diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationSitemapVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationSitemapVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..1ee34df29e0c81442293391c34f8947f08b5311e
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationSitemapVO.java
@@ -0,0 +1,36 @@
+package fr.inra.urgi.faidare.domain.data;
+
+import java.util.List;
+
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiAdditionalInfo;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiLocation;
+import fr.inra.urgi.faidare.domain.jsonld.data.HasURI;
+import fr.inra.urgi.faidare.domain.jsonld.data.HasURL;
+import fr.inra.urgi.faidare.domain.jsonld.data.IncludedInDataCatalog;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Document;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Id;
+
+/**
+ * A minimal view of a location containing only its ID, used to generate sitemaps
+ */
+@Document(type = "location", includedFields = "locationDbId")
+public class LocationSitemapVO {
+
+ @Id
+ private String locationDbId;
+
+ public LocationSitemapVO() {
+ }
+
+ public LocationSitemapVO(String locationDbId) {
+ this.locationDbId = locationDbId;
+ }
+
+ public String getLocationDbId() {
+ return locationDbId;
+ }
+
+ public void setLocationDbId(String locationDbId) {
+ this.locationDbId = locationDbId;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmSitemapVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmSitemapVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..b7dc268148ed53309a64f4fbf808d5bdec580e68
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmSitemapVO.java
@@ -0,0 +1,38 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+import java.io.Serializable;
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonSetter;
+import com.fasterxml.jackson.annotation.Nulls;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasm;
+import fr.inra.urgi.faidare.domain.jsonld.data.HasURI;
+import fr.inra.urgi.faidare.domain.jsonld.data.HasURL;
+import fr.inra.urgi.faidare.domain.jsonld.data.IncludedInDataCatalog;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Document;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Id;
+
+/**
+ * A minimal view of a germplasm, containing only its ID, used for sitemaps
+ */
+@Document(type = "germplasm", includedFields = "germplasmDbId")
+public class GermplasmSitemapVO {
+
+ @Id
+ private String germplasmDbId;
+
+ public GermplasmSitemapVO() {
+ }
+
+ public GermplasmSitemapVO(String germplasmDbId) {
+ this.germplasmDbId = germplasmDbId;
+ }
+
+ public String getGermplasmDbId() {
+ return germplasmDbId;
+ }
+
+ public void setGermplasmDbId(String germplasmDbId) {
+ this.germplasmDbId = germplasmDbId;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySitemapVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySitemapVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..c4900361a93329fa4c623b71b4cebf7a360e49d6
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySitemapVO.java
@@ -0,0 +1,40 @@
+package fr.inra.urgi.faidare.domain.data.study;
+
+import java.util.Date;
+import java.util.List;
+import java.util.Set;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiAdditionalInfo;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiStudySummary;
+import fr.inra.urgi.faidare.domain.data.GnpISInternal;
+import fr.inra.urgi.faidare.domain.jsonld.data.HasURI;
+import fr.inra.urgi.faidare.domain.jsonld.data.HasURL;
+import fr.inra.urgi.faidare.domain.jsonld.data.IncludedInDataCatalog;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Document;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Id;
+
+/**
+ * A minimal view of a study containing only its ID, used to generate sitemaps
+ */
+@Document(type = "study", includedFields = "studyDbId")
+public class StudySitemapVO {
+
+ @Id
+ private String studyDbId;
+
+ public StudySitemapVO() {
+ }
+
+ public StudySitemapVO(String studyDbId) {
+ this.studyDbId = studyDbId;
+ }
+
+ public String getStudyDbId() {
+ return studyDbId;
+ }
+
+ public void setStudyDbId(String studyDbId) {
+ this.studyDbId = studyDbId;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/ESScrollIterator.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/ESScrollIterator.java
index f106e9b7709dfc4d8e407322732e72ddd576835a..04b8d4e2993512412b57f9acedafd4217cd4c245 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/ESScrollIterator.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/ESScrollIterator.java
@@ -68,6 +68,13 @@ public class ESScrollIterator<T> implements Iterator<T> {
.size(fetchSize)
.sort(FieldSortBuilder.DOC_FIELD_NAME, SortOrder.ASC);
+ // Add included and excluded fields if requested
+ String[] includedFields = documentMetadata.getIncludedFields();
+ String[] excludedFields = documentMetadata.getExcludedFields();
+ if ((includedFields != null && includedFields.length >= 1) || (excludedFields != null && excludedFields.length >= 1)) {
+ request.source().fetchSource(includedFields, excludedFields);
+ }
+
SearchResponse response = null;
try {
response = client.search(request, RequestOptions.DEFAULT);
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtil.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtil.java
index a521970d7baafc394c027314ae554af65fac1af2..eb63d3e3424b7addbbf70f1731001c94a4959d8d 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtil.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtil.java
@@ -54,8 +54,9 @@ public class DocumentAnnotationUtil {
Map<String, DocumentMetadata.Field> fields = findDocumentFields(ImmutableList.<String>of(),
valueObjectClass);
+ String[] includedFields = document.includedFields();
String[] excludedFields = document.excludedFields();
- metadata = new DocumentMetadata<>(documentType, idFieldName, valueObjectClass, excludedFields, fields);
+ metadata = new DocumentMetadata<>(documentType, idFieldName, valueObjectClass, includedFields, excludedFields, fields);
metadataCache.put(valueObjectClass, metadata);
}
return metadata;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentMetadata.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentMetadata.java
index 6bf7389bd43b46f6dc5cd72ef5883b932788f0a5..a54e37e3c5023fcf8516a9d6e4b347ec628293da 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentMetadata.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentMetadata.java
@@ -17,15 +17,21 @@ public class DocumentMetadata<VO> {
private final String documentType;
private final String idField;
private final Class<VO> documentClass;
+ private final String[] includedFields;
private final String[] excludedFields;
private final Map<String, Field> fieldsByName;
private final Map<List<String>, Field> fieldByPath;
- public DocumentMetadata(String documentType, String idField, Class<VO> documentClass, String[] excludedFields,
+ public DocumentMetadata(String documentType,
+ String idField,
+ Class<VO> documentClass,
+ String[] includedFields,
+ String[] excludedFields,
Map<String, Field> fieldsByName) {
this.documentType = documentType;
this.idField = idField;
this.documentClass = documentClass;
+ this.includedFields = includedFields;
this.excludedFields = excludedFields;
this.fieldsByName = fieldsByName;
this.fieldByPath = flattenDocumentFieldTree(ImmutableList.<String>of(), fieldsByName);
@@ -57,6 +63,10 @@ public class DocumentMetadata<VO> {
return idField;
}
+ public String[] getIncludedFields() {
+ return includedFields;
+ }
+
public String[] getExcludedFields() {
return excludedFields;
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/annotation/Document.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/annotation/Document.java
index df4af121fa9a0f84b8b90b6ec188f6f36b17bf23..3d0585a459d0fe20a030a5b2a6e88d5217dee332 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/annotation/Document.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/document/annotation/Document.java
@@ -13,5 +13,6 @@ import java.lang.annotation.Target;
public @interface Document {
String type();
+ String[] includedFields() default {};
String[] excludedFields() default {};
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericFindRepository.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericFindRepository.java
index 54e7b287e44db289e5a83771353fc4bca487741e..e1122d86108623783ca5bf7b8d01ce3739a71796 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericFindRepository.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericFindRepository.java
@@ -90,10 +90,11 @@ public class ESGenericFindRepository<C extends PaginationCriteria, VO> implement
request.source().sort(field, order);
}
- // Add excluded fields if requested
+ // Add included and excluded fields if requested
+ String[] includedFields = documentMetadata.getIncludedFields();
String[] excludedFields = documentMetadata.getExcludedFields();
- if (excludedFields != null && excludedFields.length >= 1) {
- request.source().fetchSource(null, excludedFields);
+ if ((includedFields != null && includedFields.length >= 1) || (excludedFields != null && excludedFields.length >= 1)) {
+ request.source().fetchSource(includedFields, excludedFields);
}
Logger logger = LoggerFactory.getLogger(ESGenericFindRepository.class);
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepository.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepository.java
index dafff525774e979f20be09872e5357a888ed01c8..739feea02d0acd41ceb53c0fac02a5fd2ec0775f 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepository.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepository.java
@@ -3,6 +3,7 @@ package fr.inra.urgi.faidare.repository.es;
import fr.inra.urgi.faidare.domain.criteria.FaidareGermplasmPOSTShearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmSearchCriteria;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
@@ -31,6 +32,11 @@ public interface GermplasmRepository
*/
GermplasmVO getById(String germplasmDbId);
+ /**
+ * Scroll through all germplasms, using the given fetch size
+ */
+ Iterator<GermplasmSitemapVO> scrollAllForSitemap(int fetchSize);
+
/**
* Scroll through all germplasm matching the given criteria.
*/
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java
index 31a6e1a8c55537fb4ffe7a35b418909c3a8dfede..360087ce79e69f48685b4c2c3480b6de51766171 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java
@@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import fr.inra.urgi.faidare.domain.criteria.FaidareGermplasmPOSTShearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmSearchCriteria;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
@@ -90,6 +91,12 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
this.criteriaMapping = AnnotatedCriteriaMapper.getMapping(criteriaClass);
}
+ @Override
+ public Iterator<GermplasmSitemapVO> scrollAllForSitemap(int fetchSize) {
+ QueryBuilder query = QueryBuilders.matchAllQuery();
+ return new ESScrollIterator<>(client, requestFactory, parser, GermplasmSitemapVO.class, query, fetchSize);
+ }
+
@Override
public Iterator<GermplasmVO> scrollAll(GermplasmSearchCriteria criteria) {
QueryBuilder query = queryFactory.createQuery(criteria);
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepository.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepository.java
index 707f51bcd649768f66fdcbf99b8fee51736b5395..93e65b549079430cd2a2cfbbad8d2bb0676dd544 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepository.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepository.java
@@ -1,6 +1,9 @@
package fr.inra.urgi.faidare.repository.es;
+import java.util.Iterator;
+
import fr.inra.urgi.faidare.domain.criteria.LocationCriteria;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.LocationVO;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.elasticsearch.repository.ESFindRepository;
@@ -21,4 +24,5 @@ public interface LocationRepository
@Override
PaginatedList<LocationVO> find(LocationCriteria criteria);
+ Iterator<LocationSitemapVO> scrollAllForSitemap(int fetchSize);
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryImpl.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryImpl.java
index af74a55c2e7f9cf7e788e3905186a2bef9a66182..0a1133d75f654527a74a2bad73bc21a83763e52c 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryImpl.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryImpl.java
@@ -1,11 +1,18 @@
package fr.inra.urgi.faidare.repository.es;
+import java.util.Iterator;
+
import fr.inra.urgi.faidare.domain.criteria.LocationCriteria;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
import fr.inra.urgi.faidare.elasticsearch.ESRequestFactory;
import fr.inra.urgi.faidare.elasticsearch.ESResponseParser;
+import fr.inra.urgi.faidare.elasticsearch.ESScrollIterator;
import fr.inra.urgi.faidare.elasticsearch.repository.impl.BaseESRepository;
import org.elasticsearch.client.RestHighLevelClient;
+import org.elasticsearch.index.query.QueryBuilder;
+import org.elasticsearch.index.query.QueryBuilders;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;
@@ -17,6 +24,10 @@ public class LocationRepositoryImpl
extends BaseESRepository<LocationCriteria, LocationVO>
implements LocationRepository {
+ private final RestHighLevelClient client;
+ private final ESRequestFactory requestFactory;
+ private final ESResponseParser parser;
+
@Autowired
public LocationRepositoryImpl(
RestHighLevelClient client,
@@ -24,6 +35,14 @@ public class LocationRepositoryImpl
ESResponseParser parser
) {
super(client, requestFactory, LocationVO.class, parser);
+ this.client = client;
+ this.requestFactory = requestFactory;
+ this.parser = parser;
}
+ @Override
+ public Iterator<LocationSitemapVO> scrollAllForSitemap(int fetchSize) {
+ QueryBuilder query = QueryBuilders.matchAllQuery();
+ return new ESScrollIterator<>(client, requestFactory, parser, LocationSitemapVO.class, query, fetchSize);
+ }
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepository.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepository.java
index 6ceeca9f655fea5b94548d3c32941906c976d625..8831a8c1ff66f6a31aeac3825d690651da10c27b 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepository.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepository.java
@@ -1,12 +1,15 @@
package fr.inra.urgi.faidare.repository.es;
import fr.inra.urgi.faidare.domain.criteria.StudyCriteria;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.study.StudyDetailVO;
+import fr.inra.urgi.faidare.domain.data.study.StudySitemapVO;
import fr.inra.urgi.faidare.domain.data.study.StudySummaryVO;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.elasticsearch.repository.ESFindRepository;
import fr.inra.urgi.faidare.elasticsearch.repository.ESGetByIdRepository;
+import java.util.Iterator;
import java.util.Set;
/**
@@ -29,4 +32,5 @@ public interface StudyRepository
*/
Set<String> getVariableIds(String studyDbId);
+ Iterator<StudySitemapVO> scrollAllForSitemap(int fetchSize);
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryImpl.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryImpl.java
index d9410a871cb1c7c0f9ab3966594b523fe6d29b3b..46b0b71248b4a5498a9d24bedb3f854ce756af6f 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryImpl.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryImpl.java
@@ -2,12 +2,15 @@ package fr.inra.urgi.faidare.repository.es;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiLocation;
import fr.inra.urgi.faidare.domain.criteria.StudyCriteria;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.LocationVO;
import fr.inra.urgi.faidare.domain.data.study.StudyDetailVO;
+import fr.inra.urgi.faidare.domain.data.study.StudySitemapVO;
import fr.inra.urgi.faidare.domain.data.study.StudySummaryVO;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.elasticsearch.ESRequestFactory;
import fr.inra.urgi.faidare.elasticsearch.ESResponseParser;
+import fr.inra.urgi.faidare.elasticsearch.ESScrollIterator;
import fr.inra.urgi.faidare.elasticsearch.document.DocumentAnnotationUtil;
import fr.inra.urgi.faidare.elasticsearch.document.DocumentMetadata;
import fr.inra.urgi.faidare.elasticsearch.query.impl.ESGenericQueryFactory;
@@ -19,6 +22,8 @@ import org.elasticsearch.action.search.SearchRequest;
import org.elasticsearch.action.search.SearchResponse;
import org.elasticsearch.client.RequestOptions;
import org.elasticsearch.client.RestHighLevelClient;
+import org.elasticsearch.index.query.QueryBuilder;
+import org.elasticsearch.index.query.QueryBuilders;
import org.elasticsearch.search.aggregations.bucket.filter.FilterAggregationBuilder;
import org.elasticsearch.search.aggregations.bucket.terms.TermsAggregationBuilder;
import org.slf4j.Logger;
@@ -28,6 +33,7 @@ import org.springframework.stereotype.Repository;
import java.io.IOException;
import java.util.Arrays;
+import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
@@ -129,4 +135,9 @@ public class StudyRepositoryImpl
return new LinkedHashSet<>(ids);
}
+ @Override
+ public Iterator<StudySitemapVO> scrollAllForSitemap(int fetchSize) {
+ QueryBuilder query = QueryBuilders.matchAllQuery();
+ return new ESScrollIterator<>(client, requestFactory, parser, StudySitemapVO.class, query, fetchSize);
+ }
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/utils/Sitemaps.java b/backend/src/main/java/fr/inra/urgi/faidare/utils/Sitemaps.java
new file mode 100644
index 0000000000000000000000000000000000000000..ba32b8cf286c1c04b589e50a4338addae9df2e78
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/utils/Sitemaps.java
@@ -0,0 +1,125 @@
+package fr.inra.urgi.faidare.utils;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.UncheckedIOException;
+import java.io.Writer;
+import java.nio.charset.StandardCharsets;
+import java.util.Iterator;
+import java.util.Spliterators;
+import java.util.function.Function;
+import java.util.function.Predicate;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+import org.springframework.web.servlet.support.ServletUriComponentsBuilder;
+
+/**
+ * A generator of site maps.
+ * @author JB Nizet
+ */
+@Component
+public class Sitemaps {
+ public static final int BUCKET_COUNT = 11;
+
+ public static <T> void generateSitemap(String sitemapPath,
+ OutputStream out,
+ Iterator<T> entryIterator,
+ Predicate<T> entryPredicate,
+ Function<T, String> entryToPath) {
+ SanityChecker sanityChecker = new SanityChecker(sitemapPath);
+
+ Writer writer = new BufferedWriter(new OutputStreamWriter(out, StandardCharsets.UTF_8));
+ Stream<T> entries =
+ StreamSupport.stream(Spliterators.spliteratorUnknownSize(entryIterator, 0), false);
+ entries.filter(entryPredicate)
+ .map(entryToPath)
+ .map(entryPath -> Sitemaps.generateSitemapUrl(entryPath) + '\n')
+ .forEach(entry -> {
+ try {
+ writer.write(entry);
+ sanityChecker.addEntry(entry);
+ }
+ catch (IOException e) {
+ throw new UncheckedIOException(e);
+ }
+ });
+
+ try {
+ writer.flush();
+ } catch (IOException e) {
+ throw new UncheckedIOException(e);
+ }
+
+ sanityChecker.check();
+ }
+
+ public static String generateSitemapUrl(String path) {
+ return ServletUriComponentsBuilder
+ .fromCurrentContextPath()
+ .path(path)
+ .toUriString();
+ }
+
+ private static class SanityChecker {
+ private static final Logger LOGGER = LoggerFactory.getLogger(SanityChecker.class);
+
+ private static final int MAX_ENTRY_COUNT = 50_000;
+ private static final int MAX_BYTE_COUNT = 50 * 1024 * 1024;
+
+ private static final int DANGER_ENTRY_COUNT = 40_000;
+ private static final int DANGER_BYTE_COUNT = 40 * 1024 * 1024;
+
+ private final String sitemapPath;
+ private int entryCount = 0;
+ private int byteCount = 0;
+
+ public SanityChecker(String sitemapPath) {
+ this.sitemapPath = sitemapPath;
+ }
+
+ public void addEntry(String entry) {
+ entryCount++;
+ byteCount += entry.length();
+ }
+
+ public void check() {
+ if (entryCount > MAX_ENTRY_COUNT) {
+ LOGGER.error("The generated sitemap at path "
+ + sitemapPath +
+ " has more than "
+ + MAX_ENTRY_COUNT +
+ " entries and will thus be rejected by search engines. Increase Sitemaps.BUCKET_COUNT for a better distribution of sitemap entries.");
+ } else if (entryCount > DANGER_ENTRY_COUNT) {
+ LOGGER.warn("The generated sitemap at path "
+ + sitemapPath
+ + " has more than "
+ + DANGER_ENTRY_COUNT
+ + " entries and is thus approaching the max of "
+ + MAX_ENTRY_COUNT
+ + ". Increase Sitemaps.BUCKET_COUNT for a better distribution of sitemap entries.");
+ }
+
+ if (byteCount > MAX_BYTE_COUNT) {
+ LOGGER.error("The generated sitemap at path "
+ + sitemapPath
+ + " has more than "
+ + MAX_BYTE_COUNT
+ + " bytes and will thus be rejected by search engines. Increase Sitemaps.BUCKET_COUNT for a better distribution of sitemap entries.");
+ } else if (entryCount > DANGER_ENTRY_COUNT) {
+ LOGGER.warn("The generated sitemap at path "
+ + sitemapPath
+ + " has more than "
+ + DANGER_BYTE_COUNT
+ + " bytes and is thus approaching the max of "
+ + MAX_BYTE_COUNT
+ + ". Increase Sitemaps.BUCKET_COUNT for a better distribution of sitemap entries.");
+ }
+ }
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
index cd24d06dc61698b217db1422c9585ed4b7b97b05..973d2de38c9f3e04fb85b2b073bda308b6691719 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
@@ -4,9 +4,16 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
+import java.util.Iterator;
import java.util.List;
+import java.util.Spliterators;
import java.util.stream.Collectors;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+import javax.servlet.http.HttpServletRequest;
+
+import com.google.common.collect.Streams;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.config.FaidareProperties;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmAttributeValue;
@@ -18,25 +25,30 @@ import fr.inra.urgi.faidare.domain.data.germplasm.DonorVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GenealogyVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmAttributeValueVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmInstituteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PhotoVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PuiNameValueVO;
import fr.inra.urgi.faidare.domain.data.germplasm.SiblingVO;
-import fr.inra.urgi.faidare.domain.data.germplasm.SimpleVO;
import fr.inra.urgi.faidare.domain.data.germplasm.SiteVO;
import fr.inra.urgi.faidare.domain.data.germplasm.TaxonSourceVO;
import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
import fr.inra.urgi.faidare.repository.es.GermplasmAttributeRepository;
import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import fr.inra.urgi.faidare.utils.Sitemaps;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.ResponseBody;
import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
/**
* Controller used to display a germplasm card based on its ID.
@@ -49,7 +61,7 @@ public class GermplasmController {
private final GermplasmRepository germplasmRepository;
private final FaidareProperties faidareProperties;
private final XRefDocumentRepository xRefDocumentRepository;
- private GermplasmAttributeRepository germplasmAttributeRepository;
+ private final GermplasmAttributeRepository germplasmAttributeRepository;
public GermplasmController(GermplasmRepository germplasmRepository,
FaidareProperties faidareProperties,
@@ -87,6 +99,26 @@ public class GermplasmController {
return toModelAndView(germplasms.get(0));
}
+
+ @GetMapping(value = "/sitemap-{index}.txt")
+ @ResponseBody
+ public ResponseEntity<StreamingResponseBody> sitemap(@PathVariable("index") int index) {
+ if (index < 0 || index >= Sitemaps.BUCKET_COUNT) {
+ throw new NotFoundException("no sitemap for this index");
+ }
+ StreamingResponseBody body = out -> {
+ Iterator<GermplasmSitemapVO> iterator = germplasmRepository.scrollAllForSitemap(1000);
+ Sitemaps.generateSitemap(
+ "/germplasms/sitemap-" + index + ".txt",
+ out,
+ iterator,
+ vo -> Math.floorMod(vo.getGermplasmDbId().hashCode(), Sitemaps.BUCKET_COUNT) == index,
+ vo -> "/germplasms/" + vo.getGermplasmDbId()
+ );
+ };
+ return ResponseEntity.ok().contentType(MediaType.TEXT_PLAIN).body(body);
+ }
+
private ModelAndView toModelAndView(GermplasmVO germplasm) {
// List<BrapiGermplasmAttributeValue> attributes = getAttributes(germplasm);
// List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
index 151da527d4393d1f388de8d6098b52d4219d98b2..3b05139df1fa4e7e3584bd6695251fd9fe1bf6a9 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
@@ -1,20 +1,29 @@
package fr.inra.urgi.faidare.web.site;
import java.util.Arrays;
+import java.util.Iterator;
import java.util.List;
+import javax.servlet.http.HttpServletRequest;
+
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.config.FaidareProperties;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiAdditionalInfo;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.LocationVO;
import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
import fr.inra.urgi.faidare.repository.es.LocationRepository;
import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import fr.inra.urgi.faidare.utils.Sitemaps;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
/**
* Controller used to display a site card based on its ID.
@@ -64,6 +73,22 @@ public class SiteController {
);
}
+ @GetMapping(value = "/sitemap.txt")
+ @ResponseBody
+ public ResponseEntity<StreamingResponseBody> sitemap() {
+ StreamingResponseBody body = out -> {
+ Iterator<LocationSitemapVO> iterator = locationRepository.scrollAllForSitemap(1000);
+ Sitemaps.generateSitemap(
+ "/sites/sitemap.txt",
+ out,
+ iterator,
+ vo -> true,
+ vo -> "/sites/" + vo.getLocationDbId()
+ );
+ };
+ return ResponseEntity.ok().contentType(MediaType.TEXT_PLAIN).body(body);
+ }
+
private LocationVO createSite() {
LocationVO site = new LocationVO();
site.setLocationName("France");
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/sitemap/SitemapIndexController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/sitemap/SitemapIndexController.java
new file mode 100644
index 0000000000000000000000000000000000000000..1dd480dfbd465d243ae3b32b535c32b81c6b355a
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/sitemap/SitemapIndexController.java
@@ -0,0 +1,57 @@
+package fr.inra.urgi.faidare.web.sitemap;
+
+import java.nio.charset.StandardCharsets;
+
+import fr.inra.urgi.faidare.utils.Sitemaps;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+/**
+ * Controller used to generate the sitemap index containing links to the site sitemap
+ * (unique), the N sitemaps for the studies and the N sitemaps for the germplasms.
+ *
+ * Sitemaps for studies and germplasms are split in N buckets because sitemaps
+ * can't be more than 50 MB and can't have more than 50,000 entries.
+ * Splitting them in N sitemaps makes it almost sure that none of the sitemaps
+ * overflows those limits.
+ *
+ * The sitemaps are split based on the hashCode of the ID of the document:
+ * if a document's hash code modulo N is 0, then it's in the sitemap-0.txt, etc.
+ *
+ * @author JB Nizet
+ */
+@RestController
+@RequestMapping("")
+public class SitemapIndexController {
+ @GetMapping("/sitemap.xml")
+ public ResponseEntity<byte[]> sitemapIndex() {
+ StringBuilder builder = new StringBuilder();
+ builder
+ .append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
+ .append("<sitemapindex xmlns=\"http://www.sitemaps.org/schemas/sitemap/0.9\">\n");
+
+ appendSiteMap(builder, "/sites/sitemap.txt");
+ for (int i = 0; i < Sitemaps.BUCKET_COUNT; i++) {
+ appendSiteMap(builder, "/germplasms/sitemap-" + i + ".txt");
+ }
+ for (int i = 0; i < Sitemaps.BUCKET_COUNT; i++) {
+ appendSiteMap(builder, "/studies/sitemap-" + i + ".txt");
+ }
+ builder.append("</sitemapindex>");
+
+ return ResponseEntity.ok()
+ .contentType(MediaType.TEXT_XML)
+ .body(builder.toString().getBytes(StandardCharsets.UTF_8));
+ }
+
+ public void appendSiteMap(StringBuilder builder, String path) {
+ builder.append(" <sitemap>\n")
+ .append(" <loc>")
+ .append(Sitemaps.generateSitemapUrl(path))
+ .append("</loc>\n")
+ .append(" </sitemap>\n");
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
index 833c45471061a5ef02d7f5fc57319fc9afc8a12b..e9a9ac46f890cc8dc32c2234da82265f1cf9a37e 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
@@ -3,19 +3,24 @@ package fr.inra.urgi.faidare.web.study;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
+import java.util.Iterator;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
+import javax.servlet.http.HttpServletRequest;
+
import com.google.common.collect.Lists;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.config.FaidareProperties;
import fr.inra.urgi.faidare.domain.criteria.GermplasmPOSTSearchCriteria;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.LocationVO;
import fr.inra.urgi.faidare.domain.data.TrialVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.study.StudyDetailVO;
+import fr.inra.urgi.faidare.domain.data.study.StudySitemapVO;
import fr.inra.urgi.faidare.domain.data.variable.ObservationVariableVO;
import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
@@ -24,13 +29,18 @@ import fr.inra.urgi.faidare.repository.es.StudyRepository;
import fr.inra.urgi.faidare.repository.es.TrialRepository;
import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
import fr.inra.urgi.faidare.repository.file.CropOntologyRepository;
+import fr.inra.urgi.faidare.utils.Sitemaps;
import fr.inra.urgi.faidare.web.site.MapLocation;
import org.apache.logging.log4j.util.Strings;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
/**
* Controller used to display a study card based on its ID.
@@ -104,6 +114,24 @@ public class StudyController {
);
}
+ @GetMapping(value = "/sitemap-{index}.txt")
+ @ResponseBody
+ public ResponseEntity<StreamingResponseBody> sitemap(@PathVariable("index") int index) {
+ if (index < 0 || index >= Sitemaps.BUCKET_COUNT) {
+ throw new NotFoundException("no sitemap for this index");
+ }
+ StreamingResponseBody body = out -> {
+ Iterator<StudySitemapVO> iterator = studyRepository.scrollAllForSitemap(1000);
+ Sitemaps.generateSitemap(
+ "/sudies/sitemap-" + index + ".txt",
+ out,
+ iterator,
+ vo -> Math.floorMod(vo.getStudyDbId().hashCode(), Sitemaps.BUCKET_COUNT) == index,
+ vo -> "/studies/" + vo.getStudyDbId());
+ };
+ return ResponseEntity.ok().contentType(MediaType.TEXT_PLAIN).body(body);
+ }
+
private LocationVO getLocation(StudyDetailVO study) {
if (Strings.isBlank(study.getLocationDbId())) {
return null;
diff --git a/backend/src/main/resources/application.yml b/backend/src/main/resources/application.yml
index 2b684f600c3e548456c9e68ef473116839440929..206012ca02782c52dbdf1b27b80ac0897f351bf2 100644
--- a/backend/src/main/resources/application.yml
+++ b/backend/src/main/resources/application.yml
@@ -86,6 +86,7 @@ server:
- text/html
- text/css
- text/markdown
+ - text/plain
port: 8380
servlet:
context-path: /faidare-dev
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtilTest.java b/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtilTest.java
index b8a86407533fef5f21831fd31f01f753e8524f29..a712bfe44b6b5683c5c1f87a290e48d790136920 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtilTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/DocumentAnnotationUtilTest.java
@@ -50,6 +50,7 @@ class DocumentAnnotationUtilTest {
.getDocumentObjectMetadata(ComplexDocument.class);
assertThat(metadata).isNotNull();
assertThat(metadata.getDocumentType()).isEqualTo("dataObject4");
+ assertThat(metadata.getIncludedFields()).containsExactly("id", "nested0");
assertThat(metadata.getExcludedFields()).containsExactly("a", "b");
assertThat(metadata.getIdField()).isEqualTo("@id");
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/fixture/ComplexDocument.java b/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/fixture/ComplexDocument.java
index dd9a2c789623a79ab4101136bdbd08e21fb82703..e799a70ab4fd8f21413735811c2bd058311f61f0 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/fixture/ComplexDocument.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/document/fixture/ComplexDocument.java
@@ -11,7 +11,7 @@ import java.util.List;
/**
* @author gcornut
*/
-@Document(type = "dataObject4", excludedFields = {"a", "b"})
+@Document(type = "dataObject4", includedFields = { "id", "nested0"}, excludedFields = {"a", "b"})
public class ComplexDocument {
@Id(jsonName = "@id")
String id;
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java
index 76285c6934b21838e2af8c7c9446aafde00787e5..7705ab8afdb15a5c4ca4474a56bccb150d62073a 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java
@@ -6,12 +6,14 @@ import fr.inra.urgi.faidare.Application;
import fr.inra.urgi.faidare.domain.criteria.GermplasmGETSearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmPOSTSearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmSearchCriteria;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.domain.response.Pagination;
import fr.inra.urgi.faidare.repository.es.setup.ESSetUp;
+import org.assertj.core.data.Index;
import org.assertj.core.util.Lists;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
@@ -28,6 +30,7 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
+import java.util.Objects;
import static org.assertj.core.api.Assertions.assertThat;
import static org.assertj.core.api.Assertions.fail;
@@ -126,6 +129,12 @@ class GermplasmRepositoryTest {
assertThat(list).isNotNull().hasSize(0);
}
+ @Test
+ void shouldScrollAllForSitemap() {
+ Iterator<GermplasmSitemapVO> list = repository.scrollAllForSitemap(100);
+ assertThat(list).isNotEmpty()
+ .allMatch(vo -> !vo.getGermplasmDbId().isEmpty());
+ }
@Test
void should_Scroll_By_accessionNumber() {
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java
index 88bcef7e6130cde2111f28f0e84ab70aae2a9e73..d7700556221825480c36b8ef8c3ce78f2338eb51 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java
@@ -3,7 +3,9 @@ package fr.inra.urgi.faidare.repository.es;
import com.google.common.collect.Sets;
import fr.inra.urgi.faidare.Application;
import fr.inra.urgi.faidare.domain.criteria.LocationCriteria;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.repository.es.setup.ESSetUp;
import org.junit.jupiter.api.BeforeAll;
@@ -16,6 +18,7 @@ import org.springframework.context.annotation.Import;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit.jupiter.SpringExtension;
+import java.util.Iterator;
import java.util.Set;
import static org.assertj.core.api.Assertions.assertThat;
@@ -114,4 +117,13 @@ class LocationRepositoryTest {
assertThat(locations).isNotNull().hasSize(3);
assertThat(locations).extracting("locationType").containsOnlyElementsOf(expectedTypes);
}
+
+ @Test
+ void shouldScrollAllForSitemap() {
+ Iterator<LocationSitemapVO> list = repository.scrollAllForSitemap(100);
+ assertThat(list).isNotEmpty()
+ .allMatch(vo -> !vo.getLocationDbId().isEmpty());
+ }
+
+
}
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryTest.java
index 42b2328714b627b7b2fc2099b3614257f61c7b49..fc73d3f6515d43e9f7c0e09bc7db1b4d27c31b06 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryTest.java
@@ -4,7 +4,9 @@ import com.google.common.collect.Sets;
import fr.inra.urgi.faidare.Application;
import fr.inra.urgi.faidare.domain.criteria.StudySearchCriteria;
import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
import fr.inra.urgi.faidare.domain.data.study.StudyDetailVO;
+import fr.inra.urgi.faidare.domain.data.study.StudySitemapVO;
import fr.inra.urgi.faidare.domain.data.study.StudySummaryVO;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.repository.es.setup.ESSetUp;
@@ -20,6 +22,7 @@ import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.util.Comparator;
+import java.util.Iterator;
import java.util.Set;
import static org.assertj.core.api.AssertionsForInterfaceTypes.assertThat;
@@ -157,6 +160,13 @@ class StudyRepositoryTest {
assertThat(result).extracting(sortField).isSortedAccordingTo(new DescendingOrder());
}
+ @Test
+ void shouldScrollAllForSitemap() {
+ Iterator<StudySitemapVO> list = repository.scrollAllForSitemap(100);
+ Assertions.assertThat(list).isNotEmpty()
+ .allMatch(vo -> !vo.getStudyDbId().isEmpty());
+ }
+
private class DescendingOrder implements Comparator<Object> {
@Override
public int compare(Object o1, Object o2) {
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/web/germplasm/GermplasmControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/web/germplasm/GermplasmControllerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..75f6f3b2ce3609c627e1e1d437a530ed60d0fad5
--- /dev/null
+++ b/backend/src/test/java/fr/inra/urgi/faidare/web/germplasm/GermplasmControllerTest.java
@@ -0,0 +1,89 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.ArgumentMatchers.anyInt;
+import static org.mockito.Mockito.when;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.asyncDispatch;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+
+import java.util.Arrays;
+import java.util.List;
+
+import fr.inra.urgi.faidare.config.FaidareProperties;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmSitemapVO;
+import fr.inra.urgi.faidare.domain.data.study.StudySitemapVO;
+import fr.inra.urgi.faidare.repository.es.GermplasmAttributeRepository;
+import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
+import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import fr.inra.urgi.faidare.utils.Sitemaps;
+import fr.inra.urgi.faidare.web.study.StudyController;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.MediaType;
+import org.springframework.test.web.servlet.MockMvc;
+import org.springframework.test.web.servlet.MvcResult;
+
+/**
+ * MVC tests for {@link GermplasmController}
+ * @author JB Nizet
+ */
+@WebMvcTest(GermplasmController.class)
+public class GermplasmControllerTest {
+
+ @Autowired
+ private MockMvc mockMvc;
+
+ @MockBean
+ private GermplasmRepository mockGermplasmRepository;
+
+ @MockBean
+ private FaidareProperties mockFaidareProperties;
+
+ @MockBean
+ private XRefDocumentRepository mockXRefDocumentRepository;
+
+ @MockBean
+ private GermplasmAttributeRepository mockGermplasmAttributeRepository;
+
+
+ @Test
+ void shouldGenerateSitemap() throws Exception {
+ List<GermplasmSitemapVO> germplasms = Arrays.asList(
+ new GermplasmSitemapVO("germplasm1"),
+ new GermplasmSitemapVO("germplasm4"),
+ new GermplasmSitemapVO("germplasm45"),
+ new GermplasmSitemapVO("germplasm73")
+ );
+
+ // the hashCode algorithm is specified in the javadoc, so it's guaranteed to be
+ // the same everywhere
+ // uncomment the following line to see which sitemap index each study has
+ // germplasms.forEach(germplasm -> System.out.println(germplasm.getGermplasmDbId() + " = " + Math.floorMod(germplasm.getGermplasmDbId().hashCode(), Sitemaps.BUCKET_COUNT)));
+
+ when(mockGermplasmRepository.scrollAllForSitemap(anyInt())).thenAnswer(invocation -> germplasms.iterator());
+
+ testSitemap(6, "http://localhost/faidare/germplasms/germplasm1\nhttp://localhost/faidare/germplasms/germplasm45\n");
+ testSitemap(9, "http://localhost/faidare/germplasms/germplasm4\nhttp://localhost/faidare/germplasms/germplasm73\n");
+ testSitemap(7, "");
+
+ mockMvc.perform(get("/faidare/germplasms/sitemap-17.txt")
+ .contextPath("/faidare"))
+ .andExpect(status().isNotFound());
+ }
+
+ private void testSitemap(int index, String expectedContent) throws Exception {
+ MvcResult mvcResult = mockMvc.perform(get("/faidare/germplasms/sitemap-" + index + ".txt")
+ .contextPath("/faidare"))
+ .andExpect(request().asyncStarted())
+ .andReturn();
+
+ this.mockMvc.perform(asyncDispatch(mvcResult))
+ .andExpect(status().isOk())
+ .andExpect(content().contentType(MediaType.TEXT_PLAIN))
+ .andExpect(content().string(expectedContent));
+
+ }
+}
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/web/site/SiteControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/web/site/SiteControllerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..a71bfa4cf3acb16dfc4b92de3cac7ccaacfb3a8f
--- /dev/null
+++ b/backend/src/test/java/fr/inra/urgi/faidare/web/site/SiteControllerTest.java
@@ -0,0 +1,62 @@
+package fr.inra.urgi.faidare.web.site;
+
+import static org.mockito.ArgumentMatchers.anyInt;
+import static org.mockito.Mockito.when;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
+import java.util.Arrays;
+import java.util.List;
+
+import fr.inra.urgi.faidare.config.FaidareProperties;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
+import fr.inra.urgi.faidare.repository.es.LocationRepository;
+import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.MediaType;
+import org.springframework.test.web.servlet.MockMvc;
+import org.springframework.test.web.servlet.MvcResult;
+import org.springframework.test.web.servlet.request.MockMvcRequestBuilders;
+import org.springframework.test.web.servlet.result.MockMvcResultMatchers;
+
+/**
+ * MVC tests for {@link SiteController}
+ * @author JB Nizet
+ */
+@WebMvcTest(SiteController.class)
+public class SiteControllerTest {
+ @Autowired
+ private MockMvc mockMvc;
+
+ @MockBean
+ private LocationRepository mockLocationRepository;
+
+ @MockBean
+ private XRefDocumentRepository mockXRefDocumentRepository;
+
+ @MockBean
+ private FaidareProperties mockFaidareProperties;
+
+ @Test
+ void shouldGenerateSitemap() throws Exception {
+ List<LocationSitemapVO> sites = Arrays.asList(
+ new LocationSitemapVO("site1"),
+ new LocationSitemapVO("site2")
+ );
+ when(mockLocationRepository.scrollAllForSitemap(anyInt())).thenReturn(sites.iterator());
+ MvcResult mvcResult = mockMvc.perform(get("/faidare/sites/sitemap.txt")
+ .contextPath("/faidare"))
+ .andExpect(request().asyncStarted())
+ .andReturn();
+
+ this.mockMvc.perform(asyncDispatch(mvcResult))
+ .andExpect(status().isOk())
+ .andExpect(content().contentType(MediaType.TEXT_PLAIN))
+ .andExpect(content().string("http://localhost/faidare/sites/site1\nhttp://localhost/faidare/sites/site2\n"));
+ }
+}
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/web/sitemap/SitemapIndexControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/web/sitemap/SitemapIndexControllerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..ea03832f41a262ea210eb6f093ef68fe5b583aab
--- /dev/null
+++ b/backend/src/test/java/fr/inra/urgi/faidare/web/sitemap/SitemapIndexControllerTest.java
@@ -0,0 +1,34 @@
+package fr.inra.urgi.faidare.web.sitemap;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+
+import fr.inra.urgi.faidare.utils.Sitemaps;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
+import org.springframework.http.MediaType;
+import org.springframework.test.web.servlet.MockMvc;
+
+/**
+ * MVC tests for {@link SitemapIndexController}
+ * @author JB Nizet
+ */
+@WebMvcTest(SitemapIndexController.class)
+class SitemapIndexControllerTest {
+ @Autowired
+ private MockMvc mockMvc;
+
+ @Test
+ void shouldGenerateSitemapIndex() throws Exception {
+ mockMvc.perform(get("/faidare/sitemap.xml").contextPath("/faidare"))
+ .andExpect(status().isOk())
+ .andExpect(content().contentType(MediaType.TEXT_XML))
+ .andExpect(xpath("/sitemapindex/sitemap[1]/loc").string("http://localhost/faidare/sites/sitemap.txt"))
+ .andExpect(xpath("/sitemapindex/sitemap[2]/loc").string("http://localhost/faidare/germplasms/sitemap-0.txt"))
+ .andExpect(xpath("/sitemapindex/sitemap[3]/loc").string("http://localhost/faidare/germplasms/sitemap-1.txt"))
+ .andExpect(xpath("/sitemapindex/sitemap[" + (Sitemaps.BUCKET_COUNT + 2) + "]/loc").string("http://localhost/faidare/studies/sitemap-0.txt"))
+ .andExpect(xpath("/sitemapindex/sitemap[" + (Sitemaps.BUCKET_COUNT + 3) + "]/loc").string("http://localhost/faidare/studies/sitemap-1.txt"));
+ }
+}
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/web/study/StudyControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/web/study/StudyControllerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..cfa58e320cd6dc55d7ae41a7c24d778c61c448d3
--- /dev/null
+++ b/backend/src/test/java/fr/inra/urgi/faidare/web/study/StudyControllerTest.java
@@ -0,0 +1,97 @@
+package fr.inra.urgi.faidare.web.study;
+
+import static org.mockito.ArgumentMatchers.anyInt;
+import static org.mockito.Mockito.when;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.asyncDispatch;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+
+import java.util.Arrays;
+import java.util.List;
+
+import fr.inra.urgi.faidare.config.FaidareProperties;
+import fr.inra.urgi.faidare.domain.data.LocationSitemapVO;
+import fr.inra.urgi.faidare.domain.data.study.StudySitemapVO;
+import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
+import fr.inra.urgi.faidare.repository.es.LocationRepository;
+import fr.inra.urgi.faidare.repository.es.StudyRepository;
+import fr.inra.urgi.faidare.repository.es.TrialRepository;
+import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import fr.inra.urgi.faidare.repository.file.CropOntologyRepository;
+import fr.inra.urgi.faidare.utils.Sitemaps;
+import fr.inra.urgi.faidare.web.site.SiteController;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.MediaType;
+import org.springframework.test.web.servlet.MockMvc;
+import org.springframework.test.web.servlet.MvcResult;
+
+/**
+ * MVC tests for {@link StudyController}
+ * @author JB Nizet
+ */
+@WebMvcTest(StudyController.class)
+public class StudyControllerTest {
+ @Autowired
+ private MockMvc mockMvc;
+
+ @MockBean
+ private StudyRepository mockStudyRepository;
+
+ @MockBean
+ private FaidareProperties mockFaidareProperties;
+
+ @MockBean
+ private XRefDocumentRepository mockXRefDocumentRepository;
+
+ @MockBean
+ private GermplasmRepository mockGermplasmRepository;
+
+ @MockBean
+ private CropOntologyRepository mockCropOntologyRepository;
+
+ @MockBean
+ private TrialRepository mockTrialRepository;
+
+ @MockBean
+ private LocationRepository mockLocationRepository;
+
+ @Test
+ void shouldGenerateSitemap() throws Exception {
+ List<StudySitemapVO> studies = Arrays.asList(
+ new StudySitemapVO("study1"),
+ new StudySitemapVO("study4"),
+ new StudySitemapVO("study51"),
+ new StudySitemapVO("study72")
+ );
+
+ // the hashCode algorithm is specified in the javadoc, so it's guaranteed to be
+ // the same everywhere
+ // uncomment the following line to see which sitemap index each study has
+ // studies.forEach(study -> System.out.println(study.getStudyDbId() + " = " + Math.floorMod(study.getStudyDbId().hashCode(), Sitemaps.BUCKET_COUNT)));
+
+ when(mockStudyRepository.scrollAllForSitemap(anyInt())).thenAnswer(invocation -> studies.iterator());
+ testSitemap(6, "http://localhost/faidare/studies/study1\nhttp://localhost/faidare/studies/study72\n");
+ testSitemap(9, "http://localhost/faidare/studies/study4\nhttp://localhost/faidare/studies/study51\n");
+ testSitemap(7, "");
+
+ mockMvc.perform(get("/faidare/studies/sitemap-17.txt")
+ .contextPath("/faidare"))
+ .andExpect(status().isNotFound());
+ }
+
+ private void testSitemap(int index, String expectedContent) throws Exception {
+ MvcResult mvcResult = mockMvc.perform(get("/faidare/studies/sitemap-" + index + ".txt")
+ .contextPath("/faidare"))
+ .andExpect(request().asyncStarted())
+ .andReturn();
+
+ this.mockMvc.perform(asyncDispatch(mvcResult))
+ .andExpect(status().isOk())
+ .andExpect(content().contentType(MediaType.TEXT_PLAIN))
+ .andExpect(content().string(expectedContent));
+
+ }
+}