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Genesys Backend
Commit a20b5f93 authored by Matija Obreza's avatar Matija Obreza
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Merge branch 'crop-relink-accessions' into 'master' 

Crops: relink accessions with Crop by #cropName

See merge request genesys-pgr/genesys-server!327
parents d5e87016 d8c98197
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Showing with 182 additions and 32 deletions
src/main/java/org/genesys2/server/api/v1/CropsController.java
View file @ a20b5f93
......@@ -31,7 +31,6 @@ 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;
......@@ -39,6 +38,7 @@ 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.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;
......@@ -61,13 +61,13 @@ public class CropsController extends ApiBaseController {
public static final String CONTROLLER_URL = ApiBaseController.APIv1_BASE + "/crops";
@Autowired
GenesysService genesysService;
private TraitService traitService;
@Autowired
TraitService traitService;
private CropService cropService;
@Autowired
CropService cropService;
private ThreadPoolTaskExecutor threadPoolTaskExecutor;
/**
* List of Crop details
......@@ -258,4 +258,24 @@ public class CropsController extends ApiBaseController {
cropService.rebuildTaxonomies(crop);
}
/**
* Link accession#cropName with crop
*
* @return
* @throws AuthorizationException
*/
@PreAuthorize("hasRole('ADMINISTRATOR')")
@RequestMapping(value = "{shortName}/relink", params= { "accessions" }, method = RequestMethod.POST, produces = { MediaType.APPLICATION_JSON_VALUE })
public void relinkAccessions(@PathVariable("shortName") String shortName) {
LOG.info("Linking accessions to crop {}", shortName);
final Crop crop = cropService.getCrop(shortName);
if (crop == null)
throw new ResourceNotFoundException("No crop " + shortName);
threadPoolTaskExecutor.execute(() -> {
cropService.unlinkAccessionsForCrop(crop);
cropService.linkAccessionsWithCrop(crop);
});
}
}
src/main/java/org/genesys2/server/model/impl/Crop.java
View file @ a20b5f93
......@@ -35,29 +35,32 @@ import javax.persistence.JoinColumn;
import javax.persistence.Lob;
import javax.persistence.OneToMany;
import javax.persistence.OrderBy;
import javax.persistence.PrePersist;
import javax.persistence.PreUpdate;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
import javax.validation.constraints.NotNull;
import javax.validation.constraints.Size;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonView;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.lang3.StringUtils;
import org.genesys.blocks.model.JsonViews;
import org.genesys.blocks.model.SelfCleaning;
import org.genesys.blocks.security.model.AclAwareModel;
import org.genesys2.server.model.GlobalVersionedAuditedModel;
import org.hibernate.annotations.Type;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonView;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
@Cacheable
@Entity
@Table(name = "crop")
public class Crop extends GlobalVersionedAuditedModel implements AclAwareModel {
public class Crop extends GlobalVersionedAuditedModel implements SelfCleaning, AclAwareModel {
private static final long serialVersionUID = -2686341831839109257L;
......@@ -117,6 +120,13 @@ public class Crop extends GlobalVersionedAuditedModel implements AclAwareModel {
@JsonIgnore
private transient JsonNode i18nJU;
@PrePersist
@PreUpdate
private void prePersist() {
trimStringsToNull();
this.shortName = this.shortName.toLowerCase();
}
public String getName() {
return name;
......
src/main/java/org/genesys2/server/service/CropService.java
View file @ a20b5f93
/**
* 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;
......@@ -128,6 +128,21 @@ public interface CropService {
*/
Crop updateAliases(Crop crop, List<String> otherNames);
/**
* Unlink accessions from crop where accession#cropName doesn't match
*
* @param crop
*/
void unlinkAccessionsForCrop(Crop crop);
/**
* Link accessions to Crop by accession#cropName
*
* @param crop
*/
void linkAccessionsWithCrop(Crop crop);
public static class CropDetails implements Serializable {
private static final long serialVersionUID = 1622015024393351713L;
......@@ -152,4 +167,6 @@ public interface CropService {
return cropDetails;
}
}
}
src/main/java/org/genesys2/server/service/impl/CropServiceImpl.java
View file @ a20b5f93
......@@ -27,6 +27,8 @@ import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import javax.validation.Valid;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.Predicate;
import org.apache.commons.lang3.StringUtils;
......@@ -35,12 +37,15 @@ 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.component.security.AsAdminInvoker;
import org.genesys2.server.model.genesys.Accession;
import org.genesys2.server.model.genesys.QAccession;
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;
import org.genesys2.server.persistence.AccessionRepository;
import org.genesys2.server.persistence.CropRepository;
import org.genesys2.server.persistence.CropRuleRepository;
import org.genesys2.server.persistence.CropTaxonomyRepository;
......@@ -52,6 +57,7 @@ import org.genesys2.server.service.CropService;
import org.genesys2.server.service.ElasticsearchService;
import org.genesys2.server.service.HtmlSanitizer;
import org.genesys2.server.service.filter.AccessionFilter;
import org.genesys2.server.service.worker.AccessionProcessor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
......@@ -65,7 +71,8 @@ import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.validation.annotation.Validated;
import javax.validation.Valid;
import com.google.common.collect.Sets;
import com.querydsl.core.BooleanBuilder;
@Service
@Transactional(readOnly = true)
......@@ -103,26 +110,49 @@ public class CropServiceImpl implements CropService {
@Autowired
private Taxonomy2Repository taxonomy2Repository;
@Autowired
private AccessionProcessor accessionProcessor;
@Autowired
private AccessionRepository accessionRepository;
@Autowired
protected AsAdminInvoker asAdminInvoker;
/**
* @param shortName the crop name ("groundnuts") as provided by partners, but
* can also be a list of names ("peanut,goober,groundnut")
*/
@Override
@Cacheable(value = CACHE_CROPS, key = "#shortName", unless = "#result == null || #shortName == null")
public Crop getCrop(String shortName) {
if (StringUtils.isBlank(shortName)) {
return null;
}
Crop crop = cropRepository.findByShortName(shortName);
// Find crop by alias when null
if (crop == null) {
crop = cropRepository.findByOtherNames(shortName);
for (String cropName : shortName.split(",;")) {
cropName = StringUtils.trimToNull(cropName);
if (cropName != null) {
Crop crop = cropRepository.findByShortName(cropName);
// Find crop by alias when null
if (crop == null) {
crop = cropRepository.findByOtherNames(cropName);
}
if (crop != null) {
// Lazy load otherNames
if (crop.getOtherNames() != null) {
crop.getOtherNames().size();
}
return crop;
}
}
}
// Lazy load otherNames
if (crop != null && crop.getOtherNames() != null)
crop.getOtherNames().size();
return crop;
return null;
}
@Override
......@@ -134,7 +164,7 @@ public class CropServiceImpl implements CropService {
Article article = contentService.getArticle(crop, "blurp", locale);
LOG.trace("got article after {}ms", stopWatch.getTime());
AccessionFilter byCrop = new AccessionFilter();
byCrop.cropName = crop.getShortName();
byCrop.crop = Sets.newHashSet(crop.getShortName());
long accessionCount = accessionService.countAccessions(byCrop);
LOG.trace("got count after {}ms", stopWatch.getTime());
......@@ -535,6 +565,67 @@ public class CropServiceImpl implements CropService {
cropTaxonomyRepository.save(toAdd);
}
}
@Override
public void unlinkAccessionsForCrop(Crop crop) {
final BooleanBuilder predicate = new BooleanBuilder();
// accessions with selected crop
predicate.and(QAccession.accession.crop.eq(crop));
final BooleanBuilder cropNames = new BooleanBuilder();
cropNames.or(QAccession.accession.cropName.equalsIgnoreCase(crop.getShortName()));
cropNames.or(QAccession.accession.cropName.likeIgnoreCase(crop.getShortName()));
crop.getOtherNames().forEach(otherName -> {
cropNames.or(QAccession.accession.cropName.equalsIgnoreCase(otherName));
cropNames.or(QAccession.accession.cropName.likeIgnoreCase(otherName));
});
// accession#cropName not one of valid names
predicate.andNot(cropNames);
accessionProcessor.apply(predicate, (accessions) -> {
accessions.forEach(accession -> {
Crop newCrop = getCrop(accession.getCropName());
LOG.debug("{} from {}: {} -> {}", accession.getUuid(), accession.getInstCode(), accession.getCropName(), newCrop == null ? "null" : newCrop.getShortName());
// assign new crop
accession.setCrop(newCrop);
});
asAdminInvoker.invoke(() -> {
accessionRepository.save(accessions);
return true;
});
return accessions;
});
}
@Override
public void linkAccessionsWithCrop(Crop crop) {
final BooleanBuilder predicate = new BooleanBuilder();
// accepted crop names
predicate.or(QAccession.accession.cropName.equalsIgnoreCase(crop.getShortName()));
predicate.or(QAccession.accession.cropName.likeIgnoreCase(crop.getShortName()));
crop.getOtherNames().forEach(otherName -> {
predicate.or(QAccession.accession.cropName.equalsIgnoreCase(otherName));
predicate.or(QAccession.accession.cropName.likeIgnoreCase(otherName));
});
// but not assigned to this crop
predicate.andAnyOf(QAccession.accession.crop.isNull(), QAccession.accession.crop.ne(crop));
accessionProcessor.apply(predicate, (accessions) -> {
accessions.forEach(accession -> {
Crop newCrop = getCrop(accession.getCropName());
LOG.debug("{} from {}: {} -> {}", accession.getUuid(), accession.getInstCode(), accession.getCropName(), newCrop == null ? "null" : newCrop.getShortName());
// assign crop
accession.setCrop(newCrop);
});
asAdminInvoker.invoke(() -> {
accessionRepository.save(accessions);
return true;
});
return accessions;
});
}
private Map<String, ElasticsearchService.TermResult> getOverviewData(AccessionFilter byCropFilter) {
String[] terms = new String[] {"taxonomy.genus", "taxonomy.genusSpecies", "institute.code",
......@@ -558,7 +649,8 @@ public class CropServiceImpl implements CropService {
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());
if (source.getCropRules() != null) {
target.getCropRules().addAll(source.getCropRules());
}
}
}
src/main/java/org/genesys2/server/service/worker/AccessionProcessor.java
View file @ a20b5f93
......@@ -127,7 +127,6 @@ public class AccessionProcessor {
action.apply(a);
}
}
/**
* Apply action on accessions matching the provided filter.
*
......@@ -137,8 +136,20 @@ public class AccessionProcessor {
@Transactional(readOnly = true, propagation = Propagation.REQUIRES_NEW)
public void apply(AccessionFilter filter, IAccessionBatchAction action) {
Predicate predicate = filter.buildQuery();
apply(filter.buildQuery(), action);
}
/**
* Apply action on accessions matching the provided filter.
*
* @param predicate JPA query predicate on Accession
* @param action the action
*/
@Transactional(readOnly = true, propagation = Propagation.REQUIRES_NEW)
public void apply(Predicate predicate, IAccessionBatchAction action) {
long count = accessionRepository.count(predicate);
LOG.info("{} accessions match the query", count);
PathBuilder<Accession> builder = new PathBuilderFactory().create(Accession.class);
Querydsl querydsl = new Querydsl(em, builder);
......@@ -174,7 +185,7 @@ public class AccessionProcessor {
} while (results.size() > 0);
stopWatch.stop();
LOG.info("Processing Accessions for filter {} took {}ms", filter, stopWatch.getTime());
LOG.info("Processing Accessions took {}ms", stopWatch.getTime());
}
private void asyncUpdate(List<Long> accessionIds, IAccessionBatchAction action) {
......
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