Feat: Add web service for mcpd export.

backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmController.java

@@ -126,6 +126,27 @@ public class GnpISGermplasmController {
         return null;
     }
 
+
+
+    @PostMapping(value = "/germplasm-mcpd-csv", produces = "text/csv", consumes = APPLICATION_JSON_VALUE)
+    public FileSystemResource exportMcpd(@RequestBody @Valid FaidareGermplasmPOSTShearchCriteria criteria, HttpServletResponse response) {
+
+        long limitResult = 50000L;
+        long nbResult = germplasmService.germplasmFind(criteria).getMetadata().getPagination().getTotalCount();
+
+        if (!(nbResult > limitResult)) {
+            try {
+                File exportFile = germplasmService.exportGermplasmMcpd(criteria);
+                response.setHeader("Content-Disposition", "attachment; filename=germplasm.gnpis.csv");
+                return new FileSystemResource(exportFile);
+            } catch (Exception e) {
+                e.printStackTrace();
+                throw new RuntimeException("An error occurred when exporting germplasm: " + e.getMessage() + ".", e);
+            }
+        }
+        return null;
+    }
+
     @ApiOperation("Search list of germplasm")
     @PostMapping(value = "/search", consumes = APPLICATION_JSON_VALUE)
     public GermplasmSearchResponse germplasmSearch(@RequestBody @Valid FaidareGermplasmPOSTShearchCriteria criteria) {

backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericGetByIdRepository.java

 package fr.inra.urgi.faidare.elasticsearch.repository.impl;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import fr.inra.urgi.faidare.elasticsearch.ESRequestFactory;
 import fr.inra.urgi.faidare.elasticsearch.ESResponseParser;
 import fr.inra.urgi.faidare.elasticsearch.document.DocumentAnnotationUtil;
@@ -65,6 +67,18 @@ public class ESGenericGetByIdRepository<VO> implements ESGetByIdRepository<VO> {
             // Parse result list
             List<? extends VO> resultList = parser.parseHits(result, voClass);
 
+
+            System.out.println("");
+            System.out.println("BEGIN");
+            System.out.println("");
+
+            ObjectWriter ow = new ObjectMapper().writer().withDefaultPrettyPrinter();
+            String json = ow.writeValueAsString(result);
+            System.out.println(json);
+
+            System.out.println("END");
+            System.out.println("");
+
             if (resultList != null && !resultList.isEmpty()) {
                 if (resultList.size() > 1) {
                     // Should never happen

backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepository.java

@@ -2,13 +2,13 @@ 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.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.datadiscovery.response.GermplasmSearchResponse;
 import fr.inra.urgi.faidare.domain.response.PaginatedList;
 import fr.inra.urgi.faidare.elasticsearch.repository.ESFindRepository;
-import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
 
 import java.util.Iterator;
 
@@ -41,6 +41,11 @@ public interface GermplasmRepository
      */
     Iterator<GermplasmVO> scrollAllGermplasm(FaidareGermplasmPOSTShearchCriteria criteria);
 
+    /**
+     * Scroll through all germplasmMcpd matching the given FAIDARE search criteria.
+     */
+    Iterator<GermplasmMcpdVO> scrollAllGermplasmMcpd(FaidareGermplasmPOSTShearchCriteria criteria);
+
     /**
      * Find pedigree for germplasm by id.
      */

backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java

@@ -3,6 +3,7 @@ package fr.inra.urgi.faidare.repository.es;
 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.GermplasmVO;
 import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
 import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
@@ -38,8 +39,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
-import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
-
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -105,6 +104,13 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
         return new ESScrollIterator<>(client, requestFactory, parser, GermplasmVO.class, query, fetchSize);
     }
 
+    @Override
+    public Iterator<GermplasmMcpdVO> scrollAllGermplasmMcpd(FaidareGermplasmPOSTShearchCriteria criteria) {
+        QueryBuilder query = queryFactory.createShouldFilterQuery(criteria);
+        int fetchSize = criteria.getPageSize().intValue();
+        return new ESScrollIterator<>(client, requestFactory, parser, GermplasmMcpdVO.class, query, fetchSize);
+    }
+
     @Override
     public GermplasmVO getById(String germplasmDbId) {
         return getByIdRepository.getById(germplasmDbId);

backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmService.java

@@ -2,12 +2,12 @@ package fr.inra.urgi.faidare.service.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.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.datadiscovery.response.GermplasmSearchResponse;
 import fr.inra.urgi.faidare.domain.response.PaginatedList;
-import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
 
 import java.io.File;
 
@@ -34,5 +34,7 @@ public interface GermplasmService {
 
     GermplasmMcpdVO getMcpdById(String germplasmDbId);
 
+    File exportGermplasmMcpd(FaidareGermplasmPOSTShearchCriteria criteria);
+
 
 }

backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmServiceImpl.java

@@ -4,18 +4,13 @@ import com.opencsv.CSVWriter;
 import fr.inra.urgi.faidare.api.faidare.v1.GnpISGermplasmController;
 import fr.inra.urgi.faidare.domain.criteria.FaidareGermplasmPOSTShearchCriteria;
 import fr.inra.urgi.faidare.domain.criteria.GermplasmSearchCriteria;
-import fr.inra.urgi.faidare.domain.data.germplasm.CollPopVO;
-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.data.germplasm.*;
 import fr.inra.urgi.faidare.domain.datadiscovery.response.GermplasmSearchResponse;
 import fr.inra.urgi.faidare.domain.response.PaginatedList;
 import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Service;
-import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
-
 
 import javax.annotation.Resource;
 import java.io.*;
@@ -68,6 +63,19 @@ public class GermplasmServiceImpl implements GermplasmService {
         return germplasmRepository.getMcpdById(germplasmDbId);
     }
 
+    @Override
+    public File exportGermplasmMcpd(FaidareGermplasmPOSTShearchCriteria criteria) {
+        try {
+            Iterator<GermplasmMcpdVO> allGermplasm = germplasmRepository.scrollAllGermplasmMcpd(criteria);
+            Path tmpDirPath = Files.createTempDirectory("germplasm");
+            Path tmpFile = Files.createTempFile(tmpDirPath, "germplasm_", ".csv");
+            writeMcpdToCSV(tmpFile, allGermplasm);
+            return tmpFile.toFile();
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
 
     private void writeToCSV(Path tmpFile, Iterator<GermplasmVO> germplasms) throws IOException {
         Writer fileStream = new OutputStreamWriter(new FileOutputStream(tmpFile.toFile()), StandardCharsets.UTF_8);
@@ -107,6 +115,41 @@ public class GermplasmServiceImpl implements GermplasmService {
         csvWriter.close();
     }
 
+
+
+
+    private void writeMcpdToCSV(Path tmpFile, Iterator<GermplasmMcpdVO> germplasms) throws IOException {
+        Writer fileStream = new OutputStreamWriter(new FileOutputStream(tmpFile.toFile()), StandardCharsets.UTF_8);
+        CSVWriter csvWriter = new CSVWriter(fileStream, ';', '"', '\\', "\n");
+        String[] header = new String[]{
+            "PUI", "AccessionNumber", "AccessionNames", "TaxonGroup", "geneticNature", "HoldingInstitution",
+            "mls"
+            };
+        csvWriter.writeNext(header);
+
+        while (germplasms.hasNext()) {
+            List<String> collectionNames = new ArrayList<>();
+            List<String> panelNames = new ArrayList<>();
+            GermplasmMcpdVO germplasmMcpdVO = germplasms.next();
+
+
+            String[] line = new String[header.length];
+            line[0] = germplasmMcpdVO.getGermplasmPUI();
+            line[1] = germplasmMcpdVO.getAccessionNumber();
+            line[2] = String.join(", ", germplasmMcpdVO.getAccessionNames());
+            line[3] = germplasmMcpdVO.getCommonCropName();
+            line[4] = germplasmMcpdVO.getGeneticNature();
+            line[5] = germplasmMcpdVO.getHoldingInstitute().getInstituteName();
+            line[5] = germplasmMcpdVO.getMlsStatus();
+            csvWriter.writeNext(line);
+        }
+        csvWriter.close();
+    }
+
+
+
+
+
     @Override
     public GermplasmVO getById(String germplasmDbId) {
         return germplasmRepository.getById(germplasmDbId);