Merge branch 'genesys-ui-92-geo-module' into 'master'

API endpoints for Geo module

See merge request genesys-pgr/genesys-server!266

src/main/java/org/genesys2/server/api/v1/GeoController.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.util.List;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import io.swagger.annotations.Api;
+import org.genesys.blocks.model.JsonViews;
+import org.genesys2.server.api.ApiBaseController;
+import org.genesys2.server.model.impl.Country;
+import org.genesys2.server.model.impl.GeoRegion;
+import org.genesys2.server.service.GeoRegionService;
+import org.genesys2.server.service.GeoService;
+import org.genesys2.spring.ResourceNotFoundException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.i18n.LocaleContextHolder;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+@RestController("geoApi1")
+@RequestMapping(value = { org.genesys2.server.api.v1.GeoController.CONTROLLER_URL })
+@Api(tags = { "geo" })
+public class GeoController extends ApiBaseController {
+
+	public static final String CONTROLLER_URL = ApiBaseController.APIv1_BASE + "/geo";
+
+	@Autowired
+	private GeoService geoService;
+
+	@Autowired
+	private GeoRegionService geoRegionService;
+
+	@RequestMapping(value = "/countries", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public List<Country> listCountries() {
+		LOG.info("Listing countries");
+		return geoService.listActive(LocaleContextHolder.getLocale());
+	}
+
+	@JsonView(JsonViews.Public.class)
+	@RequestMapping(value = "/country/details/{iso3code}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public GeoService.CountryDetails getCountryDetails(@PathVariable("iso3code") String iso3code) {
+		LOG.info("Getting country details bu ISO3 code {}", iso3code);
+		return geoService.getDetails(iso3code);
+	}
+
+	@RequestMapping(value = "/country/{iso3code}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Country getCountry(@PathVariable("iso3code") String iso3code) {
+		LOG.info("Getting country {}", iso3code);
+		Country country = geoService.getCountry(iso3code);
+		if (country == null) {
+			throw new ResourceNotFoundException();
+		}
+		return country;
+	}
+
+	@RequestMapping(value = "/regions", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public List<GeoRegion> getGeoRegions() {
+		LOG.info("Listing regions");
+		return geoRegionService.findAll();
+	}
+
+	@RequestMapping(value = "/region/details/{isoCode}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public GeoRegionService.RegionDetails getGeoRegionDetails(@PathVariable("isoCode") String isoCode) {
+		LOG.info("Getting region {}", isoCode);
+		return geoRegionService.getDetails(isoCode);
+	}
+}
\ No newline at end of file

src/main/java/org/genesys2/server/mvc/GeoRegionController.java

@@ -3,6 +3,7 @@ package org.genesys2.server.mvc;
 import java.util.List;
 import java.util.stream.Collectors;
 
+import org.genesys2.server.exception.NotFoundElement;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.GeoRegion;
 import org.genesys2.server.persistence.CountryRepository;
@@ -38,15 +39,10 @@ public class GeoRegionController extends BaseController {
     }
 
     @RequestMapping("/{isoCode}")
-    public String view(ModelMap model, @PathVariable(value = "isoCode") String code) {
+    public String view(ModelMap model, @PathVariable(value = "isoCode") String code) throws NotFoundElement {
 
         GeoRegion geoRegion = geoRegionService.find(code);
 
-        if (geoRegion == null) {
-            LOG.error("Can't find region for region code {}", code);
-            throw new ResourceNotFoundException("Can't find region for region code " + code);
-        }
-
         List<Country> countryList = geoRegion.getCountries().stream().filter(country -> isCurrent(country)).collect(Collectors.toList());
         Country.sort(countryList, getLocale());
 

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

 package org.genesys2.server.service;
 
-import org.genesys2.server.model.impl.Country;
-import org.genesys2.server.model.impl.GeoRegion;
-import org.xml.sax.SAXException;
-
 import javax.xml.parsers.ParserConfigurationException;
 import java.io.IOException;
+import java.io.Serializable;
 import java.util.Collection;
 import java.util.List;
 import java.util.Locale;
 import java.util.Set;
 
+import com.fasterxml.jackson.annotation.JsonUnwrapped;
+import org.genesys2.server.model.impl.Country;
+import org.genesys2.server.model.impl.GeoRegion;
+import org.xml.sax.SAXException;
+
 public interface GeoRegionService {
 
 	GeoRegion find(String regionIsoCode);
@@ -41,4 +43,21 @@ public interface GeoRegionService {
 	 */
 	Collection<String> countryCodesFor(Set<String> regionCodes);
 
+	RegionDetails getDetails(String isoCode);
+
+	public static class RegionDetails implements Serializable {
+		private static final long serialVersionUID = -8652090344263391432L;
+
+		@JsonUnwrapped
+		public GeoRegion region;
+		public List<GeoRegion> subRegions;
+
+		public static RegionDetails from(GeoRegion region, List<GeoRegion> subRegions) {
+			RegionDetails regionDetails = new RegionDetails();
+			regionDetails.region = region;
+			regionDetails.subRegions = subRegions;
+			return regionDetails;
+		}
+	}
+
 }

src/main/java/org/genesys2/server/service/GeoService.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.
@@ -12,14 +12,19 @@
  * 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;
 
 import java.io.IOException;
+import java.io.Serializable;
 import java.util.List;
 import java.util.Locale;
+import java.util.Map;
 
+import com.fasterxml.jackson.annotation.JsonUnwrapped;
+import com.fasterxml.jackson.annotation.JsonView;
+import org.genesys.blocks.model.JsonViews;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.ITPGRFAStatus;
@@ -129,4 +134,33 @@ public interface GeoService {
 	 */
 	String getBoundingBox(AppliedFilters filters);
 
+	CountryDetails getDetails(String iso3code);
+
+	public static class CountryDetails implements Serializable {
+		private static final long serialVersionUID = -1556370638451781192L;
+
+		@JsonUnwrapped
+		public Country country;
+
+		@JsonView({ JsonViews.Public.class })
+		public List<FaoInstitute> faoInstitutes;
+		public List<FaoInstitute> genesysInstitutes;
+		@JsonView({ JsonViews.Public.class })
+		public Map<String, ElasticsearchService.TermResult> overview;
+		public Long accessionCount;
+		public Long countByLocation;
+
+		public static CountryDetails from(Country country, Long accessionCount, Long countByLocation, List<FaoInstitute> faoInstitutes, List<FaoInstitute> genesysInstitutes, Map<String, ElasticsearchService.TermResult> overview) {
+			CountryDetails countryDetails = new CountryDetails();
+			countryDetails.country = country;
+			countryDetails.accessionCount = accessionCount;
+			countryDetails.countByLocation = countByLocation;
+			countryDetails.faoInstitutes = faoInstitutes;
+			countryDetails.genesysInstitutes = genesysInstitutes;
+			countryDetails.overview = overview;
+
+			return countryDetails;
+		}
+	}
+
 }

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

@@ -28,6 +28,7 @@ import java.util.stream.Collectors;
 
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.genesys2.server.exception.NotFoundElement;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.GeoRegion;
 import org.genesys2.server.model.impl.QGeoRegion;
@@ -78,6 +79,9 @@ public class GeoRegionServiceImpl implements GeoRegionService {
 	@Override
 	public GeoRegion find(String regionIsoCode) {
 		GeoRegion geoRegion = geoRegionRepository.findByIsoCode(regionIsoCode);
+		if (geoRegion == null) {
+			throw new NotFoundElement("Can't find region for region code " + regionIsoCode);
+		}
 		geoRegion.getCountries().size();
 		return geoRegion;
 	}
@@ -238,6 +242,14 @@ public class GeoRegionServiceImpl implements GeoRegionService {
 		return x.fetch();
 	}
 
+	@Override
+	public RegionDetails getDetails(final String isoCode) {
+		GeoRegion region = find(isoCode);
+		region.setCountries(region.getCountries().stream().filter(Country::isCurrent).collect(Collectors.toList()));
+		List<GeoRegion> subRegions = getChildren(region.getIsoCode());
+		return RegionDetails.from(region, subRegions);
+	}
+
 	/* (non-Javadoc)
 	 * @see org.genesys2.server.service.GeoRegionService#conversionToSubRegionsList(org.genesys2.server.model.impl.GeoRegion)
 	 */

src/main/java/org/genesys2/server/service/impl/GeoServiceImpl.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.
@@ -12,7 +12,7 @@
  * 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.impl;
 
@@ -24,20 +24,29 @@ import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
+import java.util.Map;
 import java.util.Set;
 import java.util.TreeSet;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
+import org.genesys2.server.exception.NotFoundElement;
+import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.ITPGRFAStatus;
 import org.genesys2.server.persistence.CountryRepository;
 import org.genesys2.server.persistence.ITPGRFAStatusRepository;
+import org.genesys2.server.service.AccessionService;
 import org.genesys2.server.service.CRMException;
 import org.genesys2.server.service.ContentService;
+import org.genesys2.server.service.ElasticsearchService;
 import org.genesys2.server.service.GenesysFilterService;
+import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
+import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.filter.AccessionFilter;
+import org.genesys2.server.service.filter.CountryFilter;
 import org.genesys2.server.service.worker.CountryInfo;
 import org.genesys2.server.service.worker.DavrosCountrySource;
 import org.genesys2.server.service.worker.GeoNamesCountrySource;
@@ -81,6 +90,18 @@ public class GeoServiceImpl implements GeoService {
 	@Autowired
 	private GenesysFilterService filterService;
 
+	@Autowired
+	private ElasticsearchService elasticsearchService;
+
+	@Autowired
+	private InstituteService instituteService;
+
+	@Autowired
+	private AccessionService accessionService;
+
+	@Autowired
+	private GenesysService genesysService;
+
 	private final ObjectMapper mapper = new ObjectMapper();
 
 	@Override
@@ -450,6 +471,38 @@ public class GeoServiceImpl implements GeoService {
 		return countryRepository.autocomplete("%" + term + "%", new PageRequest(0, 10));
 	}
 
+	@Override
+	public CountryDetails getDetails(String iso3code) {
+		Country country = getCountry(iso3code);
+		if (country == null) {
+			throw new NotFoundElement("Cannot find country by ISO code " + iso3code);
+		}
+
+		AccessionFilter byCountry = new AccessionFilter();
+		byCountry.origin = new CountryFilter();
+		byCountry.origin.iso3 = new HashSet<String>(){{ add(country.getCode3()); }};
+		long accessionCount = accessionService.countAccessions(byCountry);
+		long countByLocation = genesysService.countByLocation(country);
+
+		Map<String, ElasticsearchService.TermResult> overview = getOverviewData(byCountry);
+		List<FaoInstitute> genesysInstitutes = instituteService.listByCountryActive(country);
+		List<FaoInstitute> faoInstitutes = instituteService.listByCountry(country);
+
+		return CountryDetails.from(country, accessionCount, countByLocation, faoInstitutes, genesysInstitutes, overview);
+	}
+
+	private Map<String, ElasticsearchService.TermResult> getOverviewData(AccessionFilter byCountryFilter) {
+		String[] terms = new String[] {"taxonomy.genus", "taxonomy.genusSpecies", "institute.code",
+			"institute.country.code3", "mlsStatus", "available"};
+
+		try {
+			return elasticsearchService.termStatisticsAuto(Accession.class, byCountryFilter, 10, terms);
+		} catch (SearchException e) {
+			LOG.error("Error occurred during search", e);
+			return null;
+		}
+	}
+
 	@Override
 	public String getBoundingBox(final AppliedFilters filters) {
 		filterService.transformFiltersIfNeed(filters);

src/test/java/org/genesys/test/server/api/v1/GeoControllerTest.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.v1;
+
+import java.util.Collections;
+
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.notNullValue;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
+import org.genesys.test.base.AbstractApiTest;
+import org.genesys2.server.api.v1.GeoController;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.Country;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.model.impl.GeoRegion;
+import org.genesys2.server.persistence.AccessionRepository;
+import org.genesys2.server.persistence.CountryRepository;
+import org.genesys2.server.persistence.FaoInstituteRepository;
+import org.genesys2.server.persistence.GeoRegionRepository;
+import org.genesys2.server.service.TaxonomyService;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.test.web.servlet.result.MockMvcResultHandlers;
+import org.springframework.transaction.annotation.Transactional;
+
+/**
+ * @author Maxym Borodenko
+ */
+@Transactional(transactionManager = "transactionManager")
+public class GeoControllerTest extends AbstractApiTest {
+
+	@Autowired
+	private TaxonomyService taxonomyService;
+
+	@Autowired
+	private CountryRepository countryRepository;
+	@Autowired
+	private GeoRegionRepository geoRegionRepository;
+	@Autowired
+	private AccessionRepository accessionRepository;
+	@Autowired
+	private FaoInstituteRepository instituteRepository;
+
+	private Country country;
+	private GeoRegion region;
+
+	@Transactional
+	@Before
+	@Override
+	public void beforeTest() throws Exception {
+		super.beforeTest();
+		country = setupCountry("UKR", "Ukraine");
+		region = setupRegion("001", "Europe", null, null);
+	}
+
+	@Transactional
+	@After
+	@Override
+	public void cleanup() throws Exception {
+		geoRegionRepository.deleteAll();
+		accessionRepository.deleteAll();
+		super.cleanup();
+		countryRepository.deleteAll();
+	}
+
+	@Test
+	public void listCountriesTest() throws Exception {
+		mockMvc.perform(get(GeoController.CONTROLLER_URL.concat("/countries"))
+			.contentType(MediaType.APPLICATION_JSON_UTF8))
+//			.andDo(MockMvcResultHandlers.print())
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+			.andExpect(jsonPath("$", hasSize(1)))
+			.andExpect(jsonPath("$[0].id", is(country.getId().intValue())))
+			.andExpect(jsonPath("$[0].name", is(country.getName())))
+			.andExpect(jsonPath("$[0].code3", is(country.getCode3())))
+			.andDo(document("country-list"));
+	}
+
+	@Test
+	public void getCountryDetailsTest() throws Exception {
+		setupAccession();
+		mockMvc.perform(get(GeoController.CONTROLLER_URL.concat("/country/details/{iso3code}"), country.getCode3())
+			.contentType(MediaType.APPLICATION_JSON_UTF8))
+//			.andDo(MockMvcResultHandlers.print())
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+			.andExpect(jsonPath("$.id", is(country.getId().intValue())))
+			.andExpect(jsonPath("$.name", is(country.getName())))
+			.andExpect(jsonPath("$.code3", is(country.getCode3())))
+			.andExpect(jsonPath("$.overview", notNullValue()))
+			.andExpect(jsonPath("$.countByLocation", is(1)))
+			.andExpect(jsonPath("$.accessionCount", is(1)));
+	}
+
+	@Test
+	public void getGeoRegionsTest() throws Exception {
+		mockMvc.perform(get(GeoController.CONTROLLER_URL.concat("/regions"))
+			.contentType(MediaType.APPLICATION_JSON_UTF8))
+//			.andDo(MockMvcResultHandlers.print())
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+			.andExpect(jsonPath("$", hasSize(1)))
+			.andExpect(jsonPath("$[0].id", is(region.getId().intValue())))
+			.andExpect(jsonPath("$[0].name", is(region.getName())))
+			.andExpect(jsonPath("$[0].isoCode", is(region.getIsoCode())))
+			.andDo(document("region-list"));
+	}
+
+	@Test
+	public void getGeoRegionDetailsTest() throws Exception {
+		GeoRegion geoRegion = setupRegion("003", "Eastern Europe", country, region);
+		mockMvc.perform(get(GeoController.CONTROLLER_URL.concat("/region/details/{isoCode}"), geoRegion.getIsoCode())
+			.contentType(MediaType.APPLICATION_JSON_UTF8))
+//			.andDo(MockMvcResultHandlers.print())
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+			.andExpect(jsonPath("$.id", is(geoRegion.getId().intValue())))
+			.andExpect(jsonPath("$.name", is(geoRegion.getName())))
+			.andExpect(jsonPath("$.isoCode", is(geoRegion.getIsoCode())))
+			.andExpect(jsonPath("$.parentRegion.isoCode", is(geoRegion.getParentRegion().getIsoCode())))
+			.andExpect(jsonPath("$.countries[0].code3", is(country.getCode3())))
+			.andExpect(jsonPath("$.subRegions", hasSize(0)));
+	}
+
+	private Country setupCountry(String isoCode, String name){
+		Country country = new Country();
+		country.setCode3(isoCode);
+		country.setName(name);
+		country.setCurrent(true);
+		return countryRepository.save(country);
+	}
+
+	private GeoRegion setupRegion(String isoCode, String name, Country country, GeoRegion parentRegion) {
+		GeoRegion region = new GeoRegion();
+		region.setCountries(Collections.singletonList(country));
+		region.setIsoCode(isoCode);
+		region.setName(name);
+		region.setParentRegion(parentRegion);
+		return geoRegionRepository.save(region);
+	}
+
+	private Accession setupAccession() {
+		Accession a = new Accession();
+		a.setAccessionId(new AccessionId());
+		a.setInstitute(setupInstitute("INS001"));
+		a.setAccessionNumber("ACC001");
+		a.setCountryOfOrigin(country);
+		Taxonomy2 taxon = new Taxonomy2();
+		taxon.setGenus("Hordeum");
+		a.setTaxonomy(taxonomyService.ensureTaxonomy(taxon));
+		return accessionRepository.save(a);
+	}
+
+	private FaoInstitute setupInstitute(String instCode){
+		FaoInstitute institute = new FaoInstitute();
+		institute.setCode(instCode);
+		institute.setCountry(country);
+		institute.setAccessionCount(1);
+		institute.setPgrActivity(true);
+		return instituteRepository.save(institute);
+	}
+}