Commit 8384033f authored by Raphaël Flores's avatar Raphaël Flores
Browse files

Merge branch 'chore/rename_gpds' into 'master'

Rename GPDS application in FAIDARE. GNP-5519.

See merge request !25
parents 50513533 4ecc3432
......@@ -16,7 +16,7 @@ image: urgi/docker-browsers:latest
variables:
GRADLE_OPTS: "-Dorg.gradle.daemon=false"
GRADLE_USER_HOME: $CI_PROJECT_DIR/.gradle
APP_NAME: gpds
APP_NAME: faidare
JAR_PATH: "backend/build/libs/${APP_NAME}.jar"
......
# How to contribute to GPDS
# How to contribute to FAIDARE
## Git management
......@@ -27,9 +27,9 @@
Total 0 (delta 0), reused 0 (delta 0)
remote:
remote: To create a merge request for chore/explaining_how_to_merge, visit:
remote:   https://forgemia.inra.fr/urgi-is/gpds/merge_requests/new?merge_request%5Bsource_branch%5D=chore/explaining_how_to_merge
remote:   https://forgemia.inra.fr/urgi-is/faidare/merge_requests/new?merge_request%5Bsource_branch%5D=chore/explaining_how_to_merge
remote:
To forgemia.inra.fr:urgi-is/gpds.git
To forgemia.inra.fr:urgi-is/faidare.git
* [new branch]      chore/explaining_how_to_merge -> chore/explaining_how_to_merge
La branche 'chore/explaining_how_to_merge' est paramétrée pour suivre la branche distante 'chore/explaining_how_to_merge' depuis 'origin'.
```
......
......@@ -65,10 +65,10 @@ If you just need access to API (to run the `ng serve` on top of it), you can run
Otherwise, for the complete server (backend APIs + frontend interface), you can run:
```sh
./gradlew assemble && java -jar backend/build/libs/gpds.jar
./gradlew assemble && java -jar backend/build/libs/faidare.jar
```
The server should then be accessible at http://localhost:8380/gpds-dev
The server should then be accessible at http://localhost:8380/faidare-dev
## Run frontend development server
......@@ -105,7 +105,7 @@ The details of this remote server are filled in the `bootstrap.yml` file.
By default, it tries to connect to the remote server on http://localhost:8888
but it can of course be changed, or even configured via the `SPRING_CONFIG_URI` environment variable.
It will try to fetch the configuration for the application name `gpds`, and the default profile.
It will try to fetch the configuration for the application name `faidare`, and the default profile.
If such a configuration is not found, it will then fallback to the local `application.yml` properties.
To avoid running the Spring Cloud config server every time when developing the application,
all the properties are still available in `application.yml` even if they are configured on the remote Spring Cloud server as well.
......
package fr.inra.urgi.gpds;
package fr.inra.urgi.faidare;
import fr.inra.urgi.gpds.config.GPDSProperties;
import fr.inra.urgi.faidare.config.FaidareProperties;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.boot.context.properties.EnableConfigurationProperties;
import org.springframework.scheduling.annotation.EnableAsync;
/**
* The main gpds Application
* The main faidare Application
*
* @author gcornut
*/
@SpringBootApplication
@EnableAsync
@EnableConfigurationProperties(GPDSProperties.class)
@EnableConfigurationProperties(FaidareProperties.class)
public class Application {
public static void main(String[] args) {
SpringApplication.run(Application.class, args);
......
package fr.inra.urgi.gpds.api;
package fr.inra.urgi.faidare.api;
import org.springframework.http.HttpStatus;
import org.springframework.web.bind.annotation.ResponseStatus;
......
package fr.inra.urgi.gpds.api;
package fr.inra.urgi.faidare.api;
import org.springframework.http.HttpStatus;
import org.springframework.web.bind.annotation.ResponseStatus;
......
package fr.inra.urgi.gpds.api.brapi.v1;
import fr.inra.urgi.gpds.api.BadRequestException;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.gpds.api.brapi.v1.exception.BrapiPaginationException;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiPagination;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiStatus;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.faidare.api.BadRequestException;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.api.brapi.v1.exception.BrapiPaginationException;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiPagination;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiStatus;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.validation.BindException;
......@@ -26,7 +26,7 @@ import java.util.List;
*
* @author gcornut
*/
@ControllerAdvice(basePackages = "fr.inra.urgi.gpds.api.brapi.v1")
@ControllerAdvice(basePackages = "fr.inra.urgi.faidare.api.brapi.v1")
public class BrapiExceptionHandler {
private static ResponseEntity<Object> createErrorResponse(
......
package fr.inra.urgi.gpds.api.brapi.v1;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.gpds.domain.JSONView;
import fr.inra.urgi.faidare.domain.JSONView;
import org.springframework.core.MethodParameter;
import org.springframework.core.Ordered;
import org.springframework.core.annotation.Order;
......@@ -20,7 +20,7 @@ import java.util.List;
*
* @author gcornut
*/
@ControllerAdvice(basePackages = "fr.inra.urgi.gpds.api.brapi.v1")
@ControllerAdvice(basePackages = "fr.inra.urgi.faidare.api.brapi.v1")
@Order(Ordered.HIGHEST_PRECEDENCE)
public class BrapiJSONViewHandler extends AbstractMappingJacksonResponseBodyAdvice {
......
package fr.inra.urgi.gpds.api.brapi.v1;
package fr.inra.urgi.faidare.api.brapi.v1;
import com.google.common.collect.ImmutableSet;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiCall;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.gpds.domain.data.CallVO;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiCall;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.faidare.domain.data.CallVO;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
......
package fr.inra.urgi.gpds.api.brapi.v1;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiGermplasm;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiGermplasmAttributeValueList;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiPedigree;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiProgeny;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.gpds.domain.criteria.GermplasmAttributeCriteria;
import fr.inra.urgi.gpds.domain.criteria.GermplasmGETSearchCriteria;
import fr.inra.urgi.gpds.domain.criteria.GermplasmPOSTSearchCriteria;
import fr.inra.urgi.gpds.domain.criteria.GermplasmSearchCriteria;
import fr.inra.urgi.gpds.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.domain.response.PaginatedList;
import fr.inra.urgi.gpds.domain.response.Pagination;
import fr.inra.urgi.gpds.repository.es.GermplasmAttributeRepository;
import fr.inra.urgi.gpds.service.es.GermplasmService;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasm;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmAttributeValueList;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiPedigree;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiProgeny;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.faidare.domain.criteria.GermplasmAttributeCriteria;
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.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.domain.response.Pagination;
import fr.inra.urgi.faidare.repository.es.GermplasmAttributeRepository;
import fr.inra.urgi.faidare.service.es.GermplasmService;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.slf4j.Logger;
......
package fr.inra.urgi.gpds.api.brapi.v1;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiLocation;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.gpds.domain.criteria.LocationCriteria;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.domain.response.PaginatedList;
import fr.inra.urgi.gpds.repository.es.LocationRepository;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiLocation;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.faidare.domain.criteria.LocationCriteria;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.repository.es.LocationRepository;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
......
package fr.inra.urgi.gpds.api.brapi.v1;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiObservationVariable;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiOntology;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.gpds.domain.criteria.ObservationVariableCriteria;
import fr.inra.urgi.gpds.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.repository.file.CropOntologyRepository;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiObservationVariable;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiOntology;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.faidare.domain.criteria.ObservationVariableCriteria;
import fr.inra.urgi.faidare.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.repository.file.CropOntologyRepository;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
......
package fr.inra.urgi.gpds.api.brapi.v1;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiObservationUnit;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.criteria.ObservationUnitCriteria;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.domain.response.PaginatedList;
import fr.inra.urgi.gpds.repository.es.ObservationUnitRepository;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiObservationUnit;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.criteria.ObservationUnitCriteria;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.repository.es.ObservationUnitRepository;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
......
package fr.inra.urgi.gpds.api.brapi.v1;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiProgram;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.gpds.domain.criteria.ProgramCriteria;
import fr.inra.urgi.gpds.domain.data.ProgramVO;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.domain.response.PaginatedList;
import fr.inra.urgi.gpds.repository.es.ProgramRepository;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiProgram;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.faidare.domain.criteria.ProgramCriteria;
import fr.inra.urgi.faidare.domain.data.ProgramVO;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.repository.es.ProgramRepository;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
......
package fr.inra.urgi.gpds.api.brapi.v1;
package fr.inra.urgi.faidare.api.brapi.v1;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.gpds.domain.brapi.v1.data.*;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.gpds.domain.criteria.*;
import fr.inra.urgi.gpds.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.gpds.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.gpds.domain.data.phenotype.ObservationUnitVO;
import fr.inra.urgi.gpds.domain.data.study.StudyDetailVO;
import fr.inra.urgi.gpds.domain.data.study.StudySummaryVO;
import fr.inra.urgi.gpds.domain.data.variable.ObservationVariableVO;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.domain.response.PaginatedList;
import fr.inra.urgi.gpds.domain.response.Pagination;
import fr.inra.urgi.gpds.repository.es.GermplasmRepository;
import fr.inra.urgi.gpds.repository.es.ObservationUnitRepository;
import fr.inra.urgi.gpds.repository.es.StudyRepository;
import fr.inra.urgi.gpds.repository.file.CropOntologyRepository;
import fr.inra.urgi.gpds.utils.StringFunctions;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.domain.brapi.v1.data.*;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.faidare.domain.criteria.*;
import fr.inra.urgi.faidare.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.phenotype.ObservationUnitVO;
import fr.inra.urgi.faidare.domain.data.study.StudyDetailVO;
import fr.inra.urgi.faidare.domain.data.study.StudySummaryVO;
import fr.inra.urgi.faidare.domain.data.variable.ObservationVariableVO;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.domain.response.Pagination;
import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
import fr.inra.urgi.faidare.repository.es.ObservationUnitRepository;
import fr.inra.urgi.faidare.repository.es.StudyRepository;
import fr.inra.urgi.faidare.repository.file.CropOntologyRepository;
import fr.inra.urgi.faidare.utils.StringFunctions;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.apache.commons.collections.CollectionUtils;
......
package fr.inra.urgi.gpds.api.brapi.v1;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiTrial;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.gpds.domain.criteria.TrialCriteria;
import fr.inra.urgi.gpds.domain.data.TrialVO;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.domain.response.PaginatedList;
import fr.inra.urgi.gpds.repository.es.TrialRepository;
package fr.inra.urgi.faidare.api.brapi.v1;
import fr.inra.urgi.faidare.api.NotFoundException;
import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiTrial;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiResponse;
import fr.inra.urgi.faidare.domain.criteria.TrialCriteria;
import fr.inra.urgi.faidare.domain.data.TrialVO;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.repository.es.TrialRepository;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
......
package fr.inra.urgi.gpds.api.brapi.v1.exception;
package fr.inra.urgi.faidare.api.brapi.v1.exception;
/**
* @author gcornut
......
package fr.inra.urgi.gpds.api.brapi.v1.exception;
package fr.inra.urgi.faidare.api.brapi.v1.exception;
import fr.inra.urgi.gpds.api.BadRequestException;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiPagination;
import fr.inra.urgi.faidare.api.BadRequestException;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiPagination;
/**
* @author gcornut
......
package fr.inra.urgi.gpds.api.gnpis.v1;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.datadiscovery.criteria.DataDiscoveryCriteriaImpl;
import fr.inra.urgi.gpds.domain.datadiscovery.data.DataSource;
import fr.inra.urgi.gpds.domain.datadiscovery.response.DataDiscoveryResponse;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import fr.inra.urgi.gpds.repository.es.DataDiscoveryRepository;
import fr.inra.urgi.gpds.repository.file.DataSourceRepository;
import fr.inra.urgi.gpds.utils.StringFunctions;
package fr.inra.urgi.faidare.api.gnpis.v1;
import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.faidare.domain.datadiscovery.criteria.DataDiscoveryCriteriaImpl;
import fr.inra.urgi.faidare.domain.datadiscovery.data.DataSource;
import fr.inra.urgi.faidare.domain.datadiscovery.response.DataDiscoveryResponse;
import fr.inra.urgi.faidare.domain.response.ApiResponseFactory;
import fr.inra.urgi.faidare.repository.es.DataDiscoveryRepository;
import fr.inra.urgi.faidare.repository.file.DataSourceRepository;
import fr.inra.urgi.faidare.utils.StringFunctions;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
......
package fr.inra.urgi.gpds.api.gnpis.v1;
package fr.inra.urgi.faidare.api.gnpis.v1;
import fr.inra.urgi.gpds.api.BadRequestException;
import fr.inra.urgi.gpds.api.NotFoundException;
import fr.inra.urgi.faidare.api.BadRequestException;
import fr.inra.urgi.faidare.api.NotFoundException;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.validation.BindException;
......@@ -18,7 +18,7 @@ import org.springframework.web.bind.annotation.ExceptionHandler;
*
* @author gcornut
*/
@ControllerAdvice(basePackages = "fr.inra.urgi.gpds.api.gnpis.v1")
@ControllerAdvice(basePackages = "fr.inra.urgi.faidare.api.gnpis.v1")
public class GnpISExceptionHandler {
/**
......
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