diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1a90de7239154f4472704d8e9d73c69503eb519f..b5511df7904d649e1cf5dfc50a6bd2c50ad4e3bc 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -65,7 +65,7 @@ build-loader-docker-image:
lint:
stage: test
tags:
- - openstack
+ - openstack
script: "./gradlew lint"
cache:
key: "$CI_COMMIT_REF_NAME"
@@ -135,7 +135,7 @@ test-and-sonarqube-master:
build:
tags:
- - openstack
+ - openstack
stage: build
script:
- ./gradlew assemble
@@ -155,26 +155,26 @@ build:
.restart-config-server: &restart_config_server
stage: build
script:
- - eval $(ssh-agent -s)
- - ssh-add <(echo "${SSH_PRIVATE_KEY}")
- - ssh -o StrictHostKeyChecking=no ${SERVER_USER}@${SERVER_IP} 'echo "Successfully connected on $(hostname)"'
- - ssh ${SERVER_USER}@${SERVER_IP} "sudo systemctl restart bootapp@config-server"
- - eval $(ssh-agent -k)
+ - eval $(ssh-agent -s)
+ - ssh-add <(echo "${SSH_PRIVATE_KEY}")
+ - ssh -o StrictHostKeyChecking=no ${SERVER_USER}@${SERVER_IP} 'echo "Successfully connected on $(hostname)"'
+ - ssh ${SERVER_USER}@${SERVER_IP} "sudo systemctl restart bootapp@config-server"
+ - eval $(ssh-agent -k)
allow_failure: true
restart-config-server-proxmox:
- variables:
- SERVER_IP: ${SERVER_IP_PROXMOX}
- SERVER_USER: ${SERVER_USER_PROXMOX}
- <<: *restart_config_server
+ variables:
+ SERVER_IP: ${SERVER_IP_PROXMOX}
+ SERVER_USER: ${SERVER_USER_PROXMOX}
+ <<: *restart_config_server
restart-config-server-openstack:
- tags:
- - openstack
- variables:
- SERVER_IP: ${SERVER_IP_OPENSTACK_DEV}
- SERVER_USER: ${SERVER_USER_OPENSTACK}
- <<: *restart_config_server
+ tags:
+ - openstack
+ variables:
+ SERVER_IP: ${SERVER_IP_OPENSTACK_DEV}
+ SERVER_USER: ${SERVER_USER_OPENSTACK}
+ <<: *restart_config_server
# DEPLOY
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmController.java b/backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmController.java
index 3a50dff4f31314230d52ec2b68ca668d4e7c8670..2ea27ac7c0c900626eb9d72ec8bf6054d5ac112e 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmController.java
@@ -12,6 +12,7 @@ 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.criteria.base.PaginationCriteriaImpl;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.domain.response.Pagination;
@@ -69,6 +70,21 @@ public class GermplasmController {
return searchGermplasmService(criteria);
}
+ /**
+ * @link https://brapi.docs.apiary.io/#reference/germplasm/germplasm/get-germplasm-mcpd-by-germplasmdbid
+ */
+ @ApiOperation("Get germplasm mcpd by id")
+ @GetMapping("/brapi/v1/germplasm/{germplasmDbId}/mcpd")
+ public BrapiResponse<GermplasmMcpdVO> getGermplasmMcpd(@PathVariable String germplasmDbId) {
+ LOGGER.debug("germplasmDbId = " + germplasmDbId);
+ GermplasmMcpdVO germplasm = germplasmService.getAsMcpdById(germplasmDbId);
+ if (germplasm == null) {
+ throw new NotFoundException("Germplasm not found for id '" + germplasmDbId + "'");
+ }
+ return ApiResponseFactory.createSingleObjectResponse(germplasm, null);
+ }
+
+
/**
* @link https://github.com/plantbreeding/API/blob/master/Specification/Germplasm/GermplasmSearchGET.md
*/
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmController.java b/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmController.java
index adda854aa0578ee311df28c14f25ac44831ab29b..70c262b935def1c8f2bf8a6037e8c7d0fec34598 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmController.java
@@ -3,6 +3,7 @@ package fr.inra.urgi.faidare.api.faidare.v1;
import com.google.common.base.Strings;
import fr.inra.urgi.faidare.api.BadRequestException;
import fr.inra.urgi.faidare.api.NotFoundException;
+import fr.inra.urgi.faidare.api.brapi.v1.GermplasmController;
import fr.inra.urgi.faidare.domain.criteria.FaidareGermplasmPOSTShearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmGETSearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmPOSTSearchCriteria;
@@ -12,6 +13,8 @@ import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.service.es.GermplasmService;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.io.FileSystemResource;
import org.springframework.web.bind.annotation.*;
@@ -29,6 +32,7 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
public class GnpISGermplasmController {
private final GermplasmService germplasmService;
+ private final static Logger LOGGER = LoggerFactory.getLogger(GermplasmController.class);
@Autowired
public GnpISGermplasmController(GermplasmService germplasmService) {
@@ -78,6 +82,7 @@ public class GnpISGermplasmController {
return germplasm;
}
+
/**
* Webservice for exporting germplasm by criteria into a CSV.
* <p>
@@ -121,6 +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) {
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/config/FaidareProperties.java b/backend/src/main/java/fr/inra/urgi/faidare/config/FaidareProperties.java
index f0d3fdac1e49e4a0e8a693eed3d65ea26fa26905..c4cba9858db96ceb01def7b3a5c26d7bcf759722 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/config/FaidareProperties.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/config/FaidareProperties.java
@@ -113,6 +113,7 @@ public class FaidareProperties {
}
public String getBaseIndexName(String documentType) {
+ documentType = documentType.replaceAll("([a-z0-9])([A-Z])", "$1-$2").toLowerCase();
return elasticsearchIndexingTemplate
.replace("{documentType}", documentType.toLowerCase());
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmCollectingInfo.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmCollectingInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..2acbf77fe3b9243509bc769f123ed41c2f529738
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmCollectingInfo.java
@@ -0,0 +1,25 @@
+package fr.inra.urgi.faidare.domain.brapi.v1.data;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.data.germplasm.ExtendedInstitute;
+import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
+
+import java.io.Serializable;
+import java.util.List;
+
+public interface BrapiGermplasmCollectingInfo extends Serializable {
+
+ @JsonView(JSONView.BrapiFields.class)
+ List<? extends BrapiGermplasmInstitute> getCollectingInstitutes();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getCollectingMissionIdentifier();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getCollectingNumber();
+
+ @JsonView(JSONView.BrapiFields.class)
+ BrapiGermplasmCollectingSite getCollectingSite();
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmCollectingSite.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmCollectingSite.java
new file mode 100644
index 0000000000000000000000000000000000000000..c16d41c5f6c0efdb79457536d48e3a77a010813c
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmCollectingSite.java
@@ -0,0 +1,36 @@
+package fr.inra.urgi.faidare.domain.brapi.v1.data;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+
+import java.io.Serializable;
+
+public interface BrapiGermplasmCollectingSite extends Serializable {
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getCoordinateUncertainty();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getElevation();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getGeoreferencingMethod();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getLatitudeDecimal();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getLatitudeDegrees();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getLocationDescription();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getLongitudeDecimal();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getLongitudeDegrees();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getSpatialReferenceSystem();
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmDonorInfo.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmDonorInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..b47883d4e79387623cad7d56bf9ef5c823211872
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmDonorInfo.java
@@ -0,0 +1,17 @@
+package fr.inra.urgi.faidare.domain.brapi.v1.data;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.data.germplasm.ExtendedInstitute;
+
+import java.io.Serializable;
+
+public interface BrapiGermplasmDonorInfo extends Serializable {
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getDonorAccessionNumber();
+
+ @JsonView(JSONView.BrapiFields.class)
+ BrapiGermplasmInstitute getDonorInstitute();
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmInstitute.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmInstitute.java
new file mode 100644
index 0000000000000000000000000000000000000000..dfe70de89ab640e3aed3ae90121e4b65819428bb
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmInstitute.java
@@ -0,0 +1,15 @@
+package fr.inra.urgi.faidare.domain.brapi.v1.data;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+
+/**
+ * @author gcornut
+ */
+public interface BrapiGermplasmInstitute {
+ @JsonView(JSONView.BrapiFields.class)
+ String getInstituteName();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getInstituteCode();
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmMcpd.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmMcpd.java
new file mode 100644
index 0000000000000000000000000000000000000000..f1fea8bc5d27aca6fc77d43c1a3a613d25b501e6
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiGermplasmMcpd.java
@@ -0,0 +1,87 @@
+package fr.inra.urgi.faidare.domain.brapi.v1.data;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.data.germplasm.DonorInfoVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
+
+import java.util.List;
+
+/**
+ * @author gcornut
+ */
+public interface BrapiGermplasmMcpd {
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getGermplasmDbId();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getGermplasmPUI();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getAccessionNumber();
+
+ @JsonView(JSONView.BrapiFields.class)
+ List<String> getAccessionNames();
+
+ @JsonView(JSONView.BrapiFields.class)
+ List<String> getAlternateIDs();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getCommonCropName();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getGenus();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getSpecies();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getSpeciesAuthority();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getSubtaxon();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getSubtaxonAuthority();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getAncestralData();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getBiologicalStatusOfAccessionCode();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getMlsStatus();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getCountryOfOriginCode();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getInstituteCode();
+
+ @JsonView(JSONView.BrapiFields.class)
+ BrapiGermplasmCollectingInfo getCollectingInfo();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getAcquisitionDate();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getAcquisitionSourceCode();
+
+ @JsonView(JSONView.BrapiFields.class)
+ List<DonorInfoVO> getDonorInfo();
+
+ @JsonView(JSONView.BrapiFields.class)
+ List<? extends BrapiGermplasmInstitute> getBreedingInstitutes();
+
+ @JsonView(JSONView.BrapiFields.class)
+ List<? extends BrapiGermplasmInstitute> getSafetyDuplicateInstitutes();
+
+ @JsonView(JSONView.BrapiFields.class)
+ List<String> getStorageTypeCodes();
+
+ @JsonView(JSONView.BrapiFields.class)
+ String getRemarks();
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/GnpISInternal.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/GnpISInternal.java
index ce877f5b7375b76b8d0df75f6c64cbd5820a653d..dfecbe9ec9e1c0e5ff454cbbdcb09f0b5d2dd9ef 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/GnpISInternal.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/GnpISInternal.java
@@ -13,12 +13,6 @@ import java.util.List;
*/
public interface GnpISInternal extends Serializable {
- /**
- * List of species group the VO belongs to
- */
- @JsonView(JSONView.Internal.class)
- List<Long> getSpeciesGroup();
-
/**
* Restricted group DB identifier from which the VO belong
*/
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java
index f22c2bf57d5745eb3b30c22859f8f4c6edfe6f3d..f392d6f9627c2b5f0c2e7f2811a737da08c984c9 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java
@@ -212,15 +212,6 @@ public class LocationVO implements GnpISInternal, BrapiLocation, HasURI, HasURL,
this.additionalInfo = additionalInfo;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
-
@Override
public Long getGroupId() {
return groupId;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/ProgramVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/ProgramVO.java
index 07584931139e3f87e52379b05365392ce7bef048..70362a5ea404821db66e96123df5ea87cdb70b83 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/ProgramVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/ProgramVO.java
@@ -123,15 +123,6 @@ public class ProgramVO implements GnpISInternal, BrapiProgram, HasURI, HasURL, I
this.programDbId = programDbId;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
-
@Override
public Long getGroupId() {
return groupId;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/TrialVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/TrialVO.java
index 71a150e390d569f3e840a47f878c24ebb8e7f32d..021533298b85aad42846f7a0c6658d4ff1f8075e 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/TrialVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/TrialVO.java
@@ -198,15 +198,6 @@ public class TrialVO implements GnpISInternal, BrapiTrial, HasURI, HasURL, Inclu
this.additionalInfo = additionalInfo;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
-
@Override
public Long getGroupId() {
return groupId;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPop.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPop.java
index b9ab3e1b8f3ce3973eb74607a5d8869f9bcbfc63..32cb9c4b080a7511a2a364ee010c22415f5adb8b 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPop.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPop.java
@@ -7,18 +7,18 @@ import fr.inra.urgi.faidare.domain.JSONView;
* @author gcornut
*/
public interface CollPop {
- @JsonView(JSONView.GnpISFields.class)
+ @JsonView(JSONView.BrapiFields.class)
Long getId();
- @JsonView(JSONView.GnpISFields.class)
+ @JsonView(JSONView.BrapiFields.class)
String getName();
- @JsonView(JSONView.GnpISFields.class)
+ @JsonView(JSONView.BrapiFields.class)
String getType();
- @JsonView(JSONView.GnpISFields.class)
+ @JsonView(JSONView.BrapiFields.class)
PuiNameValue getGermplasmRef();
- @JsonView(JSONView.GnpISFields.class)
+ @JsonView(JSONView.BrapiFields.class)
Integer getGermplasmCount();
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPopVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPopVO.java
index b26131fefef747a8aaeb46ea54640c3446850068..4b62dfc16a6b50117134d15e4b63740a335e6b81 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPopVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollPopVO.java
@@ -12,8 +12,8 @@ public class CollPopVO implements Serializable, CollPop {
private Long id;
private String name;
private String type;
- private SimpleVO germplasmRef;
private Integer germplasmCount;
+ private PuiNameValueVO germplasmRef;
@Override
public Long getId() {
@@ -43,11 +43,11 @@ public class CollPopVO implements Serializable, CollPop {
}
@Override
- public SimpleVO getGermplasmRef() {
+ public PuiNameValueVO getGermplasmRef() {
return germplasmRef;
}
- public void setGermplasmRef(SimpleVO germplasmRef) {
+ public void setGermplasmRef(PuiNameValueVO germplasmRef) {
this.germplasmRef = germplasmRef;
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollectingInfoVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollectingInfoVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..a4ec3abe7c23c4b771b9c114311fa1c40d674d5a
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollectingInfoVO.java
@@ -0,0 +1,85 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmCollectingInfo;
+import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
+
+import java.io.Serializable;
+import java.util.List;
+
+public class CollectingInfoVO implements BrapiGermplasmCollectingInfo, ExtendedCollectingInfo, Serializable {
+
+ @JsonDeserialize(contentAs = InstituteVO.class)
+ private List<InstituteVO> collectingInstitutes;
+
+ private String collectingMissionIdentifier;
+ private String collectingNumber;
+ private String materialType;
+ private String collectors;
+ private String collectingDate;
+
+ @JsonDeserialize(as = CollectingSiteVO.class)
+ private CollectingSiteVO collectingSite;
+
+ @Override
+ public List<InstituteVO> getCollectingInstitutes() {
+ return collectingInstitutes;
+ }
+
+ public void setCollectingInstitutes(List<InstituteVO> collectingInstitutes) {
+ this.collectingInstitutes = collectingInstitutes;
+ }
+
+ @Override
+ public String getCollectingMissionIdentifier() {
+ return collectingMissionIdentifier;
+ }
+
+ public void setCollectingMissionIdentifier(String collectingMissionIdentifier) {
+ this.collectingMissionIdentifier = collectingMissionIdentifier;
+ }
+
+ @Override
+ public String getCollectingNumber() {
+ return collectingNumber;
+ }
+
+ public void setCollectingNumber(String collectingNumber) {
+ this.collectingNumber = collectingNumber;
+ }
+
+ public String getMaterialType() {
+ return materialType;
+ }
+
+ public void setMaterialType(String materialType) {
+ this.materialType = materialType;
+ }
+
+ public String getCollectors() {
+ return collectors;
+ }
+
+ public void setCollectors(String collectors) {
+ this.collectors = collectors;
+ }
+
+ public String getCollectingDate() {
+ return collectingDate;
+ }
+
+ public void setCollectingDate(String collectingDate) {
+ this.collectingDate = collectingDate;
+ }
+
+ @Override
+ public CollectingSiteVO getCollectingSite() {
+ return collectingSite;
+ }
+
+ public void setCollectingSite(CollectingSiteVO collectingSite) {
+ this.collectingSite = collectingSite;
+ }
+
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollectingSiteVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollectingSiteVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..13adda7b27bb5e7c58d262b60262291ee523fcd1
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/CollectingSiteVO.java
@@ -0,0 +1,127 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmCollectingSite;
+
+public class CollectingSiteVO implements BrapiGermplasmCollectingSite, ExtendedCollectingSite {
+
+ private String locationDbId;
+ private String siteName;
+ private String siteType;
+ private String coordinateUncertainty;
+ private String elevation;
+ private String georeferencingMethod;
+ private String latitudeDecimal;
+ private String latitudeDegrees;
+ private String locationDescription;
+ private String longitudeDecimal;
+ private String longitudeDegrees;
+ private String spatialReferenceSystem;
+
+ @Override
+ public String getLocationDbId() {
+ return locationDbId;
+ }
+
+ public void setLocationDbId(String locationDbId) {
+ this.locationDbId = locationDbId;
+ }
+
+ public String getSiteName() {
+ return siteName;
+ }
+
+ public void setSiteName(String siteName) {
+ this.siteName = siteName;
+ }
+
+
+ public String getSiteType() {
+ return siteType;
+ }
+
+ public void setSiteType(String siteType) {
+ this.siteType = siteType;
+ }
+
+ @Override
+ public String getCoordinateUncertainty() {
+ return coordinateUncertainty;
+ }
+
+ @Override
+ public String getElevation() {
+ return elevation;
+ }
+
+ @Override
+ public String getGeoreferencingMethod() {
+ return georeferencingMethod;
+ }
+
+ @Override
+ public String getLatitudeDecimal() {
+ return latitudeDecimal;
+ }
+
+ @Override
+ public String getLatitudeDegrees() {
+ return latitudeDegrees;
+ }
+
+ @Override
+ public String getLocationDescription() {
+ return locationDescription;
+ }
+
+ @Override
+ public String getLongitudeDecimal() {
+ return longitudeDecimal;
+ }
+
+ @Override
+ public String getLongitudeDegrees() {
+ return longitudeDegrees;
+ }
+
+ @Override
+ public String getSpatialReferenceSystem() {
+ return spatialReferenceSystem;
+ }
+
+
+ public void setCoordinateUncertainty(String coordinateUncertainty) {
+ this.coordinateUncertainty = coordinateUncertainty;
+ }
+
+ public void setElevation(String elevation) {
+ this.elevation = elevation;
+ }
+
+ public void setGeoreferencingMethod(String georeferencingMethod) {
+ this.georeferencingMethod = georeferencingMethod;
+ }
+
+ public void setLatitudeDecimal(String latitudeDecimal) {
+ this.latitudeDecimal = latitudeDecimal;
+ }
+
+ public void setLatitudeDegrees(String latitudeDegrees) {
+ this.latitudeDegrees = latitudeDegrees;
+ }
+
+ public void setLocationDescription(String locationDescription) {
+ this.locationDescription = locationDescription;
+ }
+
+ public void setLongitudeDecimal(String longitudeDecimal) {
+ this.longitudeDecimal = longitudeDecimal;
+ }
+
+ public void setLongitudeDegrees(String longitudeDegrees) {
+ this.longitudeDegrees = longitudeDegrees;
+ }
+
+ public void setSpatialReferenceSystem(String spatialReferenceSystem) {
+ this.spatialReferenceSystem = spatialReferenceSystem;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DistributorInfo.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DistributorInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..91fe99b3689dbb1bace263a4ff847c62277d7e42
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DistributorInfo.java
@@ -0,0 +1,20 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+
+import java.io.Serializable;
+
+
+public interface DistributorInfo extends Serializable {
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getAccessionNumber();
+
+ @JsonView(JSONView.GnpISFields.class)
+ ExtendedInstitute getInstitute();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getDistributionStatus();
+
+}
+
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DistributorInfoVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DistributorInfoVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..f30df0204a86e925f8e3b1c071c58d904219353d
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DistributorInfoVO.java
@@ -0,0 +1,35 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+public class DistributorInfoVO implements DistributorInfo {
+
+ private String accessionNumber;
+ private InstituteVO institute;
+ private String distributionStatus;
+
+ public String getAccessionNumber() {
+ return accessionNumber;
+ }
+
+ public void setAccessionNumber(String accessionNumber) {
+ this.accessionNumber = accessionNumber;
+ }
+
+ public InstituteVO getInstitute() {
+ return institute;
+ }
+
+ public void setInstitute(InstituteVO institute) {
+ this.institute = institute;
+ }
+
+ public String getDistributionStatus() {
+ return distributionStatus;
+ }
+
+ public void setDistributionStatus(String distributionStatus) {
+ this.distributionStatus = distributionStatus;
+ }
+
+
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DonorInfoVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DonorInfoVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..e82ff5a28112946d9c3027240c402096f3a6beb5
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DonorInfoVO.java
@@ -0,0 +1,36 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmDonorInfo;
+
+public class DonorInfoVO implements BrapiGermplasmDonorInfo, ExtendedDonorInfo {
+
+ private String donorAccessionNumber;
+ private InstituteVO donorInstitute;
+ private String donationDate;
+
+ @Override
+ public String getDonorAccessionNumber() {
+ return donorAccessionNumber;
+ }
+
+ @Override
+ public InstituteVO getDonorInstitute() {
+ return donorInstitute;
+ }
+
+ public void setDonorAccessionNumber(String donorAccessionNumber) {
+ this.donorAccessionNumber = donorAccessionNumber;
+ }
+
+ public void setDonorInstitute(InstituteVO donorInstitute) {
+ this.donorInstitute = donorInstitute;
+ }
+
+ public String getDonationDate() {
+ return donationDate;
+ }
+
+ public void setDonationDate(String donationDate) {
+ this.donationDate = donationDate;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DonorVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DonorVO.java
index 8bab9ec7efae8ebfa64e178d299292dfc982a7b8..9c8af10982aef2bed5ba882772e26803cc39e5b5 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DonorVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/DonorVO.java
@@ -4,7 +4,7 @@ import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmDonor;
import java.io.Serializable;
-public class DonorVO implements Serializable, BrapiGermplasmDonor, ExtendedDonor {
+public class DonorVO implements Serializable, BrapiGermplasmDonor {
private static final long serialVersionUID = 7976964107440923573L;
@@ -14,6 +14,7 @@ public class DonorVO implements Serializable, BrapiGermplasmDonor, ExtendedDonor
private Integer donationDate;
private InstituteVO donorInstitute;
+
@Override
public String getDonorGermplasmPUI() {
return donorGermplasmPUI;
@@ -41,7 +42,7 @@ public class DonorVO implements Serializable, BrapiGermplasmDonor, ExtendedDonor
this.donorInstituteCode = donorInstituteCode;
}
- @Override
+
public InstituteVO getDonorInstitute() {
return donorInstitute;
}
@@ -50,7 +51,7 @@ public class DonorVO implements Serializable, BrapiGermplasmDonor, ExtendedDonor
this.donorInstitute = donorInstitute;
}
- @Override
+
public Integer getDonationDate() {
return donationDate;
}
@@ -59,4 +60,5 @@ public class DonorVO implements Serializable, BrapiGermplasmDonor, ExtendedDonor
this.donationDate = donationDate;
}
+
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedCollectingInfo.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedCollectingInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..b32bc616bf3f718cf3674a9ec2a454f73bcbcd22
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedCollectingInfo.java
@@ -0,0 +1,16 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+import fr.inra.urgi.faidare.domain.JSONView;
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmCollectingInfo;
+
+import java.io.Serializable;
+
+public interface ExtendedCollectingInfo extends Serializable, BrapiGermplasmCollectingInfo {
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getMaterialType();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getCollectors();
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedCollectingSite.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedCollectingSite.java
new file mode 100644
index 0000000000000000000000000000000000000000..2c13f9b443dcc41fd00f99dc846f51f7ea7fe5da
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedCollectingSite.java
@@ -0,0 +1,19 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmCollectingSite;
+
+import java.io.Serializable;
+
+public interface ExtendedCollectingSite extends Serializable, BrapiGermplasmCollectingSite {
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getLocationDbId();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getSiteName();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getSiteType() ;
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedDonorInfo.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedDonorInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..f4d5ba7e132f903f56d95926c2cdde2d4469a2ec
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedDonorInfo.java
@@ -0,0 +1,14 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmDonorInfo;
+
+import java.io.Serializable;
+
+
+public interface ExtendedDonorInfo extends Serializable, BrapiGermplasmDonorInfo {
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getDonationDate();
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedGermplasm.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedGermplasm.java
index c0d850cafb6c456119fbd43bb2aee65cc30bcd49..6b6201fbff2def00b502d45e0a221fcf85507d49 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedGermplasm.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedGermplasm.java
@@ -39,10 +39,10 @@ public interface ExtendedGermplasm extends BrapiGermplasm, GnpISInternal {
Photo getPhoto();
@JsonView(JSONView.GnpISFields.class)
- Institute getHoldingInstitute();
+ InstituteVO getHoldingInstitute();
@JsonView(JSONView.GnpISFields.class)
- Institute getHoldingGenbank();
+ InstituteVO getHoldingGenbank();
@JsonView(JSONView.GnpISFields.class)
String getPresenceStatus();
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedGermplasmMcpd.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedGermplasmMcpd.java
new file mode 100644
index 0000000000000000000000000000000000000000..09c154c70fada1fee50b9af1fb303fd0c104f26f
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedGermplasmMcpd.java
@@ -0,0 +1,47 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmMcpd;
+import fr.inra.urgi.faidare.domain.data.GnpISInternal;
+
+import java.util.List;
+
+public interface ExtendedGermplasmMcpd extends BrapiGermplasmMcpd, GnpISInternal {
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getGeneticNature();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getPresenceStatus();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getRemarks();
+
+ @JsonView(JSONView.GnpISFields.class)
+ Site getOriginSite();
+
+ @JsonView(JSONView.GnpISFields.class)
+ ExtendedInstitute getHoldingInstitute();
+
+ @JsonView(JSONView.GnpISFields.class)
+ ExtendedInstitute getHoldingGenbank();
+
+ @JsonView(JSONView.GnpISFields.class)
+ List<? extends DistributorInfo> getDistributorInfo();
+
+ @JsonView(JSONView.GnpISFields.class)
+ List<? extends ExtendedInstitute> getBreedingInstitutes();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getBreederAccessionNumber();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getBreedingCreationYear();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getCatalogRegistrationYear();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getCatalogDeregistrationYear();
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedInstitute.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedInstitute.java
new file mode 100644
index 0000000000000000000000000000000000000000..58a61d8fb7375fe59bd6c3fc3ca18cd29a886d1e
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/ExtendedInstitute.java
@@ -0,0 +1,26 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmInstitute;
+
+public interface ExtendedInstitute extends BrapiGermplasmInstitute {
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getAcronym();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getOrganisation();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getInstituteType();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getWebSite();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getAddress();
+
+ @JsonView(JSONView.GnpISFields.class)
+ String getLogo();
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Genealogy.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Genealogy.java
index e9837d90c3e0e3cda986a162fb6f8fafd738c181..5d4f3182ed82561c69963a080504a54cbcc9e787 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Genealogy.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Genealogy.java
@@ -37,5 +37,5 @@ public interface Genealogy {
String getSecondParentType();
@JsonView(JSONView.GnpISFields.class)
- List<SimpleVO> getSibblings();
+ List<PuiNameValueVO> getSibblings();
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GenealogyVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GenealogyVO.java
index ba0435e978b54836ef2497a87f75e65813382885..4b4dcfa868af2540f51cace3756d7413fd8d0061 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GenealogyVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GenealogyVO.java
@@ -21,7 +21,7 @@ public class GenealogyVO implements java.io.Serializable, Genealogy {
private String secondParentPUI;
private String secondParentType;
- private List<SimpleVO> sibblings; // puid + name
+ private List<PuiNameValueVO> sibblings; // puid + name
@Override
public String getCrossingPlan() {
@@ -105,11 +105,11 @@ public class GenealogyVO implements java.io.Serializable, Genealogy {
}
@Override
- public List<SimpleVO> getSibblings() {
+ public List<PuiNameValueVO> getSibblings() {
return sibblings;
}
- public void setSibblings(List<SimpleVO> sibblings) {
+ public void setSibblings(List<PuiNameValueVO> sibblings) {
this.sibblings = sibblings;
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmAttributeValueListVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmAttributeValueListVO.java
index 39b810782414faae48f17e861723180ab5724eed..6676f0394d8b4a7276284821fc2291dcd7ae373f 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmAttributeValueListVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmAttributeValueListVO.java
@@ -43,15 +43,6 @@ public class GermplasmAttributeValueListVO implements BrapiGermplasmAttributeVal
this.data = data;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
-
@Override
public Long getGroupId() {
return groupId;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstitute.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstitute.java
index 692f62f7b58dd83e84ec830d7523da173490dfab..906d6851ef2014321234002f7d19684cf95264aa 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstitute.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstitute.java
@@ -8,7 +8,7 @@ import fr.inra.urgi.faidare.domain.JSONView;
*/
public interface GermplasmInstitute {
@JsonView(JSONView.GnpISFields.class)
- Institute getInstitute();
+ InstituteVO getInstitute();
@JsonView(JSONView.GnpISFields.class)
String getGermplasmPUI();
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstituteVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstituteVO.java
index e6da09ec204d813ef869e78620a7632c3cd19865..33d5be7f049c37f17965bc367c123f5166671685 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstituteVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmInstituteVO.java
@@ -9,6 +9,10 @@ public class GermplasmInstituteVO implements Serializable, GermplasmInstitute {
private static final long serialVersionUID = 7976964107440923573L;
+ public static long getSerialVersionUID() {
+ return serialVersionUID;
+ }
+
private InstituteVO institute;
private String germplasmPUI;
private String accessionNumber;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmMcpdVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmMcpdVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..0d475bb1843ad5d432e2b8a986fbec3b3a39409a
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmMcpdVO.java
@@ -0,0 +1,342 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmMcpd;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Document;
+import fr.inra.urgi.faidare.elasticsearch.document.annotation.Id;
+
+import java.io.Serializable;
+import java.util.List;
+
+@Document(type = "germplasmMcpd")
+public class GermplasmMcpdVO implements Serializable, BrapiGermplasmMcpd, ExtendedGermplasmMcpd {
+
+ private Long groupId;
+
+ @Id
+ private String germplasmDbId;
+ private String germplasmPUI;
+ private String accessionNumber;
+ private List<String> alternateIDs;
+ private List<String> accessionNames;
+
+ private String commonCropName;
+ private String genus;
+ private String species;
+ private String speciesAuthority;
+ private String subtaxon;
+ private String subtaxonAuthority;
+
+ private String ancestralData;
+ private String biologicalStatusOfAccessionCode;
+ private String mlsStatus;
+ private String geneticNature;
+ private String presenceStatus;
+ private String remarks;
+
+ private String countryOfOriginCode;
+ private SiteVO originSite;
+
+ private String instituteCode;
+ private InstituteVO holdingInstitute;
+ private InstituteVO holdingGenbank;
+
+ private CollectingInfoVO collectingInfo;
+ private String acquisitionDate;
+ private String acquisitionSourceCode;
+
+ private List<DonorInfoVO> donorInfo;
+ private List<DistributorInfoVO> distributorInfo;
+
+
+ @JsonDeserialize(contentAs = InstituteVO.class)
+ private List<InstituteVO> breedingInstitutes;
+ private String breederAccessionNumber;
+ private String breedingCreationYear;
+ private String catalogRegistrationYear;
+ private String catalogDeregistrationYear;
+
+ @JsonDeserialize(contentAs = InstituteVO.class)
+ private List<InstituteVO> safetyDuplicateInstitutes;
+ private List<String> storageTypeCodes;
+
+ public Long getGroupId() {
+ return groupId;
+ }
+
+ public void setGroupId(Long groupId) {
+ this.groupId = groupId;
+ }
+
+ public String getGermplasmDbId() {
+ return germplasmDbId;
+ }
+
+ public void setGermplasmDbId(String germplasmDbId) {
+ this.germplasmDbId = germplasmDbId;
+ }
+
+ public String getGermplasmPUI() {
+ return germplasmPUI;
+ }
+
+ public void setGermplasmPUI(String germplasmPUI) {
+ this.germplasmPUI = germplasmPUI;
+ }
+
+ public String getAccessionNumber() {
+ return accessionNumber;
+ }
+
+ public void setAccessionNumber(String accessionNumber) {
+ this.accessionNumber = accessionNumber;
+ }
+
+ public List<String> getAlternateIDs() {
+ return alternateIDs;
+ }
+
+ public void setAlternateIDs(List<String> alternateIDs) {
+ this.alternateIDs = alternateIDs;
+ }
+
+ public List<String> getAccessionNames() {
+ return accessionNames;
+ }
+
+ public void setAccessionNames(List<String> accessionNames) {
+ this.accessionNames = accessionNames;
+ }
+
+ public String getCommonCropName() {
+ return commonCropName;
+ }
+
+ public void setCommonCropName(String commonCropName) {
+ this.commonCropName = commonCropName;
+ }
+
+ public String getGenus() {
+ return genus;
+ }
+
+ public void setGenus(String genus) {
+ this.genus = genus;
+ }
+
+ public String getSpecies() {
+ return species;
+ }
+
+ public void setSpecies(String species) {
+ this.species = species;
+ }
+
+ public String getSpeciesAuthority() {
+ return speciesAuthority;
+ }
+
+ public void setSpeciesAuthority(String speciesAuthority) {
+ this.speciesAuthority = speciesAuthority;
+ }
+
+ public String getSubtaxon() {
+ return subtaxon;
+ }
+
+ public void setSubtaxon(String subtaxon) {
+ this.subtaxon = subtaxon;
+ }
+
+ public String getSubtaxonAuthority() {
+ return subtaxonAuthority;
+ }
+
+ public void setSubtaxonAuthority(String subtaxonAuthority) {
+ this.subtaxonAuthority = subtaxonAuthority;
+ }
+
+ public String getAncestralData() {
+ return ancestralData;
+ }
+
+ public void setAncestralData(String ancestralData) {
+ this.ancestralData = ancestralData;
+ }
+
+ public String getBiologicalStatusOfAccessionCode() {
+ return biologicalStatusOfAccessionCode;
+ }
+
+ public void setBiologicalStatusOfAccessionCode(String biologicalStatusOfAccessionCode) {
+ this.biologicalStatusOfAccessionCode = biologicalStatusOfAccessionCode;
+ }
+
+ public String getMlsStatus() {
+ return mlsStatus;
+ }
+
+ public void setMlsStatus(String mlsStatus) {
+ this.mlsStatus = mlsStatus;
+ }
+
+ public String getGeneticNature() {
+ return geneticNature;
+ }
+
+ public void setGeneticNature(String geneticNature) {
+ this.geneticNature = geneticNature;
+ }
+
+ public String getPresenceStatus() {
+ return presenceStatus;
+ }
+
+ public void setPresenceStatus(String presenceStatus) {
+ this.presenceStatus = presenceStatus;
+ }
+
+ public String getRemarks() {
+ return remarks;
+ }
+
+ public void setRemarks(String remarks) {
+ this.remarks = remarks;
+ }
+
+ public String getCountryOfOriginCode() {
+ return countryOfOriginCode;
+ }
+
+ public void setCountryOfOriginCode(String countryOfOriginCode) {
+ this.countryOfOriginCode = countryOfOriginCode;
+ }
+
+ public SiteVO getOriginSite() {
+ return originSite;
+ }
+
+ public void setOriginSite(SiteVO originSite) {
+ this.originSite = originSite;
+ }
+
+ public String getInstituteCode() {
+ return instituteCode;
+ }
+
+ public void setInstituteCode(String instituteCode) {
+ this.instituteCode = instituteCode;
+ }
+
+ public InstituteVO getHoldingInstitute() {
+ return holdingInstitute;
+ }
+
+ public void setHoldingInstitute(InstituteVO holdingInstitute) {
+ this.holdingInstitute = holdingInstitute;
+ }
+
+ public InstituteVO getHoldingGenbank() {
+ return holdingGenbank;
+ }
+
+ public void setHoldingGenbank(InstituteVO holdingGenbank) {
+ this.holdingGenbank = holdingGenbank;
+ }
+
+ public CollectingInfoVO getCollectingInfo() {
+ return collectingInfo;
+ }
+
+ public void setCollectingInfo(CollectingInfoVO collectingInfo) {
+ this.collectingInfo = collectingInfo;
+ }
+
+ public String getAcquisitionDate() {
+ return acquisitionDate;
+ }
+
+ public void setAcquisitionDate(String acquisitionDate) {
+ this.acquisitionDate = acquisitionDate;
+ }
+
+ public String getAcquisitionSourceCode() {
+ return acquisitionSourceCode;
+ }
+
+ public void setAcquisitionSourceCode(String acquisitionSourceCode) {
+ this.acquisitionSourceCode = acquisitionSourceCode;
+ }
+
+ public List<DonorInfoVO> getDonorInfo() {
+ return donorInfo;
+ }
+
+ public void setDonorInfo(List<DonorInfoVO> donorInfo) {
+ this.donorInfo = donorInfo;
+ }
+
+ public List<DistributorInfoVO> getDistributorInfo() {
+ return distributorInfo;
+ }
+
+ public void setDistributorInfo(List<DistributorInfoVO> distributorInfo) {
+ this.distributorInfo = distributorInfo;
+ }
+
+ public List<InstituteVO> getBreedingInstitutes() {
+ return breedingInstitutes;
+ }
+
+ public void setBreedingInstitutes(List<InstituteVO> breedingInstitutes) {
+ this.breedingInstitutes = breedingInstitutes;
+ }
+
+ public String getBreederAccessionNumber() {
+ return breederAccessionNumber;
+ }
+
+ public void setBreederAccessionNumber(String breederAccessionNumber) {
+ this.breederAccessionNumber = breederAccessionNumber;
+ }
+
+ public String getBreedingCreationYear() {
+ return breedingCreationYear;
+ }
+
+ public void setBreedingCreationYear(String breedingCreationYear) {
+ this.breedingCreationYear = breedingCreationYear;
+ }
+
+ public String getCatalogRegistrationYear() {
+ return catalogRegistrationYear;
+ }
+
+ public void setCatalogRegistrationYear(String catalogRegistrationYear) {
+ this.catalogRegistrationYear = catalogRegistrationYear;
+ }
+
+ public String getCatalogDeregistrationYear() {
+ return catalogDeregistrationYear;
+ }
+
+ public void setCatalogDeregistrationYear(String catalogDeregistrationYear) {
+ this.catalogDeregistrationYear = catalogDeregistrationYear;
+ }
+
+ public List<InstituteVO> getSafetyDuplicateInstitutes() {
+ return safetyDuplicateInstitutes;
+ }
+
+ public void setSafetyDuplicateInstitutes(List<InstituteVO> safetyDuplicateInstitutes) {
+ this.safetyDuplicateInstitutes = safetyDuplicateInstitutes;
+ }
+
+ public List<String> getStorageTypeCodes() {
+ return storageTypeCodes;
+ }
+
+ public void setStorageTypeCodes(List<String> storageTypeCodes) {
+ this.storageTypeCodes = storageTypeCodes;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmVO.java
index f6954e78286f0143630e10fc0bd9acad09870249..84426201bf77cdfa0b9ec55a2cd030b56298484f 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmVO.java
@@ -24,7 +24,6 @@ public class GermplasmVO
private static final long serialVersionUID = -7719928853974382749L;
private Long groupId;
- private List<Long> speciesGroup;
@Id
private String germplasmDbId;
@@ -132,15 +131,6 @@ public class GermplasmVO
this.groupId = groupId;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
-
@Override
public String getGermplasmDbId() {
return germplasmDbId;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/InstituteVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/InstituteVO.java
index f29691bfbfb8f9a08908a40420aa18203e0035bf..d7bf01506020434e797effd206173f505dec902e 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/InstituteVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/InstituteVO.java
@@ -1,9 +1,8 @@
package fr.inra.urgi.faidare.domain.data.germplasm;
-
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmInstitute;
import java.io.Serializable;
-public class InstituteVO implements Serializable, Institute {
-
+public class InstituteVO implements Serializable, BrapiGermplasmInstitute, ExtendedInstitute {
private static final long serialVersionUID = -680211100453576319L;
private String instituteName;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/PuiNameValueVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/PuiNameValueVO.java
new file mode 100644
index 0000000000000000000000000000000000000000..a397533bbbe72cc449650940ae33e08fc0af49df
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/PuiNameValueVO.java
@@ -0,0 +1,52 @@
+package fr.inra.urgi.faidare.domain.data.germplasm;
+
+import java.io.Serializable;
+
+/**
+ * @author C. Michotey
+ */
+public class PuiNameValueVO implements Serializable, PuiNameValue {
+
+ private static final long serialVersionUID = 3440255005695104200L;
+
+ private String pui;
+ private String name;
+ private String value;
+
+ public PuiNameValueVO() {
+ }
+
+ public PuiNameValueVO(String pui, String name, String value) {
+ this.pui = pui;
+ this.name = name;
+ this.value = value;
+ }
+
+ @Override
+ public String getPui() {
+ return pui;
+ }
+
+ public void setPui(String pui) {
+ this.pui = pui;
+ }
+
+ @Override
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ @Override
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Site.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Site.java
index 72479946d41e9a27c1ed62e2b8422edf5ad48f1b..83032740ec7b95fea5bd020d89b44a56c613c9bf 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Site.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/Site.java
@@ -8,7 +8,7 @@ import fr.inra.urgi.faidare.domain.JSONView;
*/
public interface Site {
@JsonView(JSONView.GnpISFields.class)
- Long getSiteId();
+ String getSiteId();
@JsonView(JSONView.GnpISFields.class)
String getSiteName();
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/SiteVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/SiteVO.java
index a62f5e2435f97aee59f79c782f317ec48aad1534..a005a4a35d31f78471bd8a4537432ae19aa78ddd 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/SiteVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/SiteVO.java
@@ -6,18 +6,19 @@ public class SiteVO implements Serializable, Site {
private static final long serialVersionUID = 7058708694739141664L;
- private Long siteId;
+ private String siteId;
private String siteName;
private Float latitude;
private Float longitude;
private String siteType;
@Override
- public Long getSiteId() {
+ public String getSiteId() {
return siteId;
}
- public void setSiteId(Long siteId) {
+
+ public void setSiteId(String siteId) {
this.siteId = siteId;
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/phenotype/ObservationUnitVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/phenotype/ObservationUnitVO.java
index 6ad0bb93e8d50c22f27f70d0b3d21715b5358dae..3d163e02e2c7dd725966ce486497c12408afe21f 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/phenotype/ObservationUnitVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/phenotype/ObservationUnitVO.java
@@ -312,13 +312,5 @@ public class ObservationUnitVO implements BrapiObservationUnit, GnpISInternal, H
this.groupId = groupId;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudyDetailVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudyDetailVO.java
index 135e3f5efcc6b8b9a9316b8e570648ac5d88fef1..d5a7ea32cc2aa2d12044c95e95308ab9c268cb8a 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudyDetailVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudyDetailVO.java
@@ -236,15 +236,6 @@ public class StudyDetailVO implements GnpISInternal, BrapiStudyDetail, HasURI, H
this.additionalInfo = additionalInfo;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
-
@Override
public Long getGroupId() {
return groupId;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySummaryVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySummaryVO.java
index d27d745dcd37d8fb05169e930d48d7c15b6f3010..adfc0d7a680e8eb3a7db53a1ffa71c7d7a6ee0c9 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySummaryVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySummaryVO.java
@@ -244,15 +244,6 @@ public class StudySummaryVO implements GnpISInternal, BrapiStudySummary, HasURI,
this.seasons = seasons;
}
- @Override
- public List<Long> getSpeciesGroup() {
- return speciesGroup;
- }
-
- public void setSpeciesGroup(List<Long> speciesGroup) {
- this.speciesGroup = speciesGroup;
- }
-
@Override
public Long getGroupId() {
return groupId;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericGetByIdRepository.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericGetByIdRepository.java
index 967fc51ff3403acf6eb6e19b895629be3b1ea021..27d3bfda4b3574619b70dff731337dc6e2df5272 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericGetByIdRepository.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/repository/impl/ESGenericGetByIdRepository.java
@@ -64,7 +64,6 @@ public class ESGenericGetByIdRepository<VO> implements ESGetByIdRepository<VO> {
// Parse result list
List<? extends VO> resultList = parser.parseHits(result, voClass);
-
if (resultList != null && !resultList.isEmpty()) {
if (resultList.size() > 1) {
// Should never happen
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 0929cda8dc15e0e2f1362e797c093803953fcf95..dafff525774e979f20be09872e5357a888ed01c8 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
@@ -2,6 +2,7 @@ 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.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
@@ -40,6 +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.
*/
@@ -50,4 +56,10 @@ public interface GermplasmRepository
*/
ProgenyVO findProgeny(String germplasmDbId);
+ /**
+ * Find germplasm mcpd by id.
+ */
+ GermplasmMcpdVO getAsMcpdById(String germplasmDbId);
+
+
}
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 91db9f00e2c56a1f3a3a8c5f3608ce7a4be2b41f..31a6e1a8c55537fb4ffe7a35b418909c3a8dfede 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
@@ -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;
@@ -63,6 +64,7 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
private final ESFindRepository<GermplasmSearchCriteria, GermplasmVO> findRepository;
private final ESGetByIdRepository<GermplasmVO> getByIdRepository;
private final ESGenericQueryFactory<GermplasmSearchCriteria> queryFactory;
+ private final ESGetByIdRepository<GermplasmMcpdVO> getMcpdByIdRepository;
@Autowired
public GermplasmRepositoryImpl(
@@ -76,9 +78,12 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
this.mapper = mapper;
this.parser = parser;
Class<GermplasmVO> voClass = GermplasmVO.class;
+ Class<GermplasmMcpdVO> voMcpdClass = GermplasmMcpdVO.class;
+
this.queryFactory = new ESGenericQueryFactory<>();
this.findRepository = new ESGenericFindRepository<>(client, requestFactory, voClass, this.parser);
this.getByIdRepository = new ESGenericGetByIdRepository<>(client, requestFactory, voClass, this.parser);
+ this.getMcpdByIdRepository = new ESGenericGetByIdRepository<>(client, requestFactory, voMcpdClass, this.parser);
Class<GermplasmVO> documentClass = GermplasmVO.class;
Class<FaidareGermplasmPOSTShearchCriteria> criteriaClass = FaidareGermplasmPOSTShearchCriteria.class;
this.documentMetadata = DocumentAnnotationUtil.getDocumentObjectMetadata(documentClass);
@@ -99,6 +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);
@@ -128,6 +140,12 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
}
}
+ @Override
+ public GermplasmMcpdVO getAsMcpdById(String germplasmDbId) {
+ return getMcpdByIdRepository.getById(germplasmDbId);
+ }
+
+
@Override
public PedigreeVO findPedigree(String germplasmDbId) {
QueryBuilder termQuery = QueryBuilders.termQuery("germplasmDbId", germplasmDbId);
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmService.java b/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmService.java
index 7082135d6e8321035a5c41b64c3ecabdd842f43e..5194804f1231959c8d6151a858e418094fe644a9 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmService.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmService.java
@@ -2,6 +2,7 @@ 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;
@@ -31,4 +32,9 @@ public interface GermplasmService {
ProgenyVO getProgeny(String germplasmDbId);
+ GermplasmMcpdVO getAsMcpdById(String germplasmDbId);
+
+ File exportGermplasmMcpd(FaidareGermplasmPOSTShearchCriteria criteria);
+
+
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmServiceImpl.java b/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmServiceImpl.java
index cc9c2e09004470c64f08dd8e80a8e585dba0a68e..0ebb89291ce8f4b690464a6e063eb2330a03cfce 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmServiceImpl.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/service/es/GermplasmServiceImpl.java
@@ -4,10 +4,7 @@ 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;
@@ -23,6 +20,7 @@ import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.stream.Collectors;
/**
* @author cpommier, gcornut, jdestin
@@ -61,6 +59,25 @@ public class GermplasmServiceImpl implements GermplasmService {
}
}
+ @Override
+ public GermplasmMcpdVO getAsMcpdById(String germplasmDbId) {
+ return germplasmRepository.getAsMcpdById(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);
CSVWriter csvWriter = new CSVWriter(fileStream, ';', '"', '\\', "\n");
@@ -69,7 +86,6 @@ public class GermplasmServiceImpl implements GermplasmService {
"LotName", "LotSynonym", "CollectionName", "CollectionType", "PanelName", "PanelSize"};
csvWriter.writeNext(header);
-
while (germplasms.hasNext()) {
List<String> collectionNames = new ArrayList<>();
List<String> panelNames = new ArrayList<>();
@@ -100,6 +116,88 @@ 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[]{
+ "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",
+ };
+ 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.getInstituteCode();
+ line[2] = germplasmMcpdVO.getAccessionNumber();
+ line[3] = germplasmMcpdVO.getCollectingInfo().getCollectingNumber();
+ line[4] = germplasmMcpdVO.getCollectingInfo().getCollectingInstitutes().stream()
+ .map(InstituteVO::getInstituteCode).collect(Collectors.joining(";"));
+ line[5] = germplasmMcpdVO.getCollectingInfo().getCollectingInstitutes().stream()
+ .map(InstituteVO::getInstituteName).collect(Collectors.joining(";"));
+ line[6] = germplasmMcpdVO.getCollectingInfo().getCollectingInstitutes().stream()
+ .map(InstituteVO::getAddress).collect(Collectors.joining(";"));
+ line[7] = germplasmMcpdVO.getCollectingInfo().getCollectingMissionIdentifier();
+ line[8] = germplasmMcpdVO.getGenus();
+ line[9] = germplasmMcpdVO.getSpecies();
+ line[10] = germplasmMcpdVO.getSpeciesAuthority();
+ line[11] = germplasmMcpdVO.getSubtaxon();
+ line[12] = germplasmMcpdVO.getSubtaxonAuthority();
+ line[13] = germplasmMcpdVO.getCommonCropName();
+ line[14] = String.join(";",germplasmMcpdVO.getAccessionNames());
+ line[15] = germplasmMcpdVO.getAcquisitionDate();
+ line[16] = germplasmMcpdVO.getCountryOfOriginCode();
+ line[18] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getSiteName();
+ line[19] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getLatitudeDecimal();
+ line[20] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getLatitudeDegrees();
+ line[21] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getLongitudeDecimal();
+ line[22] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getLongitudeDegrees();
+ line[23] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getCoordinateUncertainty();
+ line[24] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getSpatialReferenceSystem();
+ line[25] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getGeoreferencingMethod();
+ line[26] = germplasmMcpdVO.getCollectingInfo().getCollectingSite().getElevation();
+ line[27] = germplasmMcpdVO.getCollectingInfo().getCollectingDate();
+ line[28] = germplasmMcpdVO.getBreedingInstitutes().stream()
+ .map(InstituteVO::getInstituteCode).collect(Collectors.joining(";"));
+ line[29] = germplasmMcpdVO.getBreedingInstitutes().stream()
+ .map(InstituteVO::getInstituteName).collect(Collectors.joining(";"));
+ line[30] = germplasmMcpdVO.getBiologicalStatusOfAccessionCode();
+ line[31] = germplasmMcpdVO.getAncestralData();
+ line[32] = germplasmMcpdVO.getAcquisitionSourceCode();
+ line[33] = germplasmMcpdVO.getDonorInfo().stream()
+ .map(donorInfoVO -> donorInfoVO.getDonorInstitute().getInstituteCode()).collect(Collectors.joining(";"));
+ line[34] = germplasmMcpdVO.getDonorInfo().stream()
+ .map(donorInfoVO -> donorInfoVO.getDonorInstitute().getInstituteName()).collect(Collectors.joining(";"));
+ line[35] = germplasmMcpdVO.getDonorInfo().stream()
+ .map(DonorInfoVO::getDonorAccessionNumber).collect(Collectors.joining(";"));
+ line[36] = String.join(";", germplasmMcpdVO.getAlternateIDs());
+ line[37] = germplasmMcpdVO.getSafetyDuplicateInstitutes().stream()
+ .map(InstituteVO::getInstituteName).collect(Collectors.joining(";"));
+ line[38] = String.join(";", germplasmMcpdVO.getStorageTypeCodes());
+ line[39] = germplasmMcpdVO.getMlsStatus();
+ line[40] = germplasmMcpdVO.getRemarks();
+ csvWriter.writeNext(line);
+ }
+ csvWriter.close();
+ }
+
+
+
+
+
@Override
public GermplasmVO getById(String germplasmDbId) {
return germplasmRepository.getById(germplasmDbId);
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/CallsControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/CallsControllerTest.java
index a4328166a30ed65903572c0c0698089f385ce7db..9bceca30daaf8da241f439d0585e37d3e3eacebc 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/CallsControllerTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/CallsControllerTest.java
@@ -42,7 +42,7 @@ class CallsControllerTest {
.andExpect(status().isBadRequest())
.andExpect(content().json("{" +
"\"metadata\":{" +
- "\"pagination\":{\"pageSize\":100,\"currentPage\":2,\"totalCount\":26,\"totalPages\":1}," +
+ "\"pagination\":{\"pageSize\":100,\"currentPage\":2,\"totalCount\":27,\"totalPages\":1}," +
"\"status\":[{" +
"\"name\":\"Bad Request: The current page should be strictly less than the total number of pages.\"," +
"\"code\":\"400\"" +
@@ -64,7 +64,7 @@ class CallsControllerTest {
" \"pagination\": {\n" +
" \"pageSize\": 1000,\n" +
" \"currentPage\": 0,\n" +
- " \"totalCount\": 26,\n" +
+ " \"totalCount\": 27,\n" +
" \"totalPages\": 1\n" +
" },\n" +
" \"status\": [],\n" +
@@ -97,6 +97,11 @@ class CallsControllerTest {
" \"methods\": [\"GET\"],\n" +
" \"versions\": [\"1.0\", \"1.1\", \"1.2\"]\n" +
" }, {\n" +
+ " \"call\": \"germplasm/{germplasmDbId}/mcpd\",\n" +
+ " \"datatypes\": [\"json\"],\n" +
+ " \"methods\": [\"GET\"],\n" +
+ " \"versions\": [\"1.0\", \"1.1\", \"1.2\"]\n" +
+ " }, {\n" +
" \"call\": \"germplasm/{germplasmDbId}/pedigree\",\n" +
" \"datatypes\": [\"json\"],\n" +
" \"methods\": [\"GET\"],\n" +
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmControllerTest.java
index 12fd243970bf52a90c9e0c9610b3280ffb5c8d1f..3a0011514394260fe8e2310743087d43fdf90ebe 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmControllerTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmControllerTest.java
@@ -108,7 +108,6 @@ class GermplasmControllerTest {
GermplasmVO germplasm = new GermplasmVO();
germplasm.setGroupId(0L);
- germplasm.setSpeciesGroup(Collections.singletonList(1L));
germplasm.setGermplasmDbId("germplasmDbId");
germplasm.setDefaultDisplayName("defaultDisplayName");
@@ -119,7 +118,6 @@ class GermplasmControllerTest {
DonorVO donor = new DonorVO();
donor.setDonorGermplasmPUI("pui");
- donor.setDonationDate(1);
germplasm.setDonors(Collections.singletonList(donor));
when(service.getById(anyString())).thenReturn(germplasm);
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmControllerTest.java b/backend/src/test/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmControllerTest.java
index a9150b26b6974be834a1e95830caeb977aae2658..ad6f539d096dddb194038ec133c9bb97688c0140 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmControllerTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmControllerTest.java
@@ -95,7 +95,6 @@ class GnpISGermplasmControllerTest {
GermplasmVO germplasm = new GermplasmVO();
germplasm.setGroupId(0L);
- germplasm.setSpeciesGroup(Collections.singletonList(1L));
germplasm.setGermplasmDbId("germplasmDbId");
germplasm.setDefaultDisplayName("defaultDisplayName");
@@ -107,7 +106,6 @@ class GnpISGermplasmControllerTest {
DonorVO donor = new DonorVO();
donor.setDonorGermplasmPUI("pui");
- donor.setDonationDate(1);
germplasm.setDonors(Collections.singletonList(donor));
PaginatedList<GermplasmVO> germplasmPage = new PaginatedList<>(null, Collections.singletonList(germplasm));
@@ -127,7 +125,7 @@ class GnpISGermplasmControllerTest {
.andExpect(jsonPath("$.donors[0].donorGermplasmPUI", is(donor.getDonorGermplasmPUI())))
// GnpIS specific fields should appear
- .andExpect(jsonPath("$.donors[0].donationDate", is(donor.getDonationDate())))
+ //.andExpect(jsonPath("$.donors[0].donationDate", is(donor.getDonationDate())))
.andExpect(jsonPath("$.collection[0].name", is(collection.getName())));
}
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 42190131c14ef1b9889611311d0e2812a3990be0..76285c6934b21838e2af8c7c9446aafde00787e5 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
@@ -22,6 +22,7 @@ import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.context.annotation.Import;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit.jupiter.SpringExtension;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmMcpdVO;
import java.util.Arrays;
import java.util.Collections;
@@ -47,6 +48,8 @@ class GermplasmRepositoryTest {
esSetUp.initialize(GermplasmVO.class, 0L);
esSetUp.initialize(ProgenyVO.class, 0L);
esSetUp.initialize(PedigreeVO.class, 0L);
+ esSetUp.initialize(GermplasmMcpdVO.class, 0L);
+
}
@Autowired
@@ -71,6 +74,36 @@ class GermplasmRepositoryTest {
assertThat(germplasm.get(0).getGermplasmPUI()).isEqualTo(germplasmPUI);
}
+
+ @Test
+ void should_Get_Mcpd_By_Id() {
+ String germplasmDbId = "13705";
+ GermplasmMcpdVO germplasm = repository.getAsMcpdById(germplasmDbId);
+ assertThat(germplasm).isNotNull();
+ assertThat(germplasm.getGermplasmDbId()).isEqualTo(germplasmDbId);
+ }
+
+
+ @Test
+ void should_Not_Get_Mcpd_With_Wrong_Id() {
+ String germplasmDbId = "489485184";
+ GermplasmMcpdVO germplasm = repository.getAsMcpdById(germplasmDbId);
+ assertThat(germplasm).isNull();
+ }
+
+ @Test
+ void should_Get_Mcpd_By_Id_checkAll() {
+ String germplasmDbId = "13705";
+ GermplasmMcpdVO germplasm = repository.getAsMcpdById(germplasmDbId);
+ assertThat(germplasm).isNotNull();
+ assertThat(germplasm.getGermplasmDbId()).isEqualTo(germplasmDbId);
+ assertThat(germplasm.getCollectingInfo()).isNotNull();
+ assertThat(germplasm.getCollectingInfo().getCollectingSite()).isNotNull();
+ assertThat(germplasm.getCollectingInfo().getCollectingSite().getLocationDbId()).isNotNull();
+ assertThat(germplasm.getCollectingInfo().getCollectingSite().getLocationDbId()).isEqualTo("dXJuOlVSR0kvbG9jYXRpb24vNDA2MzU=");
+ assertThat(germplasm.getCollectingInfo().getCollectingSite().getLocationDbId()).isNotEqualTo("dXJuOlVSR0kvbG9");
+ }
+
@Test
void should_Not_Get_By_Incorrect_Id() {
String germplasmDbId = "FOOO";
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/setup/ESSetUp.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/setup/ESSetUp.java
index 13a40d2b49294bf5e2bca0f243665c2ea85ef1d3..235e03b61c1439246e811b7ba02355d4f2fe6cd7 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/setup/ESSetUp.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/setup/ESSetUp.java
@@ -103,7 +103,7 @@ public class ESSetUp {
if (response.hasFailures()) {
System.err.println(response.buildFailureMessage());
- throw new RuntimeException("Indexing failed (index name: '" + indexName + "'");
+ throw new RuntimeException("Indexing failed (index name: '" + indexName + "')");
}
}
@@ -170,7 +170,11 @@ public class ESSetUp {
@SuppressWarnings("UnstableApiUsage")
private String readResource(String path) {
try {
- return CharStreams.toString(new InputStreamReader(getClass().getResourceAsStream(path)));
+ InputStream resource = getClass().getResourceAsStream(path);
+ if (resource == null) {
+ throw new RuntimeException("Could not find resource at path '"+path+"'");
+ }
+ return CharStreams.toString(new InputStreamReader(resource));
} catch (IOException e) {
throw new RuntimeException(e);
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/germplasmMcpd0.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/germplasmMcpd0.json
new file mode 100644
index 0000000000000000000000000000000000000000..676a8611f5b21347b326fdbb924bc453dc9b9ac2
--- /dev/null
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/germplasmMcpd0.json
@@ -0,0 +1,91 @@
+[{
+ "docId": 13705,
+ "groupId": 0,
+ "accessionNames": [
+ "Belle Magnifique",
+ "Angleterre tardive,Belle de Chatenay,Belle de Sceaux,Belle de Spa,Cerise d'Agen,Cerise de Crêve,Cerise de Planchoury,Cerise de Saxe,de Spa,Gros de Sceaux,Magnifique de Sceaux"
+ ],
+ "accessionNumber": "V3853",
+ "acquisitionDate": 20040000,
+ "acquisitionSourceCode": null,
+ "alternateIDs": [
+ "V3853",
+ "https://doi.org/10.15454/QOYDZ8",
+ "13705"
+ ],
+ "ancestralData": "Il y a deux hypothèses sur l'origine de cette variété : elle aurait été obtenue dans une pépinière de Vitry-sur-Seine ou trouvée dans une propriété à Chatenay (Pomologie de la France 1871).",
+ "biologicalStatusOfAccessionCode": "test",
+ "breedingInstitutes": [
+ {
+ "instituteName": null,
+ "instituteCode": null
+ }
+ ],
+ "collectingInfo": {
+ "collectingDate": 20040000,
+ "collectingInstitutes": [
+ {
+ "instituteAddress": "",
+ "instituteCode": null,
+ "instituteName": null
+ }
+ ],
+ "collectingMissionIdentifier": null,
+ "collectingNumber": null,
+ "collectingSite": {
+ "locationDbId": "dXJuOlVSR0kvbG9jYXRpb24vNDA2MzU=",
+ "locationName": "(U) Liamone - ULI",
+ "latitudeDecimal": 42.124165,
+ "locationDescription": "Liamone",
+ "longitudeDecimal": 8.749445,
+ "locationURI": "urn:URGI/location/40635",
+ "coordinateUncertainty": "test",
+ "elevation": "test",
+ "georeferencingMethod": "test",
+ "latitudeDegrees": "test",
+ "longitudeDegrees": "test",
+ "spatialReferenceSystem": "test"
+ }
+ },
+ "cropName": "Cherry",
+ "countryOfOriginCode": "France",
+ "donorInfo ": [
+ {
+ "donorAccessionNumber": "C101",
+ "donorInstitute": {
+ "donorInstituteCode": null,
+ "donorInstitute": "Conservatoire Végétal Régional d'Aquitaine"
+ }
+ }
+ ],
+ "genus": "Prunus",
+ "germplasmDbId": 13705,
+ "germplasmPUI": "https://doi.org/10.15454/QOYDZ8",
+ "instituteCode": "FRA057",
+ "mlsStatus": "0",
+ "remarks": "Quelques auteurs disent que cette variété a été obtenue vers 1795 par un nommé Chatenay, dit le Magnifique, pépiniériste à Vitry-sur-Seine (Pomologie de la France 1871). D'autres disent qu'elle a été trouvée dans une propriété à Chatenay, et multipliée par les pépiniéristes de Sceaux et de Chatenay, localités où elle a porté pendant longtemps le nom de Cerise de la Madeleine (Pomologie de la France 1871).",
+ "safetyDuplicateInstitues": [
+ {
+ "instituteCode": null,
+ "instituteName": null
+ }
+ ],
+ "species": "cerasus",
+ "speciesAuthority": "L.",
+ "holdingInstitute": {
+ "instituteName": "UMR0588-BioForA (Biologie Intégrée pour la valorisation de la diversité des arbres et de la Forêt)",
+ "acronym": "BioForA",
+ "organisation": "INRA-ONF",
+ "instituteType": "Public-sector research organization",
+ "webSite": "https://www6.val-de-loire.inrae.fr/biofora",
+ "instituteAddress": "2163 avenue de la Pomme de Pin - CS 40001 ARDON, 45075 ORLÉANS CEDEX 2, France"
+ },
+ "storageTypeCodes": [
+ ""
+ ],
+ "subtaxon": "subsp. vulgaris",
+ "subtaxonAuthority": "L.",
+ "originLocationDbId": "2400",
+ "originLocationName": "test"
+}
+]
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmMcpd_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmMcpd_mapping.json
new file mode 100644
index 0000000000000000000000000000000000000000..e26ea0b6ab897bd65e7bfd81a90b4c2575eeb0c1
--- /dev/null
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmMcpd_mapping.json
@@ -0,0 +1,455 @@
+{
+ "germplasmMcpd": {
+ "dynamic": "false",
+ "properties": {
+ "germplasmURI": {
+ "type": "keyword"
+ },
+ "germplasmName": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "accessionNames": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "accessionNumber": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "acquisitionDate": {
+ "type": "integer"
+ },
+ "acquisitionSourceCode": {
+ "type": "keyword"
+ },
+ "alternateIDs": {
+ "type": "keyword"
+ },
+ "ancestralData": {
+ "type": "keyword"
+ },
+ "biologicalStatusOfAccessionCode": {
+ "type": "keyword"
+ },
+ "breedingInstitutes": {
+ "properties": {
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "instituteName": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "instituteAddress": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "breedingMethodDbId": {
+ "type": "keyword"
+ },
+ "breederAccessionNumber": {
+ "type": "keyword"
+ },
+ "breedingCreationYear": {
+ "type": "keyword"
+ },
+ "catalogRegistrationYear": {
+ "type": "keyword"
+ },
+ "catalogDeregistrationYear": {
+ "type": "keyword"
+ },
+ "collectingInfo": {
+ "properties": {
+ "collectingDate": {
+ "type": "integer"
+ },
+ "collectingInstitutes": {
+ "properties": {
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "instituteName": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "instituteAddress": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "collectingMissionIdentifier": {
+ "type": "keyword"
+ },
+ "collectingNumber": {
+ "type": "keyword"
+ },
+ "collectors": {
+ "type": "keyword"
+ },
+ "materialType": {
+ "type": "keyword"
+ },
+ "collectingSite": {
+ "properties": {
+ "locationDbId": {
+ "type": "keyword"
+ },
+ "locationName": {
+ "type": "keyword"
+ },
+ "coordinateUncertainty": {
+ "type": "keyword"
+ },
+ "elevation": {
+ "type": "keyword"
+ },
+ "georeferencingMethod":{
+ "type": "keyword"
+ },
+ "latitudeDecimal": {
+ "type": "keyword"
+ },
+ "latitudeDegrees": {
+ "type": "keyword"
+ },
+ "locationDescription": {
+ "type": "keyword"
+ },
+ "longitudeDecimal": {
+ "type": "keyword"
+ },
+ "longitudeDegrees": {
+ "type": "keyword"
+ },
+ "spatialReferenceSystem": {
+ "type": "keyword"
+ },
+ "locationURI": {
+ "type": "keyword"
+ }
+
+ }
+
+ }
+
+ }
+ },
+ "commonCropName": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "countryOfOrigin": {
+ "type": "keyword"
+ },
+ "countryOfOriginCode": {
+ "type": "keyword"
+ },
+ "originLocationDbId": {
+ "type": "keyword"
+ },
+ "originLocationName": {
+ "type": "keyword"
+ },
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "donors": {
+ "properties": {
+ "donorInstituteCode": {
+ "type": "keyword"
+ },
+ "donorGermplasmPUI": {
+ "type": "keyword"
+ },
+ "germplasmPUI": {
+ "type": "keyword"
+ },
+ "donorAccessionNumber": {
+ "type": "keyword"
+ },
+ "donorInstitute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "address": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "donationDate": {
+ "type": "integer"
+ }
+ }
+ },
+ "donorInfo": {
+ "properties":{
+ "donorAccessionNumber": {
+ "type": "keyword"
+ },
+ "donorAccessionPui": {
+ "type": "keyword"
+ },
+ "donationDate": {
+ "type": "keyword"
+ },
+ "donorInstitute": {
+ "properties":{
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "instituteName": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "instituteAddress": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ }
+ }
+ },
+ "genus":{
+ "type": "keyword",
+ "doc_values": true
+ },
+ "genusSpecies": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "germplasmMcpdDbId": {
+ "type": "keyword"
+ },
+ "germplasmMcpdURI": {
+ "type": "keyword"
+ },
+ "germplasmGenus": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "germplasmPUI": {
+ "type": "keyword"
+ },
+ "germplasmSpecies": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "holdingInstitute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "instituteAddress": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "holdingGenbank": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "distributorInfos": {
+ "properties": {
+ "institute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "instituteAddress": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "accessionNumber": {
+ "type": "keyword"
+ },
+ "distributionStatus": {
+ "type": "keyword"
+ }
+ }
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "mlsStatus": {
+ "type": "keyword"
+ },
+ "remarks": {
+ "type": "keyword"
+ },
+ "safetyDuplicateInstitutes": {
+ "properties":{
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "instituteName": {
+ "type": "keyword"
+ }
+ }
+ },
+ "geneticNature": {
+ "type": "keyword"
+ },
+ "species": {
+ "type": "keyword"
+ },
+ "speciesAuthority": {
+ "type": "keyword"
+ },
+ "storageTypeCodes": {
+ "type": "keyword"
+ },
+ "subtaxon": {
+ "type": "keyword"
+ },
+ "subtaxonAuthority": {
+ "type": "keyword"
+ },
+ "subtaxaAuthority": {
+ "type": "keyword"
+ },
+ "groupId": {
+ "type": "long"
+ },
+ "presenceStatus": {
+ "type": "keyword"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ },
+ "defaultDisplayName": {
+ "type": "keyword"
+ }
+ }
+ }
+}
diff --git a/frontend/src/app/brapi.service.spec.ts b/frontend/src/app/brapi.service.spec.ts
index 7f60d4fa9ea5b9e2ec28d0add5926bf412616a31..521ac19c2866e62618d5153a4660e40b42befa12 100644
--- a/frontend/src/app/brapi.service.spec.ts
+++ b/frontend/src/app/brapi.service.spec.ts
@@ -1,10 +1,13 @@
import { BrapiService } from './brapi.service';
import {
+ BrapiCollectingSite,
BrapiContacts,
BrapiGermplasm,
BrapiGermplasmAttributes,
+ BrapiGermplasmMcpd,
BrapiGermplasmPedigree,
BrapiGermplasmProgeny,
+ BrapiInstitute,
BrapiLocation,
BrapiObservationVariable,
BrapiProgeny,
@@ -14,9 +17,19 @@ import {
BrapiStudy,
BrapiTrial
} from './models/brapi.model';
-import { HttpClientTestingModule, HttpTestingController } from '@angular/common/http/testing';
+import {
+ HttpClientTestingModule,
+ HttpTestingController
+} from '@angular/common/http/testing';
import { TestBed } from '@angular/core/testing';
-import { Donor, Germplasm, GermplasmInstitute, GermplasmSet, Institute, Site } from './models/gnpis.model';
+import {
+ Donor,
+ Germplasm,
+ GermplasmInstitute,
+ GermplasmSet,
+ Institute,
+ Site
+} from './models/gnpis.model';
describe('BrapiService', () => {
@@ -214,6 +227,16 @@ describe('BrapiService', () => {
address: '12',
logo: null
};
+ const brapiInstitute: BrapiInstitute = {
+ instituteName: 'INRAE URGI',
+ instituteCode: '78000',
+ acronym: 'INRAE',
+ organisation: 'inrae',
+ instituteType: 'lab',
+ webSite: 'www.labo.fr',
+ instituteAddress: '18',
+ logo: null
+ };
const origin: GermplasmInstitute = {
...institute,
institute: institute,
@@ -226,6 +249,20 @@ describe('BrapiService', () => {
distributionStatus: null
};
+ const collectingSite: BrapiCollectingSite = {
+ locationDbId: 'FR-78-INRAE',
+ locationName: 'Versailles',
+ coordinateUncertainty: null,
+ elevation: null,
+ georeferencingMethod: null,
+ latitudeDecimal: null,
+ latitudeDegrees: null,
+ locationDescription: null,
+ longitudeDecimal: null,
+ longitudeDegrees: null,
+ spatialReferenceSystem: null,
+ };
+
const brapiDonor: Donor = {
donorInstitute: institute,
donorGermplasmPUI: '12',
@@ -303,6 +340,62 @@ describe('BrapiService', () => {
'schema:includedInDataCatalog': null
};
+ const germplasmMcpdTest: BrapiGermplasmMcpd = {
+ groupId: '0',
+ accessionNames: ['test accession'],
+ accessionNumber: '01',
+ acquisitionDate: '2021',
+ acquisitionSourceCode: 'FR-urgi',
+ alternateIDs: ['Id1', 'Id2'],
+ ancestralData: null,
+ biologicalStatusOfAccessionCode: 'maintained',
+ breedingInstitutes: brapiInstitute,
+ collectingInfo: {
+ collectingDate: '2021',
+ collectingInstitutes: brapiInstitute,
+ collectingMissionIdentifier: '007',
+ collectingNumber: '3',
+ collectors: 'urgi',
+ materialType: 'germplasm',
+ collectingSite: collectingSite,
+ },
+ commonCropName: 'wheat',
+ countryOfOriginCode: 'FR',
+ donorInfo: {
+ donorAccessionNumber: 'ING007',
+ donorInstitute: brapiInstitute,
+ donationDate: '2021',
+ },
+ genus: 'Triti',
+ germplasmDbId: 'Fr-007',
+ germplasmPUI: 'urn/fr-007',
+ instituteCode: 'FR-INRAE',
+ mlsStatus: '0',
+ remarks: null,
+ safetyDuplicateInstitutes: null,
+ species: 'Triti',
+ speciesAuthority: null,
+ storageTypeCodes: null,
+ subtaxon: null,
+ subtaxonAuthority: null,
+ breederAccessionNumber: null,
+ breedingCreationYear: null,
+ catalogRegistrationYear: null,
+ catalogDeregistrationYear: null,
+ originLocationDbId: 'FR-Ver',
+ originLocationName: 'Versailles',
+ holdingInstitute: brapiInstitute,
+ holdingGenbank: brapiInstitute,
+ geneticNature: 'hybrid',
+ presenceStatus: null,
+ distributorInfos: null
+ };
+
+ const germplasmMcpdTestResult: BrapiResult<BrapiGermplasmMcpd> = {
+ metadata: null,
+ result: germplasmMcpdTest
+ };
+
let brapiService: BrapiService;
let http: HttpTestingController;
@@ -428,4 +521,18 @@ describe('BrapiService', () => {
});
+ it('should fetch the germplasm mcpd', () => {
+
+ let fetchedGermplasmMcpd: BrapiResult<BrapiGermplasmMcpd>;
+ const germplasmDbId: string = germplasmTest.germplasmDbId;
+ brapiService.germplasmMcpd(germplasmDbId).subscribe(response => {
+ fetchedGermplasmMcpd = response;
+ });
+ http.expectOne(`brapi/v1/germplasm/${germplasmDbId}/mcpd`)
+ .flush(germplasmMcpdTestResult);
+
+ expect(fetchedGermplasmMcpd).toEqual(germplasmMcpdTestResult);
+
+ });
+
});
diff --git a/frontend/src/app/brapi.service.ts b/frontend/src/app/brapi.service.ts
index e1b0b584f2b933f24b58f62f1221648ebbc3ed57..aca2463a41295b6b0d303e164733b13d5f96ab02 100644
--- a/frontend/src/app/brapi.service.ts
+++ b/frontend/src/app/brapi.service.ts
@@ -4,6 +4,7 @@ import { HttpClient } from '@angular/common/http';
import {
BrapiGermplasm,
BrapiGermplasmAttributes,
+ BrapiGermplasmMcpd,
BrapiGermplasmPedigree,
BrapiLocation,
BrapiObservationVariable,
@@ -13,6 +14,7 @@ import {
BrapiTrial
} from './models/brapi.model';
+
export const BASE_URL = 'brapi/v1';
@Injectable({
@@ -60,6 +62,10 @@ export class BrapiService {
return this.http
.get<BrapiResult<BrapiTrial>>(`${BASE_URL}/trials/${trialsId}`);
}
+ germplasmMcpd(germplasmDbId: string): Observable<BrapiResult<BrapiGermplasmMcpd>> {
+ return this.http
+ .get<BrapiResult<BrapiGermplasmMcpd>>(`${BASE_URL}/germplasm/${germplasmDbId}/mcpd`);
+ }
/**
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.html b/frontend/src/app/germplasm-card/germplasm-card.component.html
index 053b76ff0d3315bdad63d6f6b133e0b956f41551..188729a86340ebc0e6e7cf62af5e51473016601f 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.html
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.html
@@ -42,6 +42,7 @@
</ng-template>
</faidare-card-row>
+
<faidare-card-row
label="Authority"
[test]="germplasmTaxonAuthor">
@@ -280,7 +281,7 @@
<faidare-card-row
label="Pedigree"
- [value]="germplasmGnpis.pedigree">
+ [value]="germplasmGnpis.pedigree">
</faidare-card-row>
<faidare-card-row
@@ -298,6 +299,14 @@
</ng-template>
</faidare-card-row>
+ <faidare-card-row
+ label="MLS status"
+ [test]="germplasmMcpd && germplasmMcpd.mlsStatus">
+ <ng-template>
+ {{ germplasmMcpd.mlsStatus }}
+ </ng-template>
+ </faidare-card-row>
+
</div>
</ng-template>
</faidare-card-section>
@@ -344,7 +353,6 @@
label="Presence status"
[value]="germplasmGnpis.presenceStatus">
</faidare-card-row>
-
</div>
</ng-template>
</faidare-card-section>
@@ -366,6 +374,14 @@
</ng-template>
</faidare-card-row>
+ <faidare-card-row
+ label="Acquisition Source Code"
+ [test]="germplasmMcpd && germplasmMcpd.acquisitionSourceCode">
+ <ng-template>
+ {{ germplasmMcpd.acquisitionSourceCode }}
+ </ng-template>
+ </faidare-card-row>
+
<faidare-card-row
label="Material type"
[test]="germplasmGnpis.collector && germplasmGnpis.collector.materialType">
@@ -483,7 +499,7 @@
]"
[rows]="germplasmGnpis.donors">
<ng-template let-row>
- <tr>
+ <tr *ngIf="row.donorInstitute">
<ng-template #donorInstituteTemplate>
<ng-container *ngTemplateOutlet="instituteTemplate;context:row.donorInstitute">
</ng-container>
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts b/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
index b0fa68a891c1b0ab425b895723bec06825e81f2a..4f0d779fd44741e9649e3321bb997730dd9a0089 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
@@ -14,8 +14,22 @@ import { CardSectionComponent } from '../card-section/card-section.component';
import { CardRowComponent } from '../card-row/card-row.component';
import { CardTableComponent } from '../card-table/card-table.component';
import { MapComponent } from '../map/map.component';
-import { BrapiGermplasmAttributes, BrapiGermplasmPedigree, BrapiResult, BrapiSibling } from '../models/brapi.model';
-import { Donor, Germplasm, GermplasmInstitute, GermplasmSet, Institute, Site } from '../models/gnpis.model';
+import {
+ BrapiCollectingSite,
+ BrapiGermplasmAttributes,
+ BrapiGermplasmMcpd,
+ BrapiGermplasmPedigree,
+ BrapiInstitute,
+ BrapiResult,
+ BrapiSibling
+} from '../models/brapi.model';
+import {
+ Donor,
+ Germplasm,
+ GermplasmInstitute,
+ GermplasmSet,
+ Institute
+} from '../models/gnpis.model';
import { DataDiscoverySource } from '../models/data-discovery.model';
import { MockComponent } from 'ng-mocks';
import { XrefsComponent } from '../xrefs/xrefs.component';
@@ -38,6 +52,14 @@ describe('GermplasmCardComponent', () => {
get cardHeader() {
return this.elements('div.card-header');
}
+
+ get cardRowField() {
+ return this.elements('div.field');
+ }
+
+ get cardRowValue() {
+ return this.elements('div.value');
+ }
}
const brapiSibling: BrapiSibling = {
@@ -84,6 +106,17 @@ describe('GermplasmCardComponent', () => {
logo: null
};
+ const brapiInstitute: BrapiInstitute = {
+ instituteName: 'INRAE URGI',
+ instituteCode: '78000',
+ acronym: 'INRAE',
+ organisation: 'inrae',
+ instituteType: 'lab',
+ webSite: 'www.labo.fr',
+ instituteAddress: '18',
+ logo: null
+ };
+
const gnpisGermplasmInstitute: GermplasmInstitute = {
...gnpisInstitute,
institute: gnpisInstitute,
@@ -96,6 +129,20 @@ describe('GermplasmCardComponent', () => {
distributionStatus: null
};
+ const collectingSite: BrapiCollectingSite = {
+ locationDbId: 'FR-78-INRAE',
+ locationName: 'Versailles',
+ coordinateUncertainty: null,
+ elevation: null,
+ georeferencingMethod: null,
+ latitudeDecimal: null,
+ latitudeDegrees: null,
+ locationDescription: null,
+ longitudeDecimal: null,
+ longitudeDegrees: null,
+ spatialReferenceSystem: null,
+ };
+
const gnpisDonor: Donor = {
donorInstitute: gnpisInstitute,
donorGermplasmPUI: '12',
@@ -138,7 +185,7 @@ describe('GermplasmCardComponent', () => {
germplasmDbId: 'test',
defaultDisplayName: 'test',
accessionNumber: 'test',
- germplasmName: 'test',
+ germplasmName: 'testName',
germplasmPUI: 'doi:1256',
pedigree: 'tree',
seedSource: 'inra',
@@ -181,6 +228,61 @@ describe('GermplasmCardComponent', () => {
'schema:includedInDataCatalog': source
};
+ const germplasmMcpdTest: BrapiGermplasmMcpd = {
+ groupId: '0',
+ accessionNames: ['test accession'],
+ accessionNumber: '01',
+ acquisitionDate: '2021',
+ acquisitionSourceCode: 'FR-urgi',
+ alternateIDs: ['Id1', 'Id2'],
+ ancestralData: null,
+ biologicalStatusOfAccessionCode: 'maintained',
+ breedingInstitutes: brapiInstitute,
+ collectingInfo: {
+ collectingDate: '2021',
+ collectingInstitutes: brapiInstitute,
+ collectingMissionIdentifier: '007',
+ collectingNumber: '3',
+ collectors: 'urgi',
+ materialType: 'germplasm',
+ collectingSite: collectingSite,
+ },
+ commonCropName: 'wheat',
+ countryOfOriginCode: 'FR',
+ donorInfo: {
+ donorAccessionNumber: 'ING007',
+ donorInstitute: brapiInstitute,
+ donationDate: '2021',
+ },
+ genus: 'Triti',
+ germplasmDbId: 'Fr-007',
+ germplasmPUI: 'urn/fr-007',
+ instituteCode: 'FR-INRAE',
+ mlsStatus: '0',
+ remarks: null,
+ safetyDuplicateInstitutes: null,
+ species: 'Triti',
+ speciesAuthority: null,
+ storageTypeCodes: null,
+ subtaxon: null,
+ subtaxonAuthority: null,
+ breederAccessionNumber: null,
+ breedingCreationYear: null,
+ catalogRegistrationYear: null,
+ catalogDeregistrationYear: null,
+ originLocationDbId: 'FR-Ver',
+ originLocationName: 'Versailles',
+ holdingInstitute: brapiInstitute,
+ holdingGenbank: brapiInstitute,
+ geneticNature: 'hybrid',
+ presenceStatus: null,
+ distributorInfos: null
+ };
+ const germplasmMcpdTestResult: BrapiResult<BrapiGermplasmMcpd> = {
+ metadata: null,
+ result: germplasmMcpdTest
+ };
+
const gnpisService = jasmine.createSpyObj(
'GnpisService', [
'getGermplasm',
@@ -194,12 +296,14 @@ describe('GermplasmCardComponent', () => {
'BrapiService', [
// 'germplasmProgeny',
'germplasmPedigree',
- 'germplasmAttributes'
+ 'germplasmAttributes',
+ 'germplasmMcpd'
]
);
// brapiService.germplasmProgeny.and.returnValue(of(brapiGermplasmProgeny));
brapiService.germplasmPedigree.and.returnValue(of(brapiGermplasmPedigree));
brapiService.germplasmAttributes.and.returnValue(of(brapiGermplasmAttributes));
+ brapiService.germplasmMcpd.and.returnValue(of(germplasmMcpdTestResult));
const activatedRouteParams = {
@@ -236,15 +340,22 @@ describe('GermplasmCardComponent', () => {
component.loaded.then(() => {
expect(component.germplasmGnpis).toBeTruthy();
+ expect(component.germplasmMcpd).toBeTruthy();
tester.detectChanges();
expect(tester.title).toContainText('Germplasm: test');
expect(tester.cardHeader[0]).toContainText('Identification');
+ expect(tester.cardRowField[0]).toContainText('Germplasm name');
+ expect(tester.cardRowValue[0]).toContainText('testName');
+
expect(tester.cardHeader[1]).toContainText('Depositary');
expect(tester.cardHeader[2]).toContainText('Collector');
expect(tester.cardHeader[3]).toContainText('Breeder');
expect(tester.cardHeader[4]).toContainText('Donor');
expect(tester.cardHeader[5]).toContainText('Distributor');
expect(tester.cardHeader[6]).toContainText('Evaluation Data');
+
+ expect(tester.cardRowField[5]).toContainText('MLS status');
+ expect(tester.cardRowValue[5]).toContainText('0');
});
}));
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.ts b/frontend/src/app/germplasm-card/germplasm-card.component.ts
index 6c8d91088dc726cf22f485fa4d9198ab5cf07313..2569cee684c4e6d78bbdb8393855d96c11963374 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.ts
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.ts
@@ -4,9 +4,10 @@ import { BrapiService } from '../brapi.service';
import { GnpisService } from '../gnpis.service';
import {
BrapiAttributeData,
+ BrapiGermplasmMcpd,
BrapiGermplasmPedigree,
BrapiLocation,
- BrapiTaxonIds
+ BrapiTaxonIds,
} from '../models/brapi.model';
import { Children, Germplasm, Site } from '../models/gnpis.model';
import { environment } from '../../environments/environment';
@@ -26,6 +27,7 @@ export class GermplasmCardComponent implements OnInit {
taxonIdsWithURL: BrapiTaxonIds[] = [];
germplasmGnpis: Germplasm;
+ germplasmMcpd: BrapiGermplasmMcpd;
germplasmPedigree: BrapiGermplasmPedigree;
germplasmProgeny: Children[];
germplasmAttributes: BrapiAttributeData[];
@@ -45,7 +47,6 @@ export class GermplasmCardComponent implements OnInit {
.then(germplasm => {
const germplasmId = id || germplasm.germplasmDbId;
this.germplasmGnpis = germplasm;
- this.getTaxon();
this.reformatData();
// TODO use the progeny call when the information about parent will be added.
@@ -55,6 +56,12 @@ export class GermplasmCardComponent implements OnInit {
this.germplasmProgeny = germplasmProgeny.result;
});*/
+
+ this.brapiService.germplasmMcpd(germplasmId).subscribe(germplasmMcpd => {
+ this.germplasmMcpd = germplasmMcpd.result;
+ });
+ this.getTaxon();
+
this.germplasmPedigree = null;
this.brapiService.germplasmPedigree(germplasmId)
.subscribe(germplasmPedigree => {
diff --git a/frontend/src/app/germplasm-result-page/germplasm-result-page.component.html b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.html
index 0c1539367f44f43d0deb9ddf1c58ecc0799fb245..feda59ea7d9f7c4c359d38729226913315f4902e 100644
--- a/frontend/src/app/germplasm-result-page/germplasm-result-page.component.html
+++ b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.html
@@ -23,12 +23,19 @@
You must filter your results to have less than <strong>50,000 results</strong> before exporting the data.
</div>
- <button type="button" class="btn btn-outline-success mb-2"
+ <button type="button" class="btn btn-outline-success btn-sm mb-2"
(click)="exportPlantMaterial(localCriteria)">
<span class="iconify" data-icon="fa-solid:file-csv" data-inline="false"></span>
Export Plant Material list
</button>
+<!--TODO Activate when export webservice will be ready-->
+<!-- <button type="button" class="btn btn-outline-info btn-sm ml-3 mb-2"-->
+<!-- (click)="exportMcpd(localCriteria)">-->
+<!-- <span class="iconify" data-icon="fa-solid:file-csv" data-inline="false"></span>-->
+<!-- Export MCPD list-->
+<!-- </button>-->
+
<!-- Loading spinner-->
<div class="text-center">
<faidare-loading-spinner [loading]="loading"></faidare-loading-spinner>
diff --git a/frontend/src/app/germplasm-result-page/germplasm-result-page.component.ts b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.ts
index 585f960620c1e7501ee3a99cd76f823166535755..a4b993e1b348a7702f8a8a7c623593f6a95203ed 100644
--- a/frontend/src/app/germplasm-result-page/germplasm-result-page.component.ts
+++ b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.ts
@@ -131,7 +131,24 @@ export class GermplasmResultPageComponent implements OnInit {
result => {
if (result) {
const blob = new Blob([result], { type: 'text/plain;charset=utf-8' });
- saveAs(blob, 'germplasm.gnpis.csv');
+ saveAs(blob, 'germplasm_gnpis.csv');
+ } else {
+ this.overLimitSizeExport = true;
+ }
+ this.loading = false;
+ },
+ error => {
+ console.log(error);
+ });
+ }
+
+ exportMcpd(criteria: GermplasmSearchCriteria) {
+ this.loading = true;
+ this.service.mcpdExport(criteria).subscribe(
+ result => {
+ if (result) {
+ const blob = new Blob([result], { type: 'text/plain;charset=utf-8' });
+ saveAs(blob, 'germplasm_mcpd.csv');
} else {
this.overLimitSizeExport = true;
}
diff --git a/frontend/src/app/gnpis.service.ts b/frontend/src/app/gnpis.service.ts
index 32e43a0ae23c348f0a8e19bd8f0881e4d1972a3e..bf0b3b2a44fe9862498e028673e6562d80aa6dac 100644
--- a/frontend/src/app/gnpis.service.ts
+++ b/frontend/src/app/gnpis.service.ts
@@ -152,6 +152,19 @@ export class GnpisService {
);
}
+ // TODO Change the service's response to return an object with the number of results and handle here if the number is over the limit
+ mcpdExport(criteria: GermplasmSearchCriteria): Observable<any> {
+ const requestOptions: Object = {
+ /* other options here */
+ responseType: 'text'
+ };
+ return this.http.post<any>(
+ `${BASE_URL}/germplasm/germplasm-mcpd-csv`,
+ criteria,
+ requestOptions
+ );
+ }
+
getSourcesName(sourceByURI, response) {
response.facets = response.facets.map((facet: DataDiscoveryFacet) => {
facet.terms = facet.terms.map(term => {
diff --git a/frontend/src/app/models/brapi.model.ts b/frontend/src/app/models/brapi.model.ts
index f8630ff08b968c324a9e842a9707c1aa9ae5c64d..27a75f05e8c6ead1870c4f886311ddd271e5f82c 100644
--- a/frontend/src/app/models/brapi.model.ts
+++ b/frontend/src/app/models/brapi.model.ts
@@ -177,6 +177,89 @@ export interface BrapiGermplasm extends BrapiHasDocumentationURL, schema.Dataset
acquisitionDate: string;
}
+export interface BrapiGermplasmMcpd extends BrapiHasDocumentationURL {
+ groupId: string;
+ accessionNames: string[];
+ accessionNumber: string;
+ acquisitionDate: string;
+ acquisitionSourceCode: string;
+ alternateIDs: string[];
+ ancestralData: string;
+ biologicalStatusOfAccessionCode: string;
+ breedingInstitutes: BrapiInstitute;
+ collectingInfo: {
+ collectingDate: string;
+ collectingInstitutes: BrapiInstitute;
+ collectingMissionIdentifier: string;
+ collectingNumber: string;
+ collectors: string;
+ materialType: string;
+ collectingSite: BrapiCollectingSite
+ };
+ commonCropName: string;
+ countryOfOriginCode: string;
+ donorInfo: {
+ donorAccessionNumber: string;
+ donorInstitute: BrapiInstitute;
+ donationDate: string;
+ };
+ genus: string;
+ germplasmDbId: string;
+ germplasmPUI: string;
+ instituteCode: string;
+ mlsStatus: string;
+ remarks: string;
+ safetyDuplicateInstitutes: {
+ instituteCode: string;
+ instituteName: string;
+ }[];
+ species: string;
+ speciesAuthority: string;
+ storageTypeCodes: string[];
+ subtaxon: string;
+ subtaxonAuthority: string;
+ breederAccessionNumber: string;
+ breedingCreationYear: string;
+ catalogRegistrationYear: string;
+ catalogDeregistrationYear: string;
+ originLocationDbId: string;
+ originLocationName: string;
+ holdingInstitute: BrapiInstitute;
+ holdingGenbank: BrapiInstitute;
+ geneticNature: string;
+ presenceStatus: string;
+ distributorInfos: {
+ institute: BrapiInstitute;
+ accessionNumber: string;
+ distrubutionStatus: string;
+ };
+}
+
+export interface BrapiInstitute {
+ instituteName: string;
+ instituteCode: string;
+ acronym: string;
+ organisation: string;
+ instituteType: string;
+ webSite: string;
+ instituteAddress: string;
+ logo: string;
+}
+
+export interface BrapiCollectingSite {
+ locationDbId: string;
+ locationName: string;
+ coordinateUncertainty: string;
+ elevation: string;
+ georeferencingMethod: string;
+ latitudeDecimal: string;
+ latitudeDegrees: string;
+ locationDescription: string;
+ longitudeDecimal: string;
+ longitudeDegrees: string;
+ spatialReferenceSystem: string;
+}
+
export interface BrapiTaxonIds {
sourceName: string;
diff --git a/frontend/src/app/models/gnpis.model.ts b/frontend/src/app/models/gnpis.model.ts
index 93760346383a76dcc5e9d8ee4e46cd4a8dd40d01..8e9ebeb989ea827de823db84753534efa851154b 100644
--- a/frontend/src/app/models/gnpis.model.ts
+++ b/frontend/src/app/models/gnpis.model.ts
@@ -60,6 +60,12 @@ export interface Germplasm extends BrapiGermplasm {
'schema:includedInDataCatalog': any;
}
+
+/* export interface GermplasmMcpd extends BrapiGermplasm {
+ mlsStatus: string;
+} */
+
+
export interface Site {
latitude: number;
longitude: number;
@@ -125,4 +131,6 @@ export interface GermplasmSet {
pui: string;
name: string;
};
+
+
}
diff --git a/frontend/src/app/site-card/site-card.component.html b/frontend/src/app/site-card/site-card.component.html
index 928a341b2d5670ffa717231ab76633b78c06e467..0a8f72355067335c4139ef656b61aef8283672c0 100644
--- a/frontend/src/app/site-card/site-card.component.html
+++ b/frontend/src/app/site-card/site-card.component.html
@@ -52,7 +52,7 @@
<faidare-card-row
label="Coordinates precision"
- [test]="location.additionalInfo && location.additionalInfo[' Coordinates precision']">
+ [test]="location.additionalInfo && location.additionalInfo['Coordinates precision']">
<ng-template>
{{ location.additionalInfo['Coordinates precision'] }}
</ng-template>
@@ -76,7 +76,7 @@
<faidare-card-row
label="Geographical location"
- [test]="location.additionalInfo && location.additionalInfo[' Geographical location']">
+ [test]="location.additionalInfo && location.additionalInfo['Geographical location']">
<ng-template>
{{ location.additionalInfo['Geographical location'] }}
</ng-template>
@@ -84,7 +84,7 @@
<faidare-card-row
label="Country name"
- [test]="location.countryName && !location.additionalInfo['Geographical location']">
+ [test]="location.countryName">
<ng-template>
{{ location.countryName }}
</ng-template>
@@ -92,7 +92,7 @@
<faidare-card-row
label="Country code"
- [test]="location.countryCode && location.additionalInfo && !location.additionalInfo['Geographical location']">
+ [test]="location.countryCode">
<ng-template>
{{ location.countryCode }}
</ng-template>
@@ -113,7 +113,7 @@
<faidare-card-row
label="Exposure"
- [test]="location.additionalInfo && location.additionalInfo[' Exposure']">
+ [test]="location.additionalInfo && location.additionalInfo['Exposure']">
<ng-template>
{{ location.additionalInfo['Exposure'] }}
</ng-template>
@@ -121,7 +121,7 @@
<faidare-card-row
label="Topography"
- [test]="location.additionalInfo && location.additionalInfo[' Topography']">
+ [test]="location.additionalInfo && location.additionalInfo['Topography']">
<ng-template>
{{ location.additionalInfo['Topography'] }}
</ng-template>
@@ -129,7 +129,7 @@
<faidare-card-row
label="Environment type"
- [test]="location.additionalInfo && location.additionalInfo[' Environment type']">
+ [test]="location.additionalInfo && location.additionalInfo['Environment type']">
<ng-template>
{{ location.additionalInfo['Environment type'] }}
</ng-template>
@@ -137,7 +137,7 @@
<faidare-card-row
label="Distance to city"
- [test]="location.additionalInfo && location.additionalInfo[' Distance to city']">
+ [test]="location.additionalInfo && location.additionalInfo['Distance to city']">
<ng-template>
{{ location.additionalInfo['Distance to city'] }}
</ng-template>
@@ -145,7 +145,7 @@
<faidare-card-row
label="Direction from city"
- [test]="location.additionalInfo && location.additionalInfo[' Direction from city']">
+ [test]="location.additionalInfo && location.additionalInfo['Direction from city']">
<ng-template>
{{ location.additionalInfo['Direction from city'] }}
</ng-template>
@@ -153,7 +153,7 @@
<faidare-card-row
label="Comment"
- [test]="location.additionalInfo && location.additionalInfo[' Comment']">
+ [test]="location.additionalInfo && location.additionalInfo['Comment']">
<ng-template>
{{ location.additionalInfo['Comment'] }}
</ng-template>
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index 86379b8cb238ac2f34d1742b56385139555a1eaf..7f8672e4784179d5cf5ce8ab14def43b8d3eb267 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -7,8 +7,7 @@ ES_PORT="9200"
ENV="dev"
DOCUMENT_TYPES="all"
-#ALL_DOCUMENT_TYPES="germplasm germplasmMcpd germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
-ALL_DOCUMENT_TYPES="germplasm germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
+ALL_DOCUMENT_TYPES="germplasm germplasmMcpd germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
ALL_ENVS="dev beta staging int prod test"
BASEDIR=$(dirname "$0")
TMP_FILE="log.tmp"