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 7c12185204b63e1ed9a3ccd6e6c9da7092a91dca..8fbd47d1273fcd733a96d6c0543bc5b1d6a133d1 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
@@ -58,6 +58,11 @@ public interface GermplasmRepository
*/
Iterator<GermplasmMcpdVO> scrollGermplasmMcpdsByIds(Set<String> ids, int fetchSize);
+ /**
+ * Scroll through all germplasm having one of the given IDs.
+ */
+ Iterator<GermplasmVO> scrollGermplasmsByIds(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 616a33d7e6083e9f1abc027f590b692a9a17573e..d5af326a0bb8df2f51206c0408ac2c6cc060255c 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
@@ -125,6 +125,13 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
return new ESScrollIterator<>(client, requestFactory, parser, GermplasmMcpdVO.class, query, fetchSize);
}
+ @Override
+ public Iterator<GermplasmVO> scrollGermplasmsByIds(Set<String> ids,
+ int fetchSize) {
+ QueryBuilder query = QueryBuilders.termsQuery("germplasmDbId", ids);
+ return new ESScrollIterator<>(client, requestFactory, parser, GermplasmVO.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 bfe7d484cb1b5afaed7e17f239db0c29ec5e8153..9cf89be05915532b1bc418c32108f865dfd330ac 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
@@ -49,17 +49,20 @@ public class GermplasmController {
private final FaidareProperties faidareProperties;
private final XRefDocumentRepository xRefDocumentRepository;
private final GermplasmAttributeRepository germplasmAttributeRepository;
+ private final GermplasmMcpdExportService germplasmMcpdExportService;
private final GermplasmExportService germplasmExportService;
public GermplasmController(GermplasmRepository germplasmRepository,
FaidareProperties faidareProperties,
XRefDocumentRepository xRefDocumentRepository,
GermplasmAttributeRepository germplasmAttributeRepository,
+ GermplasmMcpdExportService germplasmMcpdExportService,
GermplasmExportService germplasmExportService) {
this.germplasmRepository = germplasmRepository;
this.faidareProperties = faidareProperties;
this.xRefDocumentRepository = xRefDocumentRepository;
this.germplasmAttributeRepository = germplasmAttributeRepository;
+ this.germplasmMcpdExportService = germplasmMcpdExportService;
this.germplasmExportService = germplasmExportService;
}
@@ -86,13 +89,25 @@ public class GermplasmController {
return toModelAndView(germplasms.get(0));
}
- @PostMapping("/exports")
+ @PostMapping("/exports/mcpd")
+ @ResponseBody
+ public ResponseEntity<StreamingResponseBody> export(@Validated @RequestBody GermplasmMcpdExportCommand command) {
+ List<GermplasmMcpdExportableField> fields = getFieldsToExport(command);
+
+ StreamingResponseBody body = out -> {
+ Iterator<GermplasmMcpdVO> iterator = germplasmRepository.scrollGermplasmMcpdsByIds(command.getIds(), 1000);
+ germplasmMcpdExportService.export(out, iterator, fields);
+ };
+ return ResponseEntity.ok().contentType(MediaType.parseMediaType("text/csv")).body(body);
+ }
+
+ @PostMapping("/exports/plant-material")
@ResponseBody
public ResponseEntity<StreamingResponseBody> export(@Validated @RequestBody GermplasmExportCommand command) {
List<GermplasmExportableField> fields = getFieldsToExport(command);
StreamingResponseBody body = out -> {
- Iterator<GermplasmMcpdVO> iterator = germplasmRepository.scrollGermplasmMcpdsByIds(command.getIds(), 1000);
+ Iterator<GermplasmVO> iterator = germplasmRepository.scrollGermplasmsByIds(command.getIds(), 1000);
germplasmExportService.export(out, iterator, fields);
};
return ResponseEntity.ok().contentType(MediaType.parseMediaType("text/csv")).body(body);
@@ -192,7 +207,17 @@ public class GermplasmController {
return germplasmRepository.findPedigree(germplasm.getGermplasmDbId());
}
- private List<GermplasmExportableField> getFieldsToExport(GermplasmExportCommand command) {
+ private List<GermplasmMcpdExportableField> getFieldsToExport(
+ GermplasmMcpdExportCommand command) {
+ List<GermplasmMcpdExportableField> fields = command.getFields();
+ if (fields.isEmpty()) {
+ fields = Arrays.asList(GermplasmMcpdExportableField.values());
+ }
+ return fields;
+ }
+
+ private List<GermplasmExportableField> getFieldsToExport(
+ GermplasmExportCommand command) {
List<GermplasmExportableField> fields = command.getFields();
if (fields.isEmpty()) {
fields = Arrays.asList(GermplasmExportableField.values());
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
index dc8289ffdeff97c140b4f298ed62f0ae03dc2a82..b17538a92f5edf80493c0dcdf6374a3118030e95 100644
--- 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
@@ -17,9 +17,9 @@ 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.CollPopVO;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
-import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import org.springframework.stereotype.Component;
/**
@@ -34,85 +34,19 @@ public class GermplasmExportService {
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 -> null)); // no value available for DUPLSITE
- 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()));
+ map.put(DOI, new GermplasmExportableFieldDescriptor("DOI", vo -> vo.getGermplasmPUI()));
+ map.put(ACCESSION_NUMBER, new GermplasmExportableFieldDescriptor("Accession number", vo -> vo.getAccessionNumber()));
+ map.put(ACCESSION_NAME, new GermplasmExportableFieldDescriptor("Accession name", vo -> vo.getGermplasmName()));
+ map.put(TAXON_GROUP, new GermplasmExportableFieldDescriptor("Taxon group", vo -> vo.getCommonCropName()));
+ map.put(HOLDING_INSTITUTION, new GermplasmExportableFieldDescriptor("Holding institution", vo -> vo.getInstituteName()));
+ map.put(LOT_NAME, new GermplasmExportableFieldDescriptor("Lot name", vo -> null));
+ map.put(LOT_SYNONYM, new GermplasmExportableFieldDescriptor("Lot synonym", vo -> null));
+ map.put(COLLECTION_NAME, new GermplasmExportableFieldDescriptor("Collection name", vo -> vo.getCollection().stream().map(
+ CollPopVO::getName).collect(Collectors.joining(", "))));
+ map.put(COLLECTION_TYPE, new GermplasmExportableFieldDescriptor("Collection type", vo -> null));
+ map.put(PANEL_NAME, new GermplasmExportableFieldDescriptor("Panel name", vo -> vo.getPanel().stream().map(CollPopVO::getName).collect(
+ Collectors.joining(", "))));
+ map.put(PANEL_SIZE, new GermplasmExportableFieldDescriptor("Panel size", vo -> null));
this.descriptors = Collections.unmodifiableMap(map);
if (map.size() != GermplasmExportableField.values().length) {
@@ -120,7 +54,7 @@ public class GermplasmExportService {
}
}
- public void export(OutputStream out, Iterator<GermplasmMcpdVO> germplasms, List<GermplasmExportableField> fields) {
+ public void export(OutputStream out, Iterator<GermplasmVO> germplasms, List<GermplasmExportableField> fields) {
try {
CSVWriter csvWriter = new CSVWriter(new BufferedWriter(new OutputStreamWriter(out, StandardCharsets.UTF_8)), ';', '"', '\\', "\n");
String[] header = fields.stream()
@@ -130,7 +64,7 @@ public class GermplasmExportService {
csvWriter.writeNext(header);
while (germplasms.hasNext()) {
- GermplasmMcpdVO vo = germplasms.next();
+ GermplasmVO vo = germplasms.next();
String[] line =
fields.stream()
.map(descriptors::get)
@@ -144,17 +78,12 @@ public class GermplasmExportService {
}
}
- 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;
+ private final Function<GermplasmVO, String> exporter;
public GermplasmExportableFieldDescriptor(String header,
- Function<GermplasmMcpdVO, String> exporter) {
+ Function<GermplasmVO, String> exporter) {
this.header = header;
this.exporter = exporter;
}
@@ -163,7 +92,7 @@ public class GermplasmExportService {
return this.header;
}
- public String export(GermplasmMcpdVO germplasm) {
+ public String export(GermplasmVO 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
index 5835bf3aedbf98b67d7d1a0eff4d49f0348b86e7..ecda40cbcdd5fb14532d9b4d9f37eb09b85d90ae 100644
--- 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
@@ -1,52 +1,20 @@
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
+ DOI,
+ ACCESSION_NUMBER,
+ ACCESSION_NAME,
+ TAXON_GROUP,
+ HOLDING_INSTITUTION,
+ LOT_NAME,
+ LOT_SYNONYM,
+ COLLECTION_NAME,
+ COLLECTION_TYPE,
+ PANEL_NAME,
+ PANEL_SIZE
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportCommand.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportCommand.java
new file mode 100644
index 0000000000000000000000000000000000000000..deefb113622f13aa13c55187b2f61a16b96ac041
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportCommand.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 MCPD IDs
+ * @author JB Nizet
+ */
+public class GermplasmMcpdExportCommand {
+
+ @NotEmpty
+ private final Set<String> ids;
+
+ /**
+ * The ordered list of fields to export. If empty, all fields are exported
+ */
+ private final List<GermplasmMcpdExportableField> fields;
+
+ @JsonCreator
+ public GermplasmMcpdExportCommand(@JsonProperty("ids") Set<String> ids,
+ @JsonProperty("fields") List<GermplasmMcpdExportableField> fields) {
+ this.ids = ids;
+ this.fields = fields == null ? Collections.emptyList() : fields;
+ }
+
+ public Set<String> getIds() {
+ return ids;
+ }
+
+ public List<GermplasmMcpdExportableField> getFields() {
+ return fields;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportService.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportService.java
new file mode 100644
index 0000000000000000000000000000000000000000..764eaf9fe40272333e7ac6c725c0c58f24b9d927
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportService.java
@@ -0,0 +1,178 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import static fr.inra.urgi.faidare.web.germplasm.GermplasmMcpdExportableField.*;
+
+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 germplasm MCPDs as CSV
+ * @author JB Nizet
+ */
+@Component
+public class GermplasmMcpdExportService {
+
+ private final Map<GermplasmMcpdExportableField, GermplasmMcpdExportableFieldDescriptor> descriptors;
+
+ public GermplasmMcpdExportService() {
+ Map<GermplasmMcpdExportableField, GermplasmMcpdExportableFieldDescriptor> 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() != GermplasmMcpdExportableField.values().length) {
+ throw new IllegalStateException("Missing field descriptor");
+ }
+ }
+
+ public void export(OutputStream out, Iterator<GermplasmMcpdVO> germplasms, List<GermplasmMcpdExportableField> fields) {
+ try {
+ CSVWriter csvWriter = new CSVWriter(new BufferedWriter(new OutputStreamWriter(out, StandardCharsets.UTF_8)), ';', '"', '\\', "\n");
+ String[] header = fields.stream()
+ .map(descriptors::get)
+ .map(GermplasmMcpdExportableFieldDescriptor::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 GermplasmMcpdExportableFieldDescriptor withFieldAsHeader(
+ GermplasmMcpdExportableField field,
+ Function<GermplasmMcpdVO, String> exporter) {
+ return new GermplasmMcpdExportableFieldDescriptor(field.name(), exporter);
+ }
+
+ private static class GermplasmMcpdExportableFieldDescriptor {
+ private final String header;
+ private final Function<GermplasmMcpdVO, String> exporter;
+
+ public GermplasmMcpdExportableFieldDescriptor(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/GermplasmMcpdExportableField.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportableField.java
new file mode 100644
index 0000000000000000000000000000000000000000..860003663cd5b5397bf1b7f59434e98acb46f972
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmMcpdExportableField.java
@@ -0,0 +1,52 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import com.fasterxml.jackson.annotation.JsonValue;
+
+/**
+ * The fields of a germplasm MCPD that can be exported
+ *
+ * @author JB Nizet
+ */
+public enum GermplasmMcpdExportableField {
+ 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/repository/es/GermplasmRepositoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java
index 7ec9bb8e27fa23dbdb2a84b87e5c116334fae20c..4ba1d45b622eea6310e5e7bb99bc234201ace801 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
@@ -28,6 +28,7 @@ import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
import java.util.Arrays;
import java.util.Collections;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Objects;
@@ -140,7 +141,7 @@ class GermplasmRepositoryTest {
void shouldScrollGermplasmMcpdsByIds() {
Iterator<GermplasmMcpdVO> list = repository.scrollGermplasmMcpdsByIds(Collections.singleton("13705"), 1000);
assertThat(list).toIterable()
- .isNotEmpty()
+ .hasSize(1)
.allMatch(vo -> !vo.getGermplasmDbId().isEmpty());
list = repository.scrollGermplasmMcpdsByIds(Collections.singleton("1370"), 1000);
@@ -152,6 +153,27 @@ class GermplasmRepositoryTest {
.isEmpty();
}
+ @Test
+ void shouldScrollGermplasmsByIds() {
+ Iterator<GermplasmVO> list = repository.scrollGermplasmsByIds(
+ new HashSet<>(
+ Arrays.asList(
+ "ZG9pOjEwLjE1NDU0LzEuNDkyMTc4NjM4MTc4MzY5NkUxMg==",
+ "ZG9pOjEwLjE1NDU0LzEuNDkyMTc4NjM4NDcyNjA1MkUxMg==")
+ ), 1000);
+ assertThat(list).toIterable()
+ .hasSize(2)
+ .allMatch(vo -> !vo.getGermplasmDbId().isEmpty());
+
+ list = repository.scrollGermplasmsByIds(Collections.singleton("ZG9pOjEwL"), 1000);
+ assertThat(list).toIterable()
+ .isEmpty();
+
+ list = repository.scrollGermplasmsByIds(Collections.singleton("ZG9pOjEwL"), 1000);
+ assertThat(list).toIterable()
+ .isEmpty();
+ }
+
@Test
void should_Scroll_By_accessionNumber() {
GermplasmPOSTSearchCriteria criteria = new GermplasmPOSTSearchCriteria();
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 47695c75fe427ea226d278736d0ed05fd7c1e38b..37595c9b7669d49f357f49a4f365ebc12d0a3561 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
@@ -8,7 +8,6 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.
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;
@@ -40,7 +39,7 @@ import org.springframework.test.web.servlet.MvcResult;
* @author JB Nizet
*/
@WebMvcTest(GermplasmController.class)
-@Import(GermplasmExportService.class)
+@Import({GermplasmMcpdExportService.class, GermplasmExportService.class})
public class GermplasmControllerTest {
@Autowired
@@ -131,20 +130,20 @@ public class GermplasmControllerTest {
}
@Test
- void shouldExportGermplasms() throws Exception {
+ void shouldExportMcpds() throws Exception {
List<GermplasmMcpdVO> germplasms = Arrays.asList(
Fixtures.createGermplasmMcpd(),
Fixtures.createGermplasmMcpd()
);
- GermplasmExportCommand command = new GermplasmExportCommand(
+ GermplasmMcpdExportCommand command = new GermplasmMcpdExportCommand(
Sets.newHashSet("g1", "g2"),
- Arrays.asList(GermplasmExportableField.PUID, GermplasmExportableField.INSTCODE));
+ Arrays.asList(GermplasmMcpdExportableField.PUID, GermplasmMcpdExportableField.INSTCODE));
when(mockGermplasmRepository.scrollGermplasmMcpdsByIds(eq(command.getIds()), anyInt()))
.thenAnswer(invocation -> germplasms.iterator());
- MvcResult mvcResult = mockMvc.perform(post("/germplasms/exports")
+ MvcResult mvcResult = mockMvc.perform(post("/germplasms/exports/mcpd")
.contentType(MediaType.APPLICATION_JSON)
.content(objectMapper.writeValueAsBytes(
command)))
@@ -159,6 +158,37 @@ public class GermplasmControllerTest {
"\"PUI1\";\"Inst1\"\n"));
}
+ @Test
+ void shouldExporPlantMaterials() throws Exception {
+ List<GermplasmVO> germplasms = Arrays.asList(
+ Fixtures.createGermplasm(),
+ Fixtures.createGermplasm()
+ );
+
+ GermplasmExportCommand command = new GermplasmExportCommand(
+ Sets.newHashSet("g1", "g2"),
+ Arrays.asList(GermplasmExportableField.DOI,
+ GermplasmExportableField.ACCESSION_NUMBER,
+ GermplasmExportableField.ACCESSION_NAME));
+
+ when(mockGermplasmRepository.scrollGermplasmsByIds(eq(command.getIds()), anyInt()))
+ .thenAnswer(invocation -> germplasms.iterator());
+
+ MvcResult mvcResult = mockMvc.perform(post("/germplasms/exports/plant-material")
+ .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("\"DOI\";\"Accession number\";\"Accession name\"\n" +
+ "\"germplasmPUI\";\"1408\";\"BLE BARBU DU ROUSSILLON\"\n" +
+ "\"germplasmPUI\";\"1408\";\"BLE BARBU DU ROUSSILLON\"\n"));
+ }
+
private void testSitemap(int index, String expectedContent) throws Exception {
MvcResult mvcResult = mockMvc.perform(get("/faidare/germplasms/sitemap-" + index + ".txt")
.contextPath("/faidare"))
@@ -169,6 +199,5 @@ public class GermplasmControllerTest {
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.TEXT_PLAIN))
.andExpect(content().string(expectedContent));
-
}
}