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 739feea02d0acd41ceb53c0fac02a5fd2ec0775f..7c12185204b63e1ed9a3ccd6e6c9da7092a91dca 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
@@ -12,6 +12,7 @@ import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.elasticsearch.repository.ESFindRepository;
import java.util.Iterator;
+import java.util.Set;
public interface GermplasmRepository
extends ESFindRepository<GermplasmSearchCriteria, GermplasmVO> {
@@ -52,6 +53,11 @@ public interface GermplasmRepository
*/
Iterator<GermplasmMcpdVO> scrollAllGermplasmMcpd(FaidareGermplasmPOSTShearchCriteria criteria);
+ /**
+ * Scroll through all germplasmMcpd having one of the given IDs.
+ */
+ Iterator<GermplasmMcpdVO> scrollGermplasmMcpdsByIds(Set<String> ids, int fetchSize);
+
/**
* Find pedigree for germplasm by id.
*/
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 360087ce79e69f48685b4c2c3480b6de51766171..733d1da9794950b689b43cd95ae465823f45778c 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
@@ -45,6 +45,7 @@ import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Set;
import static org.elasticsearch.search.aggregations.AggregationBuilders.filter;
import static org.elasticsearch.search.aggregations.AggregationBuilders.terms;
@@ -118,6 +119,12 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
return new ESScrollIterator<>(client, requestFactory, parser, GermplasmMcpdVO.class, query, fetchSize);
}
+ @Override
+ public Iterator<GermplasmMcpdVO> scrollGermplasmMcpdsByIds(Set<String> ids, int fetchSize) {
+ QueryBuilder query = QueryBuilders.idsQuery().addIds(ids.toArray(new String[0]));
+ return new ESScrollIterator<>(client, requestFactory, parser, GermplasmMcpdVO.class, query, fetchSize);
+ }
+
@Override
public GermplasmVO getById(String germplasmDbId) {
return getByIdRepository.getById(germplasmDbId);
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 9c126964ee66645fca5c16fbe572519caef4cf77..84da94f897426a8b78c7bc6a3dc2c62b74d4a4c3 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
@@ -6,14 +6,8 @@ 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;
@@ -25,6 +19,7 @@ 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.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.InstituteVO;
@@ -34,7 +29,6 @@ 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.SiteVO;
import fr.inra.urgi.faidare.domain.data.germplasm.TaxonSourceVO;
-import fr.inra.urgi.faidare.domain.xref.XRefDocumentSearchCriteria;
import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
import fr.inra.urgi.faidare.repository.es.GermplasmAttributeRepository;
import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
@@ -43,8 +37,11 @@ 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.validation.annotation.Validated;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.ResponseBody;
@@ -63,15 +60,18 @@ public class GermplasmController {
private final FaidareProperties faidareProperties;
private final XRefDocumentRepository xRefDocumentRepository;
private final GermplasmAttributeRepository germplasmAttributeRepository;
+ private final GermplasmExportService germplasmExportService;
public GermplasmController(GermplasmRepository germplasmRepository,
FaidareProperties faidareProperties,
XRefDocumentRepository xRefDocumentRepository,
- GermplasmAttributeRepository germplasmAttributeRepository) {
+ GermplasmAttributeRepository germplasmAttributeRepository,
+ GermplasmExportService germplasmExportService) {
this.germplasmRepository = germplasmRepository;
this.faidareProperties = faidareProperties;
this.xRefDocumentRepository = xRefDocumentRepository;
this.germplasmAttributeRepository = germplasmAttributeRepository;
+ this.germplasmExportService = germplasmExportService;
}
@GetMapping("/{germplasmId}")
@@ -100,8 +100,19 @@ public class GermplasmController {
return toModelAndView(germplasms.get(0));
}
+ @PostMapping("/exports")
+ @ResponseBody
+ public ResponseEntity<StreamingResponseBody> export(@Validated @RequestBody GermplasmExportCommand command) {
+ List<GermplasmExportableField> fields = getFieldsToExport(command);
- @GetMapping(value = "/sitemap-{index}.txt")
+ StreamingResponseBody body = out -> {
+ Iterator<GermplasmMcpdVO> iterator = germplasmRepository.scrollGermplasmMcpdsByIds(command.getIds(), 1000);
+ germplasmExportService.export(out, iterator, fields);
+ };
+ return ResponseEntity.ok().contentType(MediaType.parseMediaType("text/csv")).body(body);
+ }
+
+ @GetMapping("/sitemap-{index}.txt")
@ResponseBody
public ResponseEntity<StreamingResponseBody> sitemap(@PathVariable("index") int index) {
if (index < 0 || index >= Sitemaps.BUCKET_COUNT) {
@@ -440,4 +451,12 @@ public class GermplasmController {
xref.setEntryType("type " + name);
return xref;
}
+
+ private List<GermplasmExportableField> getFieldsToExport(GermplasmExportCommand command) {
+ List<GermplasmExportableField> fields = command.getFields();
+ if (fields.isEmpty()) {
+ fields = Arrays.asList(GermplasmExportableField.values());
+ }
+ return fields;
+ }
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportCommand.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportCommand.java
new file mode 100644
index 0000000000000000000000000000000000000000..2ae02bdf4f7fdab3a8bf66ef35d583b863ef39f0
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportCommand.java
@@ -0,0 +1,39 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+import javax.validation.constraints.NotEmpty;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+/**
+ * Command sent to export a list of germplasm IDs
+ * @author JB Nizet
+ */
+public class GermplasmExportCommand {
+
+ @NotEmpty
+ private final Set<String> ids;
+
+ /**
+ * The ordered list of fields to export. If empty, all fields are exported
+ */
+ private final List<GermplasmExportableField> fields;
+
+ @JsonCreator
+ public GermplasmExportCommand(@JsonProperty("ids") Set<String> ids,
+ @JsonProperty("fields") List<GermplasmExportableField> fields) {
+ this.ids = ids;
+ this.fields = fields == null ? Collections.emptyList() : fields;
+ }
+
+ public Set<String> getIds() {
+ return ids;
+ }
+
+ public List<GermplasmExportableField> getFields() {
+ return fields;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportService.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportService.java
new file mode 100644
index 0000000000000000000000000000000000000000..1158bdf341b229e7c3779483fbfacc2e1467c395
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportService.java
@@ -0,0 +1,176 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import static fr.inra.urgi.faidare.web.germplasm.GermplasmExportableField.*;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.UncheckedIOException;
+import java.nio.charset.StandardCharsets;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+import com.opencsv.CSVWriter;
+import fr.inra.urgi.faidare.domain.data.germplasm.DonorInfoVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
+import org.springframework.stereotype.Component;
+
+/**
+ * Service allowing to export germplasms as CSV
+ * @author JB Nizet
+ */
+@Component
+public class GermplasmExportService {
+
+ private final Map<GermplasmExportableField, GermplasmExportableFieldDescriptor> descriptors;
+
+ public GermplasmExportService() {
+ Map<GermplasmExportableField, GermplasmExportableFieldDescriptor> map = new HashMap<>();
+
+ map.put(PUID, withFieldAsHeader(PUID, vo -> vo.getGermplasmPUI()));
+ map.put(INSTCODE, withFieldAsHeader(INSTCODE, vo -> vo.getInstituteCode()));
+ map.put(ACCENUMB, withFieldAsHeader(ACCENUMB, vo -> vo.getAccessionNumber()));
+ map.put(COLLNUMB, withFieldAsHeader(COLLNUMB, vo -> vo.getCollectingInfo().getCollectingNumber()));
+ map.put(COLLCODE, withFieldAsHeader(COLLCODE, vo ->
+ vo.getCollectingInfo()
+ .getCollectingInstitutes()
+ .stream()
+ .map(InstituteVO::getInstituteCode).collect(Collectors.joining(";"))));
+ map.put(COLLNAME, withFieldAsHeader(COLLNAME, vo ->
+ vo.getCollectingInfo()
+ .getCollectingInstitutes()
+ .stream()
+ .map(InstituteVO::getInstituteName)
+ .collect(Collectors.joining(";"))));
+ map.put(COLLINSTADDRESS, withFieldAsHeader(COLLINSTADDRESS, vo ->
+ vo.getCollectingInfo()
+ .getCollectingInstitutes()
+ .stream()
+ .map(InstituteVO::getAddress)
+ .collect(Collectors.joining(";"))));
+ map.put(COLLMISSID, withFieldAsHeader(COLLMISSID, vo -> vo.getCollectingInfo().getCollectingMissionIdentifier()));
+ map.put(GENUS, withFieldAsHeader(GENUS, vo -> vo.getGenus()));
+ map.put(SPECIES, withFieldAsHeader(SPECIES, vo -> vo.getSpecies()));
+ map.put(SPAUTHOR, withFieldAsHeader(SPAUTHOR, vo -> vo.getSpeciesAuthority()));
+ map.put(SUBTAXA, withFieldAsHeader(SUBTAXA, vo -> vo.getSubtaxon()));
+ map.put(SUBTAUTHOR, withFieldAsHeader(SUBTAUTHOR, vo -> vo.getSubtaxonAuthority()));
+ map.put(CROPNAME, withFieldAsHeader(CROPNAME, vo -> vo.getCommonCropName()));
+ map.put(ACCENAME, withFieldAsHeader(ACCENAME, vo -> String.join(";", vo.getAccessionNames())));
+ map.put(ACQDATE, withFieldAsHeader(ACQDATE, vo -> vo.getAcquisitionDate()));
+ map.put(ORIGCTY, withFieldAsHeader(ORIGCTY, vo -> vo.getCountryOfOriginCode()));
+ map.put(COLLSITE, withFieldAsHeader(COLLSITE, vo -> vo.getCollectingInfo().getCollectingSite().getSiteName()));
+ map.put(DECLATITUDE, withFieldAsHeader(DECLATITUDE, vo -> vo.getCollectingInfo().getCollectingSite().getLatitudeDecimal()));
+ map.put(LATITUDE, withFieldAsHeader(LATITUDE, vo -> vo.getCollectingInfo().getCollectingSite().getLatitudeDegrees()));
+ map.put(DECLONGITUDE, withFieldAsHeader(DECLONGITUDE, vo -> vo.getCollectingInfo().getCollectingSite().getLongitudeDecimal()));
+ map.put(LONGITUDE, withFieldAsHeader(LONGITUDE, vo -> vo.getCollectingInfo().getCollectingSite().getLongitudeDegrees()));
+ map.put(COORDUNCERT, withFieldAsHeader(COORDUNCERT, vo -> vo.getCollectingInfo().getCollectingSite().getCoordinateUncertainty()));
+ map.put(COORDDATUM, withFieldAsHeader(COORDDATUM, vo -> vo.getCollectingInfo().getCollectingSite().getSpatialReferenceSystem()));
+ map.put(GEOREFMETH, withFieldAsHeader(GEOREFMETH, vo -> vo.getCollectingInfo().getCollectingSite().getGeoreferencingMethod()));
+ map.put(ELEVATION, withFieldAsHeader(ELEVATION, vo -> vo.getCollectingInfo().getCollectingSite().getElevation()));
+ map.put(COLLDATE, withFieldAsHeader(COLLDATE, vo -> vo.getCollectingInfo().getCollectingDate()));
+ map.put(BREDCODE, withFieldAsHeader(BREDCODE, vo ->
+ vo.getBreedingInstitutes()
+ .stream()
+ .map(InstituteVO::getInstituteCode)
+ .collect(Collectors.joining(";"))));
+ map.put(BREDNAME, withFieldAsHeader(BREDNAME, vo ->
+ vo.getBreedingInstitutes()
+ .stream()
+ .map(InstituteVO::getInstituteName)
+ .collect(Collectors.joining(";"))));
+ map.put(SAMPSTAT, withFieldAsHeader(SAMPSTAT, vo -> vo.getBiologicalStatusOfAccessionCode()));
+ map.put(ANCEST, withFieldAsHeader(ANCEST, vo -> vo.getAncestralData()));
+ map.put(COLLSRC, withFieldAsHeader(COLLSRC, vo -> vo.getAcquisitionSourceCode()));
+ map.put(DONORCODE, withFieldAsHeader(DONORCODE, vo ->
+ vo.getDonorInfo()
+ .stream()
+ .map(donorInfoVO -> donorInfoVO.getDonorInstitute().getInstituteCode())
+ .collect(Collectors.joining(";"))));
+ map.put(DONORNAME, withFieldAsHeader(DONORNAME, vo ->
+ vo.getDonorInfo()
+ .stream()
+ .map(donorInfoVO -> donorInfoVO.getDonorInstitute().getInstituteName())
+ .collect(Collectors.joining(";"))));
+ map.put(DONORNUMB, withFieldAsHeader(DONORNUMB, vo ->
+ vo.getDonorInfo()
+ .stream()
+ .map(DonorInfoVO::getDonorAccessionNumber)
+ .collect(Collectors.joining(";"))));
+ map.put(OTHERNUMB, withFieldAsHeader(OTHERNUMB, vo -> String.join(";", vo.getAlternateIDs())));
+ map.put(DUPLSITE, withFieldAsHeader(DUPLSITE, vo ->
+ vo.getSafetyDuplicateInstitutes()
+ .stream()
+ .map(InstituteVO::getInstituteCode)
+ .collect(Collectors.joining(";"))));
+ map.put(DUPLINSTNAME, withFieldAsHeader(DUPLINSTNAME, vo ->
+ vo.getSafetyDuplicateInstitutes()
+ .stream()
+ .map(InstituteVO::getInstituteName)
+ .collect(Collectors.joining(";"))));
+ map.put(STORAGE, withFieldAsHeader(STORAGE, vo -> String.join(";", vo.getStorageTypeCodes())));
+ map.put(MLSSTAT, withFieldAsHeader(MLSSTAT, vo -> vo.getMlsStatus()));
+ map.put(REMARKS, withFieldAsHeader(REMARKS, vo -> vo.getRemarks()));
+
+ this.descriptors = Collections.unmodifiableMap(map);
+ if (map.size() != GermplasmExportableField.values().length) {
+ throw new IllegalStateException("Missing field descriptor");
+ }
+ }
+
+ public void export(OutputStream out, Iterator<GermplasmMcpdVO> germplasms, List<GermplasmExportableField> fields) {
+ try {
+ CSVWriter csvWriter = new CSVWriter(new BufferedWriter(new OutputStreamWriter(out, StandardCharsets.UTF_8)), ';', '"', '\\', "\n");
+ String[] header = fields.stream()
+ .map(descriptors::get)
+ .map(GermplasmExportableFieldDescriptor::getHeader)
+ .toArray(String[]::new);
+ csvWriter.writeNext(header);
+
+ while (germplasms.hasNext()) {
+ GermplasmMcpdVO vo = germplasms.next();
+ String[] line =
+ fields.stream()
+ .map(descriptors::get)
+ .map(descriptor -> descriptor.export(vo))
+ .toArray(String[]::new);
+ csvWriter.writeNext(line);
+ }
+ csvWriter.flush();
+ } catch (IOException e) {
+ throw new UncheckedIOException(e);
+ }
+ }
+
+ private GermplasmExportableFieldDescriptor withFieldAsHeader(GermplasmExportableField field,
+ Function<GermplasmMcpdVO, String> exporter) {
+ return new GermplasmExportableFieldDescriptor(field.name(), exporter);
+ }
+
+ private static class GermplasmExportableFieldDescriptor {
+ private final String header;
+ private final Function<GermplasmMcpdVO, String> exporter;
+
+ public GermplasmExportableFieldDescriptor(String header,
+ Function<GermplasmMcpdVO, String> exporter) {
+ this.header = header;
+ this.exporter = exporter;
+ }
+
+ public String getHeader() {
+ return this.header;
+ }
+
+ public String export(GermplasmMcpdVO germplasm) {
+ return this.exporter.apply(germplasm);
+ }
+ }
+}
+
+
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportableField.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportableField.java
new file mode 100644
index 0000000000000000000000000000000000000000..5835bf3aedbf98b67d7d1a0eff4d49f0348b86e7
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmExportableField.java
@@ -0,0 +1,52 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import com.fasterxml.jackson.annotation.JsonValue;
+
+/**
+ * The fields of a germplasm that can be exported
+ *
+ * @author JB Nizet
+ */
+public enum GermplasmExportableField {
+ PUID,
+ INSTCODE,
+ ACCENUMB,
+ COLLNUMB,
+ COLLCODE,
+ COLLNAME,
+ COLLINSTADDRESS,
+ COLLMISSID,
+ GENUS,
+ SPECIES,
+ SPAUTHOR,
+ SUBTAXA,
+ SUBTAUTHOR,
+ CROPNAME,
+ ACCENAME,
+ ACQDATE,
+ ORIGCTY,
+ COLLSITE,
+ DECLATITUDE,
+ LATITUDE,
+ DECLONGITUDE,
+ LONGITUDE,
+ COORDUNCERT,
+ COORDDATUM,
+ GEOREFMETH,
+ ELEVATION,
+ COLLDATE,
+ BREDCODE,
+ BREDNAME,
+ SAMPSTAT,
+ ANCEST,
+ COLLSRC,
+ DONORCODE,
+ DONORNAME,
+ DONORNUMB,
+ OTHERNUMB,
+ DUPLSITE,
+ DUPLINSTNAME,
+ STORAGE,
+ MLSSTAT,
+ REMARKS
+}
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/web/Fixtures.java b/backend/src/test/java/fr/inra/urgi/faidare/web/Fixtures.java
index ea15e50aa6c909c466ae6f1f090d6c0e9d414f26..fb746865de7e9f6581ccca286360f4e89ccf4633 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/web/Fixtures.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/web/Fixtures.java
@@ -20,6 +20,7 @@ import fr.inra.urgi.faidare.domain.data.germplasm.GenealogyVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmAttributeValueListVO;
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.GermplasmMcpdVO;
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;
@@ -384,4 +385,11 @@ public class Fixtures {
variable.setTrait(trait);
return variable;
}
+
+ public static GermplasmMcpdVO createGermplasmMcpd() {
+ GermplasmMcpdVO result = new GermplasmMcpdVO();
+ result.setGermplasmPUI("PUI1");
+ result.setInstituteCode("Inst1");
+ return result;
+ }
}
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
index 1fbe843db8013edb9b88e9418674891ca68fa3f6..47695c75fe427ea226d278736d0ed05fd7c1e38b 100644
--- 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
@@ -1,35 +1,30 @@
package fr.inra.urgi.faidare.web.germplasm;
import static fr.inra.urgi.faidare.web.Fixtures.htmlContent;
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.ArgumentMatchers.anyInt;
+import static org.mockito.ArgumentMatchers.*;
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.request.MockMvcRequestBuilders.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.request;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Sets;
import fr.inra.urgi.faidare.config.FaidareProperties;
-import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmAttributeValue;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmAttributeValueListVO;
+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.study.StudySitemapVO;
import fr.inra.urgi.faidare.domain.datadiscovery.data.DataSource;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
-import fr.inra.urgi.faidare.domain.xref.XRefDocumentSearchCriteria;
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 fr.inra.urgi.faidare.web.Fixtures;
-import fr.inra.urgi.faidare.web.study.StudyController;
-import fr.inra.urgi.faidare.web.thymeleaf.CoordinatesDialect;
-import fr.inra.urgi.faidare.web.thymeleaf.FaidareDialect;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
@@ -45,11 +40,15 @@ import org.springframework.test.web.servlet.MvcResult;
* @author JB Nizet
*/
@WebMvcTest(GermplasmController.class)
+@Import(GermplasmExportService.class)
public class GermplasmControllerTest {
@Autowired
private MockMvc mockMvc;
+ @Autowired
+ private ObjectMapper objectMapper;
+
@MockBean
private GermplasmRepository mockGermplasmRepository;
@@ -131,6 +130,35 @@ public class GermplasmControllerTest {
.andExpect(status().isNotFound());
}
+ @Test
+ void shouldExportGermplasms() throws Exception {
+ List<GermplasmMcpdVO> germplasms = Arrays.asList(
+ Fixtures.createGermplasmMcpd(),
+ Fixtures.createGermplasmMcpd()
+ );
+
+ GermplasmExportCommand command = new GermplasmExportCommand(
+ Sets.newHashSet("g1", "g2"),
+ Arrays.asList(GermplasmExportableField.PUID, GermplasmExportableField.INSTCODE));
+
+ when(mockGermplasmRepository.scrollGermplasmMcpdsByIds(eq(command.getIds()), anyInt()))
+ .thenAnswer(invocation -> germplasms.iterator());
+
+ MvcResult mvcResult = mockMvc.perform(post("/germplasms/exports")
+ .contentType(MediaType.APPLICATION_JSON)
+ .content(objectMapper.writeValueAsBytes(
+ command)))
+ .andExpect(request().asyncStarted())
+ .andReturn();
+
+ this.mockMvc.perform(asyncDispatch(mvcResult))
+ .andExpect(status().isOk())
+ .andExpect(content().contentType("text/csv"))
+ .andExpect(content().string("\"PUID\";\"INSTCODE\"\n" +
+ "\"PUI1\";\"Inst1\"\n" +
+ "\"PUI1\";\"Inst1\"\n"));
+ }
+
private void testSitemap(int index, String expectedContent) throws Exception {
MvcResult mvcResult = mockMvc.perform(get("/faidare/germplasms/sitemap-" + index + ".txt")
.contextPath("/faidare"))