.setOtherNames(source.getOtherNames().stream().distinct().map(otherName -> StringUtils.trim(otherName)).filter(otherName -> StringUtils.isNotBlank(otherName)).sorted().collect(Collectors.toList()));
+		}
+		if (source.getCropRules() != null)
+		target.getCropRules().addAll(source.getCropRules());
+	}
 }

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

@@ -4373,6 +4373,19 @@ databaseChangeLog:
           indexName: IX_id3
           tableName: accession
 
+- changeSet:
+      id: 1539794655476-1
+      author: vpavlov
+      comment: added annex1 to crop
+      changes:
+      - addColumn:
+          columns:
+          - column:
+              name:  annex1
+              type:  boolean
+              defaultValue: false
+          tableName: crop
+
 
 # ENABLE AFTER SOME TIME
 # - changeSet:

src/test/java/org/genesys/test/server/api/v0/CropsControllerTest.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.genesys.test.server.api.v0;
 
 import static org.hamcrest.Matchers.*;
@@ -154,6 +169,7 @@ public class CropsControllerTest extends AbstractApiTest {
                                 fieldWithPath("active").ignored(),
                                 fieldWithPath("_class").ignored(),
                                 fieldWithPath("_permissions.*").ignored(),
+                                fieldWithPath("annex1").ignored(),
 		                        fieldWithPath("createdBy").ignored(),
 		                        fieldWithPath("createdDate").ignored(),
 		                        fieldWithPath("lastModifiedBy").ignored(),
@@ -193,6 +209,7 @@ public class CropsControllerTest extends AbstractApiTest {
                         fieldWithPath("active").ignored(),
                         fieldWithPath("_class").ignored(),
                         fieldWithPath("_permissions.*").ignored(),
+                        fieldWithPath("annex1").ignored(),
                         fieldWithPath("createdBy").ignored(),
                         fieldWithPath("createdDate").ignored(),
                         fieldWithPath("lastModifiedBy").ignored(),

src/test/java/org/genesys/test/server/api/v0/docs/ApiCropsTest.java

@@ -142,6 +142,7 @@ public class ApiCropsTest extends AbstractApiTest {
 								fieldWithPath("active").type(JsonFieldType.BOOLEAN).description("Record is active"), 
 								fieldWithPath("_class").ignored(),
 								fieldWithPath("_permissions.*").ignored(),
+								fieldWithPath("annex1").ignored(),
 								fieldWithPath("createdDate").ignored(),
 								fieldWithPath("lastModifiedBy").ignored(),
 								fieldWithPath("lastModifiedDate").ignored())));
@@ -167,6 +168,7 @@ public class ApiCropsTest extends AbstractApiTest {
 								fieldWithPath("i18n").type(JsonFieldType.STRING).optional().description("i18n map"), fieldWithPath("createdBy").ignored(),
 								fieldWithPath("_class").ignored(),
 								fieldWithPath("_permissions.*").ignored(),
+								fieldWithPath("annex1").ignored(),
 								fieldWithPath("createdDate").ignored(), 
 								fieldWithPath("lastModifiedBy").ignored(), 
 								fieldWithPath("lastModifiedDate").ignored())));