diff --git a/.idea/compiler.xml b/.idea/compiler.xml
index 677323ac411a2e2cd554d850bdc5b9e1462eb456..8b06b9812dc5e8f580433afaed5519e9e0c32112 100644
--- a/.idea/compiler.xml
+++ b/.idea/compiler.xml
@@ -1,6 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="CompilerConfiguration">
+ <annotationProcessing>
+ <profile name="Gradle Imported" enabled="true">
+ <outputRelativeToContentRoot value="true" />
+ <processorPath useClasspath="false">
+ <entry name="$USER_HOME$/.gradle/caches/modules-2/files-2.1/org.springframework.boot/spring-boot-configuration-processor/2.1.2.RELEASE/db9671c321defb942a6700fae8a7700a137a25e/spring-boot-configuration-processor-2.1.2.RELEASE.jar" />
+ </processorPath>
+ <module name="faidare.backend.main" />
+ </profile>
+ </annotationProcessing>
<bytecodeTargetLevel>
<module name="faidare.backend.main" target="1.8" />
<module name="faidare.backend.test" target="1.8" />
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 7e6a21ff6f9dde532dc42ef9e839e19413faa40a..5a43701f7195c98eb2b222902176a2add2469f19 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
@@ -3,25 +3,25 @@ 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.domain.criteria.FaidareGermplasmPOSTShearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmGETSearchCriteria;
import fr.inra.urgi.faidare.domain.criteria.GermplasmPOSTSearchCriteria;
import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.response.GermplasmSearchResponse;
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.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.io.FileSystemResource;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.*;
import javax.servlet.http.HttpServletResponse;
+import javax.validation.Valid;
import java.io.File;
import java.util.Collections;
-import static org.springframework.web.bind.annotation.RequestMethod.GET;
+import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(tags = {"FAIDARE API"}, description = "Extended FAIDARE API")
@RestController
@@ -89,8 +89,9 @@ public class GnpISGermplasmController {
* resp.setContentType("application/zip");
* </pre>
*/
- @RequestMapping(value = "/csv", method = GET, produces = "text/csv")
- public FileSystemResource export(GermplasmPOSTSearchCriteria criteria, HttpServletResponse response) {
+ @PostMapping(value = "/csv", produces = "text/csv", consumes = APPLICATION_JSON_VALUE)
+ public FileSystemResource export(@RequestBody @Valid GermplasmPOSTSearchCriteria criteria, HttpServletResponse response) {
+
try {
File exportFile = germplasmService.exportCSV(criteria);
response.setHeader("Content-Disposition", "attachment; filename=germplasm.gnpis.csv");
@@ -101,4 +102,27 @@ public class GnpISGermplasmController {
}
}
+ @PostMapping(value = "/germplasm-list-csv", produces = "text/csv", consumes = APPLICATION_JSON_VALUE)
+ public FileSystemResource export(@RequestBody @Valid FaidareGermplasmPOSTShearchCriteria criteria, HttpServletResponse response) {
+
+ try {
+ File exportFile = germplasmService.exportListGermplasmCSV(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);
+ }
+ }
+
+ @ApiOperation("Search list of germplasm")
+ @PostMapping(value = "/search", consumes = APPLICATION_JSON_VALUE)
+ public GermplasmSearchResponse germplasmSearch(@RequestBody @Valid FaidareGermplasmPOSTShearchCriteria criteria) {
+ try {
+ return germplasmService.germplasmFind(criteria);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw new RuntimeException();
+ }
+ }
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/FaidareGermplasmPOSTShearchCriteria.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/FaidareGermplasmPOSTShearchCriteria.java
new file mode 100644
index 0000000000000000000000000000000000000000..5c46dc15d629891beb98e3b8a7dae2bf022f7509
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/FaidareGermplasmPOSTShearchCriteria.java
@@ -0,0 +1,204 @@
+package fr.inra.urgi.faidare.domain.criteria;
+
+import fr.inra.urgi.faidare.domain.criteria.base.SortCriteria;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.elasticsearch.criteria.annotation.CriteriaForDocument;
+import fr.inra.urgi.faidare.elasticsearch.criteria.annotation.DocumentPath;
+import fr.inra.urgi.faidare.elasticsearch.criteria.annotation.NoDocumentMapping;
+
+import java.util.List;
+
+/**
+ * @author jdestin
+ */
+@CriteriaForDocument(GermplasmVO.class)
+public class FaidareGermplasmPOSTShearchCriteria extends GermplasmPOSTSearchCriteria implements SortCriteria {
+
+ @DocumentPath(value = "synonyms")
+ private List<String> synonyms;
+
+ /*@DocumentPath(value = {"panel", "name"}, objectsValue = CollPopVO.class)
+ private List<String> panel;
+
+ @DocumentPath(value = {"collection", "name"}, objectsValue = CollPopVO.class)
+ private List<String> collection;
+
+ @DocumentPath(value = {"population", "name"}, objectsValue = CollPopVO.class)
+ private List<String> population;*/
+
+ @DocumentPath(value = "commonCropName")
+ private List<String> commonCropName;
+
+ @DocumentPath(value = "species")
+ private List<String> species;
+
+ @DocumentPath(value = "genus")
+ private List<String> genus;
+
+ @DocumentPath(value = "genusSpecies")
+ private List<String> genusSpecies;
+
+ @DocumentPath(value = "subtaxa")
+ private List<String> subtaxa;
+
+ @DocumentPath(value = "genusSpeciesSubtaxa")
+ private List<String> genusSpeciesSubtaxa;
+
+ @DocumentPath("taxonSynonyms")
+ private List<String> taxonSynonyms;
+
+ @DocumentPath("taxonCommonNames")
+ private List<String> taxonCommonNames;
+
+ @DocumentPath(value = {"holdingInstitute", "organisation"})
+ private List<String> holdingInstitute;
+
+ @DocumentPath("sourceUri")
+ private List<String> sources;
+
+ @DocumentPath("biologicalStatusOfAccessionCode")
+ private List<String> biologicalStatus;
+
+ @DocumentPath("geneticNature")
+ private List<String> geneticNature;
+
+ @DocumentPath("countryOfOriginCode")
+ private List<String> country;
+
+ @NoDocumentMapping
+ private List<String> facetFields;
+
+ @NoDocumentMapping
+ private String sortBy = null;// = "schema:name";
+
+ @NoDocumentMapping
+ private String sortOrder = null;// = SortOrder.ASC.name();
+
+
+
+
+ /*public List<String> getPanel() { return panel; }
+
+ public void setPanel(List<String> panel) { this.panel = panel; }
+
+ public List<String> getCollection() { return collection; }
+
+ public void setCollection(List<String> collection) { this.collection = collection; }
+
+ public List<String> getPopulation() { return population; }
+
+ public void setPopulation(List<String> population) { this.population = population; }*/
+
+ public List<String> getCommonCropName() { return commonCropName; }
+
+ public void setCommonCropName(List<String> commonCropName) {
+ this.commonCropName = commonCropName;
+ }
+
+ public List<String> getSpecies() { return species; }
+
+ public void setSpecies(List<String> species) { this.species = species; }
+
+ public List<String> getGenus() { return genus; }
+
+ public void setGenus(List<String> genus) { this.genus = genus; }
+
+ public List<String> getGenusSpecies() { return genusSpecies; }
+
+ public void setGenusSpecies(List<String> genusSpecies) {
+ this.genusSpecies = genusSpecies;
+ }
+
+ public List<String> getSubtaxa() { return subtaxa; }
+
+ public void setSubtaxa(List<String> subtaxa) { this.subtaxa = subtaxa; }
+
+ public List<String> getGenusSpeciesSubtaxa() { return genusSpeciesSubtaxa; }
+
+ public void setGenusSpeciesSubtaxa(List<String> genusSpeciesSubtaxa) {
+ this.genusSpeciesSubtaxa = genusSpeciesSubtaxa;
+ }
+
+ public List<String> getTaxonSynonyms() { return taxonSynonyms; }
+
+ public void setTaxonSynonyms(List<String> taxonSynonyms) {
+ this.taxonSynonyms = taxonSynonyms;
+ }
+
+ public List<String> getSynonyms() { return synonyms; }
+
+ public void setSynonyms(List<String> synonyms) { this.synonyms = synonyms; }
+
+ public List<String> getTaxonCommonNames() {
+ return taxonCommonNames;
+ }
+
+ public void setTaxonCommonNames(List<String> taxonCommonNames) {
+ this.taxonCommonNames = taxonCommonNames;
+ }
+
+ public List<String> getHoldingInstitute() {
+ return holdingInstitute;
+ }
+
+ public void setHoldingInstitute(List<String> holdingInstitute) {
+ this.holdingInstitute = holdingInstitute;
+ }
+
+ public List<String> getSources() {
+ return sources;
+ }
+
+ public void setSources(List<String> sources) {
+ this.sources = sources;
+ }
+
+ public List<String> getBiologicalStatus() { return biologicalStatus; }
+
+ public void setBiologicalStatus(List<String> biologicalStatus) {
+ this.biologicalStatus = biologicalStatus;
+ }
+
+ public List<String> getGeneticNature() {
+ return geneticNature;
+ }
+
+ public void setGeneticNature(List<String> geneticNature) {
+ this.geneticNature = geneticNature;
+ }
+
+ public List<String> getCountry() { return country; }
+
+ public void setCountry(List<String> country) {
+ this.country = country;
+ }
+
+
+ public void setSortBy(String sortBy) {
+ this.sortBy = sortBy;
+ }
+
+
+ public void setSortOrder(String sortOrder) {
+ this.sortOrder = sortOrder;
+ }
+
+ @Override
+ public String getSortBy() {
+ return sortBy;
+ }
+
+ @Override
+ public String getSortOrder() {
+ return sortOrder;
+ }
+
+
+ public List<String> getFacetFields() {
+ return facetFields;
+ }
+
+ public void setFacetFields(List<String> facetFields) {
+ this.facetFields = facetFields;
+ }
+}
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 4f2c156569e5653fa89831f85fda619d2ee4f641..c0d850cafb6c456119fbd43bb2aee65cc30bcd49 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
@@ -23,6 +23,12 @@ public interface ExtendedGermplasm extends BrapiGermplasm, GnpISInternal {
@JsonView(JSONView.GnpISFields.class)
String getTaxonComment();
+ @JsonView(JSONView.GnpISFields.class)
+ public String getGenusSpecies();
+
+ @JsonView(JSONView.GnpISFields.class)
+ public String getGenusSpeciesSubtaxa();
+
@JsonView(JSONView.GnpISFields.class)
String getGeneticNature();
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 6e3312fb5793b5f198f8671b74ba4f814c7fac08..f6954e78286f0143630e10fc0bd9acad09870249 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
@@ -48,8 +48,10 @@ public class GermplasmVO
private String genus;
private String species;
+ private String genusSpecies;
private String speciesAuthority;
private String subtaxa;
+ private String genusSpeciesSubtaxa;
private String subtaxaAuthority;
private String acquisitionDate;
@@ -292,6 +294,13 @@ public class GermplasmVO
this.species = species;
}
+ @Override
+ public String getGenusSpecies() { return genusSpecies; }
+
+ public void setGenusSpecies(String genusSpecies) {
+ this.genusSpecies = genusSpecies;
+ }
+
@Override
public String getSpeciesAuthority() {
return speciesAuthority;
@@ -310,6 +319,15 @@ public class GermplasmVO
this.subtaxa = subtaxa;
}
+ @Override
+ public String getGenusSpeciesSubtaxa() {
+ return genusSpeciesSubtaxa;
+ }
+
+ public void setGenusSpeciesSubtaxa(String genusSpeciesSubtaxa) {
+ this.genusSpeciesSubtaxa = genusSpeciesSubtaxa;
+ }
+
@Override
public String getSubtaxaAuthority() {
return subtaxaAuthority;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/datadiscovery/response/GermplasmSearchResponse.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/datadiscovery/response/GermplasmSearchResponse.java
new file mode 100644
index 0000000000000000000000000000000000000000..1daacd4eb8b91bd4324a6b36f59c7671567024d0
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/datadiscovery/response/GermplasmSearchResponse.java
@@ -0,0 +1,25 @@
+package fr.inra.urgi.faidare.domain.datadiscovery.response;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import fr.inra.urgi.faidare.domain.JSONView;
+import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiData;
+import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiListResponse;
+import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiMetadata;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.Facet;
+
+import java.util.List;
+
+public interface GermplasmSearchResponse extends BrapiListResponse<GermplasmVO> {
+
+ @Override
+ @JsonView(JSONView.GnpISFields.class)
+ BrapiMetadata getMetadata();
+
+ @Override
+ @JsonView(JSONView.GnpISFields.class)
+ BrapiData<GermplasmVO> getResult();
+
+ @JsonView(JSONView.GnpISFields.class)
+ List<? extends Facet> getFacets();
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/response/ApiResponseFactory.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/response/ApiResponseFactory.java
index a8a26095354ee309efb985b821163eef82890eff..b51e11234c4e5b2c99285266d1bc418365abb309 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/response/ApiResponseFactory.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/response/ApiResponseFactory.java
@@ -2,9 +2,11 @@ package fr.inra.urgi.faidare.domain.response;
import fr.inra.urgi.faidare.api.brapi.v1.exception.BrapiPaginationException;
import fr.inra.urgi.faidare.domain.brapi.v1.response.*;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
import fr.inra.urgi.faidare.domain.datadiscovery.data.DataDiscoveryDocument;
import fr.inra.urgi.faidare.domain.datadiscovery.data.FacetImpl;
import fr.inra.urgi.faidare.domain.datadiscovery.response.DataDiscoveryResponse;
+import fr.inra.urgi.faidare.domain.datadiscovery.response.GermplasmSearchResponse;
import org.springframework.http.HttpStatus;
import java.util.ArrayList;
@@ -114,4 +116,12 @@ public class ApiResponseFactory {
BrapiMetadata metadata = ApiResponseFactory.createMetadata(pagination, null);
return new DataDiscoveryResponseImpl(metadata, results, facets);
}
+
+ /**
+ * Create germplasm search response (brapi list response with facets)
+ */
+ public static GermplasmSearchResponse createGermplasmListResponseWithFacets(Pagination pagination, List<GermplasmVO> results, List<FacetImpl> facets) {
+ BrapiMetadata metadata = ApiResponseFactory.createMetadata(pagination, null);
+ return new GermplasmSearchResponseImpl(metadata, results, facets);
+ }
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/response/GermplasmSearchResponseImpl.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/response/GermplasmSearchResponseImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..430130197f65cfb3114f6547f6270969590f0552
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/response/GermplasmSearchResponseImpl.java
@@ -0,0 +1,24 @@
+package fr.inra.urgi.faidare.domain.response;
+
+import fr.inra.urgi.faidare.domain.brapi.v1.response.BrapiMetadata;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.Facet;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.FacetImpl;
+import fr.inra.urgi.faidare.domain.datadiscovery.response.GermplasmSearchResponse;
+
+import java.util.List;
+
+public class GermplasmSearchResponseImpl extends ApiListResponseImpl<GermplasmVO> implements GermplasmSearchResponse {
+
+ private final List<FacetImpl> facets;
+
+ public GermplasmSearchResponseImpl(BrapiMetadata metadata, List<GermplasmVO> result, List<FacetImpl> facets) {
+ super(metadata, result);
+ this.facets = facets;
+ }
+
+ @Override
+ public List<? extends Facet> getFacets() {
+ return facets;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/ESQueryFactory.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/ESQueryFactory.java
index 3b20638a3163b763b5c177970ccb2de290b8663b..4fccfa7c0093e145cd287d96e38bc51747f7db2d 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/ESQueryFactory.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/ESQueryFactory.java
@@ -12,4 +12,6 @@ public interface ESQueryFactory<C> {
*/
QueryBuilder createQuery(C criteria);
+ QueryBuilder createShouldFilterQuery(C criteria);
+
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactory.java b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactory.java
index e6cbe313796803e7230f3167fbf5e73bd8db0225..77ad147e1dbd047c0437e6b01e602636530db782 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactory.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactory.java
@@ -22,7 +22,7 @@ import static org.elasticsearch.index.query.QueryBuilders.*;
* Generic Elasticsearch query generator for criteria mapped on value object via
* {@link DocumentPath} annotations
*
- * @author gcornut
+ * @author gcornut, jdestin
*/
public class ESGenericQueryFactory<C> implements ESQueryFactory<C> {
@@ -55,6 +55,24 @@ public class ESGenericQueryFactory<C> implements ESQueryFactory<C> {
}
}
+ @Override
+ public QueryBuilder createShouldFilterQuery(C criteria) {
+ try {
+ CriteriaMapping voMappingToCriteria = AnnotatedCriteriaMapper.getMapping(criteria.getClass());
+ DocumentMetadata<?> documentMetadata = voMappingToCriteria.getDocumentMetadata();
+
+ List<QueryBuilder> queries = createQueryFromMapping(criteria, null, null, voMappingToCriteria, documentMetadata);
+
+ if (!queries.isEmpty()) {
+ return germplasmFilterQueries(queries);
+ } else {
+ return matchAllQuery();
+ }
+ } catch (Exception e) {
+ throw new ESQueryGenerationException(e);
+ }
+ }
+
/**
* Same as {@link ESGenericQueryFactory#createQuery(Object)} but with a list of document fields to exclude from query
*/
@@ -76,6 +94,24 @@ public class ESGenericQueryFactory<C> implements ESQueryFactory<C> {
}
}
+ public QueryBuilder createEsShouldQueryExcludingFields(C criteria, String... excludeDocumentFields) {
+ try {
+ CriteriaMapping voMappingToCriteria = AnnotatedCriteriaMapper.getMapping(criteria.getClass());
+ DocumentMetadata<?> documentMetadata = voMappingToCriteria.getDocumentMetadata();
+ Set<String> excludedDocumentFields = ImmutableSet.copyOf(excludeDocumentFields);
+
+ List<QueryBuilder> queries = createQueryFromMapping(criteria, null, excludedDocumentFields, voMappingToCriteria, documentMetadata);
+
+ if (!queries.isEmpty()) {
+ return germplasmFilterQueries(queries);
+ } else {
+ return matchAllQuery();
+ }
+ } catch (Exception e) {
+ throw new ESQueryGenerationException(e);
+ }
+ }
+
/**
* Same as {@link ESGenericQueryFactory#createQuery(Object)} but with a list of document fields to include from query (excluding all others)
*/
@@ -97,6 +133,24 @@ public class ESGenericQueryFactory<C> implements ESQueryFactory<C> {
}
}
+ public QueryBuilder createEsShouldQueryIncludingFields(C criteria, String... includeDocumentFields) {
+ try {
+ CriteriaMapping voMappingToCriteria = AnnotatedCriteriaMapper.getMapping(criteria.getClass());
+ DocumentMetadata<?> documentMetadata = voMappingToCriteria.getDocumentMetadata();
+ Set<String> includedDocumentFields = ImmutableSet.copyOf(includeDocumentFields);
+
+ List<QueryBuilder> queries = createQueryFromMapping(criteria, includedDocumentFields, null, voMappingToCriteria, documentMetadata);
+
+ if (!queries.isEmpty()) {
+ return germplasmFilterQueries(queries);
+ } else {
+ return matchAllQuery();
+ }
+ } catch (Exception e) {
+ throw new ESQueryGenerationException(e);
+ }
+ }
+
/**
* Generate a query from a criteria
*/
@@ -287,7 +341,7 @@ public class ESGenericQueryFactory<C> implements ESQueryFactory<C> {
/**
* Combine queries into a bool must query
*
- * @return null if not queries given; the first query if only only query is given; a bool query otherwise
+ * @return null if not queries given; the first query if only one query is given; a bool query otherwise
*/
public static QueryBuilder andQueries(List<QueryBuilder> queries) {
if (queries == null || queries.isEmpty()) {
@@ -306,4 +360,52 @@ public class ESGenericQueryFactory<C> implements ESQueryFactory<C> {
public static QueryBuilder andQueries(QueryBuilder... queries) {
return andQueries(Arrays.asList(queries));
}
+
+
+ /**
+ * Combine queries into a bool should query
+ *
+ * @return null if not queries given; the first query if only one query is given; a bool query otherwise
+ */
+ public static QueryBuilder germplasmFilterQueries(List<QueryBuilder> queries) {
+ if (queries == null || queries.isEmpty()) {
+ return null;
+ } else if (queries.size() == 1) {
+ return queries.get(0);
+ } else {
+ // List of the criteria that will be use in should query part, the other criteria will be used as filter.
+ List<String> shouldCriterion = Arrays.asList("commonCropName",
+ "species", "germplasmGenus", "genusSpecies", "subtaxa", "genus",
+ "genusSpeciesSubtaxa", "taxonSynonyms", "taxonCommonNames", "panel", "collection", "population",
+ "germplasmName", "accessionNumber", "synonyms");
+ BoolQueryBuilder boolQueryBuilder = QueryBuilders.boolQuery();
+ BoolQueryBuilder boolShouldQueryBuilder = QueryBuilders.boolQuery();
+ List<QueryBuilder> filterQueries = new ArrayList<>();
+ for (QueryBuilder query : queries) {
+ boolean isShouldCriterion = stringContainsItemFromList(query.toString(), shouldCriterion);
+ if (isShouldCriterion){
+ boolShouldQueryBuilder.should(query);
+ } else {
+ filterQueries.add(query);
+ }
+ }
+ boolQueryBuilder.must(boolShouldQueryBuilder);
+ for (QueryBuilder query: filterQueries) {
+ boolQueryBuilder.filter(query);
+ }
+ return boolQueryBuilder;
+ }
+ }
+
+ public static boolean stringContainsItemFromList(String inputStr, List<String> items)
+ {
+ for(String item: items)
+ {
+ if(inputStr.contains(item))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/DataDiscoveryRepositoryImpl.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/DataDiscoveryRepositoryImpl.java
index 73662c5d9787b70d4f57705fc994e6f4a572749f..559c71413eebe28b61b37e5a1dbdf533e3fb6dbc 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/DataDiscoveryRepositoryImpl.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/DataDiscoveryRepositoryImpl.java
@@ -177,7 +177,7 @@ public class DataDiscoveryRepositoryImpl implements DataDiscoveryRepository {
return ApiResponseFactory.createListResponseWithFacets(pagination, resultList, facets);
}
- private String[] criteriaFieldsToDocumentFields(List<String> criteriaFields) {
+ public String[] criteriaFieldsToDocumentFields(List<String> criteriaFields) {
List<String> fields = new ArrayList<>();
if (criteriaFields != null) {
for (String facetField : criteriaFields) {
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 d7652aab7bb15121499e67025a5d9b42d6f12906..0929cda8dc15e0e2f1362e797c093803953fcf95 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
@@ -1,9 +1,11 @@
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.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.response.GermplasmSearchResponse;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.elasticsearch.repository.ESFindRepository;
@@ -18,6 +20,11 @@ public interface GermplasmRepository
@Override
PaginatedList<GermplasmVO> find(GermplasmSearchCriteria criteria);
+ /**
+ * Find germplasm by criteria with pagination with a should query.
+ */
+ GermplasmSearchResponse germplasmFind(FaidareGermplasmPOSTShearchCriteria germSearCrit);
+
/**
* Get germplasm by id.
*/
@@ -28,6 +35,11 @@ public interface GermplasmRepository
*/
Iterator<GermplasmVO> scrollAll(GermplasmSearchCriteria criteria);
+ /**
+ * Scroll through all germplasm matching the given FAIDARE search criteria.
+ */
+ Iterator<GermplasmVO> scrollAllGermplasm(FaidareGermplasmPOSTShearchCriteria criteria);
+
/**
* Find pedigree for germplasm by id.
*/
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java b/backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java
index e89383e1706d94b7326085dc36e8aef075db6a62..91db9f00e2c56a1f3a3a8c5f3608ce7a4be2b41f 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
@@ -1,14 +1,25 @@
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.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.FacetImpl;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.FacetTermImpl;
+import fr.inra.urgi.faidare.domain.datadiscovery.response.GermplasmSearchResponse;
+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.domain.response.PaginationImpl;
import fr.inra.urgi.faidare.elasticsearch.ESRequestFactory;
import fr.inra.urgi.faidare.elasticsearch.ESResponseParser;
import fr.inra.urgi.faidare.elasticsearch.ESScrollIterator;
+import fr.inra.urgi.faidare.elasticsearch.criteria.AnnotatedCriteriaMapper;
+import fr.inra.urgi.faidare.elasticsearch.criteria.mapping.CriteriaMapping;
+import fr.inra.urgi.faidare.elasticsearch.document.DocumentAnnotationUtil;
+import fr.inra.urgi.faidare.elasticsearch.document.DocumentMetadata;
import fr.inra.urgi.faidare.elasticsearch.query.impl.ESGenericQueryFactory;
import fr.inra.urgi.faidare.elasticsearch.repository.ESFindRepository;
import fr.inra.urgi.faidare.elasticsearch.repository.ESGetByIdRepository;
@@ -22,19 +33,28 @@ import org.elasticsearch.index.query.QueryBuilder;
import org.elasticsearch.index.query.QueryBuilders;
import org.elasticsearch.search.SearchHit;
import org.elasticsearch.search.SearchHits;
+import org.elasticsearch.search.aggregations.bucket.terms.TermsAggregationBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Iterator;
+import java.util.List;
+
+import static org.elasticsearch.search.aggregations.AggregationBuilders.filter;
+import static org.elasticsearch.search.aggregations.AggregationBuilders.terms;
@Repository
public class GermplasmRepositoryImpl implements GermplasmRepository {
private static final Logger LOGGER = LoggerFactory.getLogger(GermplasmRepositoryImpl.class);
+ private final DocumentMetadata<GermplasmVO> documentMetadata;
+ private final CriteriaMapping criteriaMapping;
+
private final RestHighLevelClient client;
private final ObjectMapper mapper;
private final ESRequestFactory requestFactory;
@@ -59,6 +79,10 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
this.queryFactory = new ESGenericQueryFactory<>();
this.findRepository = new ESGenericFindRepository<>(client, requestFactory, voClass, this.parser);
this.getByIdRepository = new ESGenericGetByIdRepository<>(client, requestFactory, voClass, this.parser);
+ Class<GermplasmVO> documentClass = GermplasmVO.class;
+ Class<FaidareGermplasmPOSTShearchCriteria> criteriaClass = FaidareGermplasmPOSTShearchCriteria.class;
+ this.documentMetadata = DocumentAnnotationUtil.getDocumentObjectMetadata(documentClass);
+ this.criteriaMapping = AnnotatedCriteriaMapper.getMapping(criteriaClass);
}
@Override
@@ -68,6 +92,13 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
return new ESScrollIterator<>(client, requestFactory, parser, GermplasmVO.class, query, fetchSize);
}
+ @Override
+ public Iterator<GermplasmVO> scrollAllGermplasm(FaidareGermplasmPOSTShearchCriteria criteria) {
+ QueryBuilder query = queryFactory.createShouldFilterQuery(criteria);
+ int fetchSize = criteria.getPageSize().intValue();
+ return new ESScrollIterator<>(client, requestFactory, parser, GermplasmVO.class, query, fetchSize);
+ }
+
@Override
public GermplasmVO getById(String germplasmDbId) {
return getByIdRepository.getById(germplasmDbId);
@@ -78,11 +109,30 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
return findRepository.find(criteria);
}
+ @Override
+ public GermplasmSearchResponse germplasmFind(FaidareGermplasmPOSTShearchCriteria germplasmSearchCriteria) {
+ try {
+
+ // Prepare search request
+ SearchRequest request = prepareSearchRequest(germplasmSearchCriteria);
+
+ // Execute request
+ LOGGER.debug(request.toString());
+ SearchResponse response = client.search(request, RequestOptions.DEFAULT);
+
+ // Return paginated list
+ return parseResponse (germplasmSearchCriteria, response);
+
+ } catch (Exception e) {
+ throw new RuntimeException(e);
+ }
+ }
+
@Override
public PedigreeVO findPedigree(String germplasmDbId) {
QueryBuilder termQuery = QueryBuilders.termQuery("germplasmDbId", germplasmDbId);
SearchRequest request = requestFactory.prepareSearch("germplasmPedigree", termQuery);
- SearchResponse response = null;
+ SearchResponse response;
try {
response = client.search(request, RequestOptions.DEFAULT);
} catch (IOException e) {
@@ -112,7 +162,7 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
public ProgenyVO findProgeny(String germplasmDbId) {
QueryBuilder termQuery = QueryBuilders.termQuery("germplasmDbId", germplasmDbId);
SearchRequest request = requestFactory.prepareSearch("germplasmProgeny", termQuery);
- SearchResponse response = null;
+ SearchResponse response;
try {
response = client.search(request, RequestOptions.DEFAULT);
} catch (IOException e) {
@@ -135,4 +185,91 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
}
return progenyVO;
}
+
+
+
+
+
+ private SearchRequest prepareSearchRequest(FaidareGermplasmPOSTShearchCriteria criteria) {
+ List<String> facetFields = criteria.getFacetFields();
+ String[] documentFieldsInFacets = criteriaFieldsToDocumentFields(facetFields);
+
+ // Build search query (excluding document fields used in facets)
+ QueryBuilder query = queryFactory.createEsShouldQueryExcludingFields(criteria, documentFieldsInFacets);
+
+ // Prepare search request with query
+ SearchRequest request = ESGenericFindRepository.prepareSearchRequest(
+ query, criteria, documentMetadata, requestFactory);
+
+ // Build facet aggregations
+ if (facetFields != null) {
+ for (String facetField : facetFields) {
+ String documentPath = criteriaMapping.getDocumentPath(facetField, true);
+
+ String filterAggName = facetField + "Filter";
+
+ // Create facet term agg
+ TermsAggregationBuilder termAgg = terms(facetField)
+ .field(documentPath)
+ .size(ESRequestFactory.MAX_TERM_AGG_SIZE);
+
+ // Create filter agg for this facet excluding it self
+ QueryBuilder facetFilter = queryFactory.createEsShouldQueryExcludingFields(criteria, documentPath);
+ if (facetFilter == null) {
+ facetFilter = QueryBuilders.matchAllQuery();
+ }
+
+ request.source().aggregation(
+ filter(filterAggName, facetFilter).subAggregation(termAgg)
+ );
+ }
+ }
+
+ // Build post filter (including document fields used in facets)
+ QueryBuilder postFilter = queryFactory.createQueryIncludingFields(criteria, documentFieldsInFacets);
+ request.source().postFilter(postFilter);
+
+ return request;
+ }
+
+ private String[] criteriaFieldsToDocumentFields(List<String> criteriaFields) {
+ List<String> fields = new ArrayList<>();
+ if (criteriaFields != null) {
+ for (String facetField : criteriaFields) {
+ fields.add(criteriaMapping.getDocumentPath(facetField, true));
+ }
+ }
+ return fields.toArray(new String[]{});
+ }
+
+ /**
+ * Parse Elasticsearch search response into data discovery response
+ */
+ private GermplasmSearchResponse parseResponse(
+ FaidareGermplasmPOSTShearchCriteria criteria, SearchResponse response
+ ) throws IOException, ReflectiveOperationException {
+ // Parse pagination
+ Pagination pagination = PaginationImpl.create(criteria, parser.parseTotalHits(response));
+
+ // Parse result list
+ List<GermplasmVO> resultList = parser.parseHits(response,
+ documentMetadata.getDocumentClass());
+
+ // Parse facet terms
+ List<String> facetFields = criteria.getFacetFields();
+ List<FacetImpl> facets = null;
+ if (facetFields != null) {
+ facets = new ArrayList<>();
+ for (String facetField : facetFields) {
+ String filterAggName = facetField + "Filter";
+ List<FacetTermImpl> terms = parser.parseFacetTerms(
+ response, filterAggName, facetField
+ );
+ facets.add(new FacetImpl(facetField, terms));
+ }
+ }
+
+ // Return paginated list
+ return ApiResponseFactory.createGermplasmListResponseWithFacets(pagination, resultList, facets);
+ }
}
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 97ac680e49c3b6f0f4aa53025fc045e393b88de2..7082135d6e8321035a5c41b64c3ecabdd842f43e 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
@@ -1,9 +1,11 @@
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.GermplasmVO;
import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
import fr.inra.urgi.faidare.domain.data.germplasm.ProgenyVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.response.GermplasmSearchResponse;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import java.io.File;
@@ -15,8 +17,16 @@ public interface GermplasmService {
PaginatedList<GermplasmVO> find(GermplasmSearchCriteria criteria);
+ GermplasmSearchResponse germplasmFind(FaidareGermplasmPOSTShearchCriteria criteria);
+
+ /*LinkedHashSet<String> suggest(
+ String criteriaField, String searchText, Integer fetchSize, FaidareGermplasmPOSTShearchCriteria criteria
+ );*/
+
File exportCSV(GermplasmSearchCriteria criteria);
+ File exportListGermplasmCSV(FaidareGermplasmPOSTShearchCriteria criteria);
+
PedigreeVO getPedigree(String germplasmDbId);
ProgenyVO getProgeny(String germplasmDbId);
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 f6217f52d69eab7373977072089e30f846c7f6d7..cc9c2e09004470c64f08dd8e80a8e585dba0a68e 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
@@ -2,10 +2,13 @@ package fr.inra.urgi.faidare.service.es;
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.datadiscovery.response.GermplasmSearchResponse;
import fr.inra.urgi.faidare.domain.response.PaginatedList;
import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
import org.slf4j.Logger;
@@ -17,10 +20,12 @@ import java.io.*;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
+import java.util.ArrayList;
import java.util.Iterator;
+import java.util.List;
/**
- * @author cpommier, gcornut
+ * @author cpommier, gcornut, jdestin
*/
@Service("germplasmService")
public class GermplasmServiceImpl implements GermplasmService {
@@ -43,6 +48,19 @@ public class GermplasmServiceImpl implements GermplasmService {
}
}
+ @Override
+ public File exportListGermplasmCSV(FaidareGermplasmPOSTShearchCriteria criteria) {
+ try {
+ Iterator<GermplasmVO> allGermplasm = germplasmRepository.scrollAllGermplasm(criteria);
+ Path tmpDirPath = Files.createTempDirectory("germplasm");
+ Path tmpFile = Files.createTempFile(tmpDirPath, "germplasm_", ".csv");
+ writeToCSV(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");
@@ -51,14 +69,32 @@ 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<>();
GermplasmVO germplasmVO = germplasms.next();
+
+ if (germplasmVO.getCollection() != null) {
+ for (CollPopVO collection : germplasmVO.getCollection()) {
+ collectionNames.add(collection.getName());
+ }
+ }
+
+ if (germplasmVO.getPanel() != null) {
+ for (CollPopVO panel : germplasmVO.getPanel()) {
+ panelNames.add(panel.getName());
+ }
+ }
+
String[] line = new String[header.length];
line[0] = germplasmVO.getGermplasmPUI();
line[1] = germplasmVO.getAccessionNumber();
line[2] = germplasmVO.getGermplasmName();
line[3] = germplasmVO.getCommonCropName();
line[4] = germplasmVO.getInstituteName();
+ line[7] = (collectionNames != null) ? String.join(", ", collectionNames) : "";
+ line[9] = (panelNames != null) ? String.join(", ", panelNames) : "";
csvWriter.writeNext(line);
}
csvWriter.close();
@@ -74,6 +110,11 @@ public class GermplasmServiceImpl implements GermplasmService {
return germplasmRepository.find(sCrit);
}
+ @Override
+ public GermplasmSearchResponse germplasmFind(FaidareGermplasmPOSTShearchCriteria germplasmSearchCriteria) {
+ return germplasmRepository.germplasmFind(germplasmSearchCriteria);
+ }
+
@Override
public PedigreeVO getPedigree(String germplasmDbId) {
return germplasmRepository.findPedigree(germplasmDbId);
diff --git a/backend/src/main/main.iml b/backend/src/main/main.iml
index 908ad4f521a27722a24664f5a0adb595bf81f4e7..50f3d6bc79c58fa92df31bb59ab229d1e7c0c12e 100644
--- a/backend/src/main/main.iml
+++ b/backend/src/main/main.iml
@@ -7,5 +7,33 @@
</content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="Gradle: io.swagger:swagger-annotations:1.5.21" level="project" />
+ <orderEntry type="library" name="Gradle: org.springframework:spring-beans:5.1.4.RELEASE" level="project" />
+ <orderEntry type="library" name="Gradle: org.springframework:spring-web:5.1.4.RELEASE" level="project" />
+ <orderEntry type="library" name="Gradle: io.springfox:springfox-core:2.9.2" level="project" />
+ <orderEntry type="library" name="Gradle: io.springfox:springfox-spring-web:2.9.2" level="project" />
+ <orderEntry type="library" name="Gradle: javax.validation:validation-api:2.0.1.Final" level="project" />
+ <orderEntry type="library" name="Gradle: com.google.guava:guava:27.0.1-jre" level="project" />
+ <orderEntry type="library" name="Gradle: commons-collections:commons-collections:3.2.2" level="project" />
+ <orderEntry type="library" name="Gradle: org.apache.httpcomponents:httpcore:4.4.10" level="project" />
+ <orderEntry type="library" name="Gradle: org.elasticsearch.client:elasticsearch-rest-client:6.4.3" level="project" />
+ <orderEntry type="library" name="Gradle: org.apache.httpcomponents:httpcore-nio:4.4.10" level="project" />
+ <orderEntry type="library" name="Gradle: org.springframework.boot:spring-boot-autoconfigure:2.1.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Gradle: org.springframework:spring-context:5.1.4.RELEASE" level="project" />
+ <orderEntry type="library" name="Gradle: com.fasterxml.jackson.core:jackson-databind:2.9.8" level="project" />
+ <orderEntry type="library" name="Gradle: org.springframework.boot:spring-boot:2.1.2.RELEASE" level="project" />
+ <orderEntry type="library" name="Gradle: org.springframework.security:spring-security-config:5.1.3.RELEASE" level="project" />
+ <orderEntry type="library" name="Gradle: io.springfox:springfox-spi:2.9.2" level="project" />
+ <orderEntry type="library" name="Gradle: io.springfox:springfox-swagger2:2.9.2" level="project" />
+ <orderEntry type="library" name="Gradle: org.elasticsearch:elasticsearch:6.5.4" level="project" />
+ <orderEntry type="library" name="Gradle: org.slf4j:slf4j-api:1.7.25" level="project" />
+ <orderEntry type="library" name="Gradle: org.elasticsearch.client:elasticsearch-rest-high-level-client:6.5.4" level="project" />
+ <orderEntry type="library" name="Gradle: org.elasticsearch:elasticsearch-core:6.5.4" level="project" />
+ <orderEntry type="library" name="Gradle: org.springframework:spring-core:5.1.4.RELEASE" level="project" />
+ <orderEntry type="library" name="Gradle: org.apache.tomcat.embed:tomcat-embed-core:9.0.14" level="project" />
+ <orderEntry type="library" name="Gradle: com.opencsv:opencsv:4.4" level="project" />
+ <orderEntry type="library" name="Gradle: org.apache.commons:commons-lang3:3.8.1" level="project" />
+ <orderEntry type="library" name="Gradle: org.apache.lucene:lucene-join:7.5.0" level="project" />
+ <orderEntry type="library" name="Gradle: com.fasterxml.jackson.core:jackson-annotations:2.9.0" level="project" />
</component>
</module>
\ No newline at end of file
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactoryTest.java
index 304d2215bc94ac0555eb486386436f12eb51e882..8b6bcd21b1d74da82304944fef7d651df725224a 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactoryTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactoryTest.java
@@ -4,10 +4,7 @@ import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Sets;
import com.google.common.io.CharStreams;
-import fr.inra.urgi.faidare.domain.criteria.LocationCriteria;
-import fr.inra.urgi.faidare.domain.criteria.ObservationUnitCriteria;
-import fr.inra.urgi.faidare.domain.criteria.ProgramCriteria;
-import fr.inra.urgi.faidare.domain.criteria.StudySearchCriteria;
+import fr.inra.urgi.faidare.domain.criteria.*;
import fr.inra.urgi.faidare.domain.datadiscovery.criteria.DataDiscoveryCriteria;
import fr.inra.urgi.faidare.domain.datadiscovery.criteria.DataDiscoveryCriteriaImpl;
import fr.inra.urgi.faidare.elasticsearch.criteria.annotation.CriteriaForDocument;
@@ -292,6 +289,28 @@ public class ESGenericQueryFactoryTest {
assertJsonEquals(actualQuery, expectedQuery);
}
+
+ @Test
+ void should_Generate_Filter_Bool_Terms_Query() throws Exception {
+ FaidareGermplasmPOSTShearchCriteria criteria = new FaidareGermplasmPOSTShearchCriteria();
+
+ criteria.setSpecies(newArrayList("Triticum", "Populus"));
+ criteria.setGenus(newArrayList("Triticum", "Populus"));
+ criteria.setGenusSpecies(newArrayList("Triticum", "Populus"));
+
+ criteria.setBiologicalStatus(newArrayList("Wild"));
+
+ ESGenericQueryFactory<FaidareGermplasmPOSTShearchCriteria> queryFactory =
+ new ESGenericQueryFactory<>();
+
+ QueryBuilder query = queryFactory.createShouldFilterQuery(criteria);
+
+ String actualQuery = query.toString();
+
+ String expectedQuery = readResource("expected/query8.json");
+ assertJsonEquals(actualQuery, expectedQuery);
+ }
+
public static void assertJsonEquals(String json1, String json2) throws IOException {
ObjectMapper mapper = new ObjectMapper();
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/elasticsearch/query/impl/expected/query8.json b/backend/src/test/resources/fr/inra/urgi/faidare/elasticsearch/query/impl/expected/query8.json
new file mode 100644
index 0000000000000000000000000000000000000000..462708718ed5641b91825c6a87d77f5090538653
--- /dev/null
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/elasticsearch/query/impl/expected/query8.json
@@ -0,0 +1,89 @@
+{
+ "bool" : {
+ "must" : [
+ {
+ "bool" : {
+ "should" : [
+ {
+ "terms" : {
+ "commonCropName" : [
+ "Triticum",
+ "Populus"
+ ],
+ "boost" : 1.0
+ }
+ },
+ {
+ "terms" : {
+ "genusSpeciesSubtaxa" : [
+ "Triticum",
+ "Populus"
+ ],
+ "boost" : 1.0
+ }
+ },
+ {
+ "terms" : {
+ "species" : [
+ "Triticum",
+ "Populus"
+ ],
+ "boost" : 1.0
+ }
+ },
+ {
+ "terms" : {
+ "genus" : [
+ "Triticum",
+ "Populus"
+ ],
+ "boost" : 1.0
+ }
+ },
+ {
+ "terms" : {
+ "subtaxa" : [
+ "Triticum",
+ "Populus"
+ ],
+ "boost" : 1.0
+ }
+ },
+ {
+ "terms" : {
+ "taxonSynonyms" : [
+ "Triticum",
+ "Populus"
+ ],
+ "boost" : 1.0
+ }
+ },
+ {
+ "terms" : {
+ "genusSpecies" : [
+ "Triticum",
+ "Populus"
+ ],
+ "boost" : 1.0
+ }
+ }
+ ],
+ "adjust_pure_negative" : true,
+ "boost" : 1.0
+ }
+ }
+ ],
+ "filter" : [
+ {
+ "terms" : {
+ "biologicalStatusOfAccessionCode" : [
+ "Wild"
+ ],
+ "boost" : 1.0
+ }
+ }
+ ],
+ "adjust_pure_negative" : true,
+ "boost" : 1.0
+ }
+}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
index 359f0616b5bdab5e1d67bb9e9e7555d20c74b4ed..ab6abaf77b9fd90ccefa0eb08793644490fdb39c 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
@@ -131,7 +131,7 @@
},
"instituteName": {
"type": "keyword"
- },
+ },
"pedigree": {
"type": "keyword"
},
@@ -590,7 +590,7 @@
"source": {
"type": "keyword"
- },
+ },
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/test.iml b/backend/src/test/test.iml
index 5ebc6f48ecbe7e78271fcbb44057f6682d802638..6e30bb1c6134aa08b8bcfb9660df0484e83585c6 100644
--- a/backend/src/test/test.iml
+++ b/backend/src/test/test.iml
@@ -9,4 +9,4 @@
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="module" module-name="main" />
</component>
-</module>
\ No newline at end of file
+</module>
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
deleted file mode 100644
index aa2aa4ef5adab9259bebd7a7ad229c2a0d30d961..0000000000000000000000000000000000000000
--- a/frontend/package-lock.json
+++ /dev/null
@@ -1,10809 +0,0 @@
-{
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- "version": "0.0.0",
- "lockfileVersion": 1,
- "requires": true,
- "dependencies": {
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- "dev": true,
- "requires": {
- "@angular-devkit/core": "7.3.2",
- "rxjs": "6.3.3"
- },
- "dependencies": {
- "rxjs": {
- "version": "6.3.3",
- "resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.3.3.tgz",
- "integrity": "sha512-JTWmoY9tWCs7zvIk/CvRjhjGaOd+OVBM987mxFo+OW66cGpdKjZcpmc74ES1sB//7Kl/PAe8+wEakuhG4pcgOw==",
- "dev": true,
- "requires": {
- "tslib": "^1.9.0"
- }
- }
- }
- },
- "@angular-devkit/build-angular": {
- "version": "0.13.2",
- "resolved": "https://registry.npmjs.org/@angular-devkit/build-angular/-/build-angular-0.13.2.tgz",
- "integrity": "sha512-zRrV/dknx8891XSjXTh5JcTZnX4h+YsCHi6u8GABnIZW9JyiCl9QZpv0mRIyGTEaK2udmfMo2Yp5qZo1sd8jeQ==",
- "dev": true,
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- "@angular-devkit/build-webpack": "0.13.2",
- "@angular-devkit/core": "7.3.2",
- "@ngtools/webpack": "7.3.2",
- "ajv": "6.9.1",
- "autoprefixer": "9.4.6",
- "circular-dependency-plugin": "5.0.2",
- "clean-css": "4.2.1",
- "copy-webpack-plugin": "4.6.0",
- "file-loader": "3.0.1",
- "glob": "7.1.3",
- "istanbul-instrumenter-loader": "3.0.1",
- "karma-source-map-support": "1.3.0",
- "less": "3.9.0",
- "less-loader": "4.1.0",
- "license-webpack-plugin": "2.1.0",
- "loader-utils": "1.2.3",
- "mini-css-extract-plugin": "0.5.0",
- "minimatch": "3.0.4",
- "node-sass": "4.11.0",
- "opn": "5.4.0",
- "parse5": "4.0.0",
- "postcss": "7.0.14",
- "postcss-import": "12.0.1",
- "postcss-loader": "3.0.0",
- "raw-loader": "1.0.0",
- "rxjs": "6.3.3",
- "sass-loader": "7.1.0",
- "semver": "5.6.0",
- "source-map-loader": "0.2.4",
- "source-map-support": "0.5.10",
- "speed-measure-webpack-plugin": "1.3.0",
- "stats-webpack-plugin": "0.7.0",
- "style-loader": "0.23.1",
- "stylus": "0.54.5",
- "stylus-loader": "3.0.2",
- "terser-webpack-plugin": "1.2.2",
- "tree-kill": "1.2.1",
- "webpack": "4.29.0",
- "webpack-dev-middleware": "3.5.1",
- "webpack-dev-server": "3.1.14",
- "webpack-merge": "4.2.1",
- "webpack-sources": "1.3.0",
- "webpack-subresource-integrity": "1.1.0-rc.6"
- },
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- "dev": true,
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- "dev": true
- },
- "zone.js": {
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- "integrity": "sha512-mla2acNCMkWXBD+c+yeUrBUrzOxYMNFdQ6FGfigGGtEVBPJx07BQeJekjt9DmH1FtZek4E9rE1eRR9qQpxACOQ=="
- }
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-}
diff --git a/frontend/package.json b/frontend/package.json
index e4dc6e1e794f5866c8912d4277d045a432733841..4d1de75f06f22939692e87f5a39653a54c42aa1d 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -21,24 +21,25 @@
"@angular/platform-browser": "7.2.7",
"@angular/platform-browser-dynamic": "7.2.7",
"@angular/router": "7.2.7",
- "@ng-bootstrap/ng-bootstrap": "4.0.0",
+ "@ng-bootstrap/ng-bootstrap": "4.2.2",
"@types/leaflet": "1.2.14",
"@types/leaflet.markercluster": "1.0.3",
"angular-coordinates": "1.0.0",
"angular-mocks": "1.7.8",
- "bootstrap": "4.1.3",
+ "bootstrap": "4.3.1",
"core-js": "2.5.7",
+ "file-saver": "2.0.2",
"font-awesome": "4.7.0",
"leaflet": "1.3.4",
"leaflet.markercluster": "1.4.1",
"moment": "2.24.0",
"ng-mocks": "7.6.0",
- "ngx-markdown": "8.0.2",
+ "ngx-markdown": "8.2.1",
"ngx-moment": "3.3.0",
"popper.js": "1.14.6",
"rxjs": "6.4.0",
"trait-ontology-widget": "git+https://github.com/gnpis/trait-ontology-widget.git#v2.2.1",
- "tslib": "1.9.3",
+ "tslib": "1.11.0",
"zone.js": "0.8.29"
},
"devDependencies": {
diff --git a/frontend/src/app/app-routing.module.ts b/frontend/src/app/app-routing.module.ts
index 8c9af89d4567e7ba3f8e776fb759da3158639d7a..01ef7b6a7388a041723ef7463758aacd5e1f25dc 100644
--- a/frontend/src/app/app-routing.module.ts
+++ b/frontend/src/app/app-routing.module.ts
@@ -6,12 +6,14 @@ import { StudyCardComponent } from './study-card/study-card.component';
import { SiteCardComponent } from './site-card/site-card.component';
import { MarkdownPageComponent } from './markdown-page/markdown-page.component';
import { environment } from '../environments/environment';
+import { GermplasmResultPageComponent } from './germplasm-result-page/germplasm-result-page.component';
export const routes: Routes = [
{ path: 'studies/:id', component: StudyCardComponent },
{ path: 'sites/:id', component: SiteCardComponent },
{ path: '', component: ResultPageComponent },
{ path: 'germplasm', component: GermplasmCardComponent },
+ { path: 'germplasm-result-page', component: GermplasmResultPageComponent },
{ path: 'about', component: MarkdownPageComponent, data: { mdFile: environment.aboutUsMdFile } },
{ path: 'join', component: MarkdownPageComponent, data: { mdFile: environment.joinUsMdFile } },
{ path: 'legal', component: MarkdownPageComponent, data: { mdFile: environment.legalMentionsMdFile } },
diff --git a/frontend/src/app/app.component.html b/frontend/src/app/app.component.html
index 19054abf426f8055c7aabcaf2649a5fa00513923..e56bebd4c869ad6afbe5836c72441b80575e1ab8 100644
--- a/frontend/src/app/app.component.html
+++ b/frontend/src/app/app.component.html
@@ -1,5 +1,5 @@
<faidare-navbar></faidare-navbar>
-<div class="container" style="margin-top: 100px">
+<div style="margin-top: 100px ; margin-right: 100px ; margin-left: 100px">
<faidare-error></faidare-error>
<router-outlet></router-outlet>
</div>
diff --git a/frontend/src/app/app.module.ts b/frontend/src/app/app.module.ts
index 92d8652856c0b612140b1b328391a9809364862c..ba96c6c987c4ffb83052ea085197037a2695ef8f 100644
--- a/frontend/src/app/app.module.ts
+++ b/frontend/src/app/app.module.ts
@@ -5,19 +5,30 @@ import { AppComponent } from './app.component';
import { FormComponent } from './form/form.component';
import { ResultPageComponent } from './result-page/result-page.component';
import { GermplasmCardComponent } from './germplasm-card/germplasm-card.component';
+import { GermplasmResultPageComponent } from './germplasm-result-page/germplasm-result-page.component';
import { StudyCardComponent } from './study-card/study-card.component';
import { SiteCardComponent } from './site-card/site-card.component';
-import { HTTP_INTERCEPTORS, HttpClient, HttpClientModule } from '@angular/common/http';
+import {
+ HTTP_INTERCEPTORS,
+ HttpClient,
+ HttpClientModule
+} from '@angular/common/http';
import { NavbarComponent } from './navbar/navbar.component';
import { MapComponent } from './map/map.component';
-import { NgbAlertModule, NgbDropdownModule, NgbPaginationModule, NgbPopoverModule, NgbTypeaheadModule } from '@ng-bootstrap/ng-bootstrap';
+import {
+ NgbAlertModule,
+ NgbDropdownModule,
+ NgbPaginationModule,
+ NgbPopoverModule,
+ NgbTypeaheadModule
+} from '@ng-bootstrap/ng-bootstrap';
import { FormsModule, ReactiveFormsModule } from '@angular/forms';
import { SuggestionFieldComponent } from './form/suggestion-field/suggestion-field.component';
import { DocumentComponent } from './result-page/document/document.component';
import { ErrorComponent } from './error/error.component';
import { ErrorInterceptorService } from './error-interceptor.service';
import { TraitOntologyWidgetComponent } from './form/trait-ontology-widget/trait-ontology-widget.component';
-import { FacetsComponent } from './result-page/facets/facets.component';
+import { FacetsComponent } from './facets/facets.component';
import { CardRowComponent } from './card-row/card-row.component';
import { CardSectionComponent } from './card-section/card-section.component';
import { LoadingSpinnerComponent } from './loading-spinner/loading-spinner.component';
@@ -28,6 +39,10 @@ import { CoordinatesModule } from 'angular-coordinates';
import { CardGenericDocumentComponent } from './card-generic-document/card-generic-document.component';
import { MarkdownModule, MarkedOptions, MarkedRenderer } from 'ngx-markdown';
import { MarkdownPageComponent } from './markdown-page/markdown-page.component';
+import { DecimalPipe } from '@angular/common';
+import { LargeFacetsComponent } from './facets/large-facets/large-facets.component';
+import { SmallFacetsComponent } from './facets/small-facets/small-facets.component';
+import { SwitchButtonComponent } from './facets/switch-button/switch-button.component';
@NgModule({
declarations: [
@@ -35,6 +50,8 @@ import { MarkdownPageComponent } from './markdown-page/markdown-page.component';
FormComponent,
ResultPageComponent,
GermplasmCardComponent,
+ GermplasmResultPageComponent,
+ GermplasmResultPageComponent,
StudyCardComponent,
SiteCardComponent,
NavbarComponent,
@@ -50,7 +67,10 @@ import { MarkdownPageComponent } from './markdown-page/markdown-page.component';
CardTableComponent,
XrefsComponent,
CardGenericDocumentComponent,
- MarkdownPageComponent
+ MarkdownPageComponent,
+ LargeFacetsComponent,
+ SmallFacetsComponent,
+ SwitchButtonComponent
],
imports: [
BrowserModule,
@@ -84,7 +104,12 @@ import { MarkdownPageComponent } from './markdown-page/markdown-page.component';
],
providers: [
- { provide: HTTP_INTERCEPTORS, useExisting: ErrorInterceptorService, multi: true }
+ {
+ provide: HTTP_INTERCEPTORS,
+ useExisting: ErrorInterceptorService,
+ multi: true
+ },
+ DecimalPipe
],
bootstrap: [AppComponent]
})
diff --git a/frontend/src/app/brapi.service.spec.ts b/frontend/src/app/brapi.service.spec.ts
index 5466b472d437801edf65368798316455c7506fb4..7f60d4fa9ea5b9e2ec28d0add5926bf412616a31 100644
--- a/frontend/src/app/brapi.service.spec.ts
+++ b/frontend/src/app/brapi.service.spec.ts
@@ -299,7 +299,8 @@ describe('BrapiService', () => {
distributors: [origin],
panel: [germplasmSet],
collection: [germplasmSet],
- population: [germplasmSet]
+ population: [germplasmSet],
+ 'schema:includedInDataCatalog': null
};
let brapiService: BrapiService;
diff --git a/frontend/src/app/brapi.service.ts b/frontend/src/app/brapi.service.ts
index 706b76153cf26672db977187755980f66613bd15..e1b0b584f2b933f24b58f62f1221648ebbc3ed57 100644
--- a/frontend/src/app/brapi.service.ts
+++ b/frontend/src/app/brapi.service.ts
@@ -29,9 +29,9 @@ export class BrapiService {
}
// TODO use the progeny call when the information about parent will be added
- /*germplasmProgeny(germplasmDbId: string): Observable<GermplasmResult<BrapiGermplasmProgeny>> {
+ /* germplasmProgeny(germplasmDbId: string): Observable<GermplasmResult<BrapiGermplasmProgeny>> {
return this.http.get<GermplasmResult<BrapiGermplasmProgeny>>(`${BASE_URL}/germplasm/${germplasmDbId}/progeny`);
- }*/
+ } */
germplasmAttributes(germplasmDbId: string): Observable<BrapiResult<BrapiGermplasmAttributes>> {
return this.http
@@ -61,6 +61,7 @@ export class BrapiService {
.get<BrapiResult<BrapiTrial>>(`${BASE_URL}/trials/${trialsId}`);
}
+
/**
* Get BrAPI single result response and replace the 'schema:includedInDataCatalog' URI value to the actual source object value.
*/
diff --git a/frontend/src/app/card-table/card-table.component.html b/frontend/src/app/card-table/card-table.component.html
index ad60e888ea81a3f3c4e3968e09c0055b7e79e3c4..fff69973e8fd7824626bd52051daa317c30d34cb 100644
--- a/frontend/src/app/card-table/card-table.component.html
+++ b/frontend/src/app/card-table/card-table.component.html
@@ -1,15 +1,17 @@
-<table class="table table-sm table-striped">
- <thead *ngIf="headers">
- <tr>
- <th *ngFor="let header of headers" scope="col">
- {{ header }}
- </th>
- </tr>
- </thead>
- <tbody>
- <ng-container *ngFor="let row of rows"
- [ngTemplateOutlet]="template"
- [ngTemplateOutletContext]="{$implicit: row}">
- </ng-container>
- </tbody>
-</table>
+<div class="card">
+ <table class="table table-sm table-striped">
+ <thead *ngIf="headers">
+ <tr>
+ <th *ngFor="let header of headers" scope="col">
+ {{ header }}
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+ <ng-container *ngFor="let row of rows"
+ [ngTemplateOutlet]="template"
+ [ngTemplateOutletContext]="{$implicit: row}">
+ </ng-container>
+ </tbody>
+ </table>
+</div>
diff --git a/frontend/src/app/error-interceptor.service.spec.ts b/frontend/src/app/error-interceptor.service.spec.ts
index c6ce5cc7fd419ca9e78191d1ed4628b99a112507..5b321dff20ab54e1394e59d97eee166e14415d03 100644
--- a/frontend/src/app/error-interceptor.service.spec.ts
+++ b/frontend/src/app/error-interceptor.service.spec.ts
@@ -34,7 +34,7 @@ describe('ErrorInterceptorService', () => {
error = err;
});
- httpClient.get('/test').subscribe(null, noop);
+ httpClient.get('/test').subscribe({ next: null, error: noop });
http.expectOne('/test').error(new ErrorEvent('unknown', { message: 'not good' }));
expect(error.status).toBeNull();
@@ -47,7 +47,7 @@ describe('ErrorInterceptorService', () => {
error = err;
});
- httpClient.get('/test').subscribe(null, noop);
+ httpClient.get('/test').subscribe({ next: null, error: noop });
http.expectOne('/test').flush(null, { status: 500, statusText: 'Server Error' });
expect(error.status).toBe(500);
@@ -68,7 +68,7 @@ describe('ErrorInterceptorService', () => {
}
};
- httpClient.get('/test').subscribe(null, noop);
+ httpClient.get('/test').subscribe({ next: null, error: noop });
http.expectOne('/test').flush(result, { status: 500, statusText: 'Server Error' });
expect(error.status).toBe(500);
@@ -91,7 +91,7 @@ describe('ErrorInterceptorService', () => {
}
};
- httpClient.get('/test').subscribe(null, noop);
+ httpClient.get('/test').subscribe({ next: null, error: noop });
http.expectOne('/test').flush(result, { status: 500, statusText: 'Server Error' });
expect(error.status).toBe(500);
diff --git a/frontend/src/app/error-interceptor.service.ts b/frontend/src/app/error-interceptor.service.ts
index 87fa7ff612bb6e84c6aaed41d1627d5a9989f4a7..f969531ca35aba7e6599874ab39cf7f7b22e9184 100644
--- a/frontend/src/app/error-interceptor.service.ts
+++ b/frontend/src/app/error-interceptor.service.ts
@@ -1,5 +1,11 @@
import { Injectable } from '@angular/core';
-import { HttpErrorResponse, HttpEvent, HttpHandler, HttpInterceptor, HttpRequest } from '@angular/common/http';
+import {
+ HttpErrorResponse,
+ HttpEvent,
+ HttpHandler,
+ HttpInterceptor,
+ HttpRequest
+} from '@angular/common/http';
import { Observable, Subject } from 'rxjs';
import { tap } from 'rxjs/operators';
@@ -17,7 +23,7 @@ export class ErrorInterceptorService implements HttpInterceptor {
intercept(req: HttpRequest<any>, next: HttpHandler): Observable<HttpEvent<any>> {
return next.handle(req).pipe(
- tap(null, err => this.errorSubject.next(this.toError(err)))
+ tap(() => null, err => this.errorSubject.next(this.toError(err)))
);
}
diff --git a/frontend/src/app/facets/facets.component.html b/frontend/src/app/facets/facets.component.html
new file mode 100644
index 0000000000000000000000000000000000000000..dc1554b894055e9e0d6051c7ed5b2c054a0d809c
--- /dev/null
+++ b/frontend/src/app/facets/facets.component.html
@@ -0,0 +1,23 @@
+
+
+<div class="row">
+ <faidare-small-facets
+ class="col-12 col-lg-12 col-sm-6"
+ *ngFor="let facet of facets"
+ [facet]="facet"
+ [criteria$]="criteria$"
+ [germplasmSearchCriteria$]="germplasmSearchCriteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$">
+ </faidare-small-facets>
+</div>
+
+<div class="row">
+ <faidare-large-facets
+ class="col-12 col-lg-12 col-sm-6"
+ *ngFor="let facet of facets"
+ [facet]="facet"
+ [criteria$]="criteria$"
+ [germplasmSearchCriteria$]="germplasmSearchCriteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$">
+ </faidare-large-facets>
+</div>
diff --git a/frontend/src/app/facets/facets.component.scss b/frontend/src/app/facets/facets.component.scss
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/frontend/src/app/facets/facets.component.spec.ts b/frontend/src/app/facets/facets.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2819afd6451608d1f9e73f1ce5167266a89a9889
--- /dev/null
+++ b/frontend/src/app/facets/facets.component.spec.ts
@@ -0,0 +1,38 @@
+import { async, ComponentFixture, TestBed } from '@angular/core/testing';
+import { FacetsComponent } from './facets.component';
+import { BehaviorSubject } from 'rxjs';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils
+} from '../models/data-discovery.model';
+import { GermplasmSearchCriteria } from '../models/gnpis.model';
+import { SmallFacetsComponent } from './small-facets/small-facets.component';
+import { LargeFacetsComponent } from './large-facets/large-facets.component';
+import { MockComponents } from 'ng-mocks';
+
+
+describe('FacetsComponent', () => {
+ let component: FacetsComponent;
+ let fixture: ComponentFixture<FacetsComponent>;
+
+ beforeEach(async(() => {
+ TestBed.configureTestingModule({
+ declarations: [FacetsComponent, MockComponents(SmallFacetsComponent), MockComponents(LargeFacetsComponent)]
+ })
+ .compileComponents();
+
+
+ fixture = TestBed.createComponent(FacetsComponent);
+ component = fixture.componentInstance;
+
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
+ component.germplasmSearchCriteria$ = new BehaviorSubject<GermplasmSearchCriteria>(DataDiscoveryCriteriaUtils
+ .emptyGermplasmSearchCriteria());
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+ fixture.detectChanges();
+ }));
+
+ it('should create', () => {
+ expect(component).toBeTruthy();
+ });
+});
diff --git a/frontend/src/app/facets/facets.component.ts b/frontend/src/app/facets/facets.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c1f30b80dabff41bca03b6a56f54e6479935f29b
--- /dev/null
+++ b/frontend/src/app/facets/facets.component.ts
@@ -0,0 +1,32 @@
+import { Component, Input, OnInit } from '@angular/core';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryFacet
+} from '../models/data-discovery.model';
+import { BehaviorSubject } from 'rxjs';
+import { GermplasmSearchCriteria } from '../models/gnpis.model';
+
+export const formatFacets: {[key: string]: string} = {
+ 'holdingInstitute': 'holding institute',
+ 'biologicalStatus': 'biological status',
+ 'geneticNature': 'genetic nature'
+};
+
+@Component({
+ selector: 'faidare-facets',
+ templateUrl: './facets.component.html',
+ styleUrls: ['./facets.component.scss']
+})
+export class FacetsComponent implements OnInit {
+
+ @Input() facets: DataDiscoveryFacet[];
+ @Input() criteria$: BehaviorSubject<DataDiscoveryCriteria>;
+ @Input() germplasmSearchCriteria$: BehaviorSubject<GermplasmSearchCriteria>;
+ @Input() displayGermplasmResult$: BehaviorSubject<boolean>;
+
+ constructor() {
+ }
+
+ ngOnInit(): void {
+ }
+}
diff --git a/frontend/src/app/facets/large-facets/large-facets.component.html b/frontend/src/app/facets/large-facets/large-facets.component.html
new file mode 100644
index 0000000000000000000000000000000000000000..93e0fe1e066eb31a33ad103d3eceb312cee2c738
--- /dev/null
+++ b/frontend/src/app/facets/large-facets/large-facets.component.html
@@ -0,0 +1,52 @@
+<ng-template #resultTemplate let-facet="result" let-t="term">
+ <ng-container *ngIf="facet !== 'REFINE'; else refine">
+ <ngb-highlight [result]="displayableKey(facet.label)"
+ [term]="t"></ngb-highlight>
+ <small class="ml-1 text-muted">({{ facet.count | number }})</small>
+ </ng-container>
+ <ng-template #refine>
+ <div class="text-muted small">Other results are available.<br/>Refine your
+ search.
+ </div>
+ </ng-template>
+</ng-template>
+
+<ng-container *ngIf="facet.terms.length && facet.terms.length >8">
+
+ <div class="card mb-1">
+ <div class="card-body">
+ <h3
+ class="card-title">{{ formatFacets[facet.field] ? (formatFacets[facet.field] | titlecase) : facet.field | titlecase }}</h3>
+
+ <div class="mb-2">
+ <span class="badge badge-pill badge-secondary mr-1 selectedElem"
+ style="font-size: smaller"
+ *ngFor="let term of selectedTerms[facet.field]"
+ (keydown.delete)="removeKey(term)"
+ (keydown.backspace)="removeKey(term)"> {{ displaySourceName(term) }}
+ <button tabindex="-1" type="button" class="btn btn-link"
+ (click)="removeKey(term)">×</button>
+ </span>
+ </div>
+
+ <input #typeahead class="form-control" [formControl]="criterion"
+ [ngbTypeahead]="search"
+ (selectItem)="selectKey($event)" [resultTemplate]="resultTemplate"
+
+ placeholder="Filter on {{ facet.field.toLowerCase() }}..."
+ (focus)="focus$.next($event.target.value)"/>
+ </div>
+
+ <faidare-switch-button
+ *ngIf="!criteriaIsEmpty"
+ style="margin-top: -10px; margin-left: 25px"
+ [criteria$]=criteria$
+ [germplasmSearchCriteria$]="germplasmSearchCriteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$"
+ [facetFiled]="facet.field"
+ [switchTitle]="'Germplasm details'">
+ </faidare-switch-button>
+
+ </div>
+</ng-container>
+
diff --git a/frontend/src/app/facets/large-facets/large-facets.component.scss b/frontend/src/app/facets/large-facets/large-facets.component.scss
new file mode 100644
index 0000000000000000000000000000000000000000..21fbbb7047a94af8abc939ce4f2651455b6f0492
--- /dev/null
+++ b/frontend/src/app/facets/large-facets/large-facets.component.scss
@@ -0,0 +1,17 @@
+
+.card * {
+ font-size: 1em;
+}
+
+.btn-link {
+ border-top: 0;
+ border-bottom: 0;
+ margin-top: 0;
+ margin-bottom: 0;
+ padding: 0;
+ color: white;
+ vertical-align: baseline;
+ text-decoration: none;
+ font-size: inherit;
+}
+
diff --git a/frontend/src/app/facets/large-facets/large-facets.component.spec.ts b/frontend/src/app/facets/large-facets/large-facets.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..8529e56c0c17937065c8ab2237b090e7220d5d06
--- /dev/null
+++ b/frontend/src/app/facets/large-facets/large-facets.component.spec.ts
@@ -0,0 +1,122 @@
+import { LargeFacetsComponent } from './large-facets.component';
+import { async, ComponentFixture, TestBed } from '@angular/core/testing';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils,
+ DataDiscoveryFacet
+} from '../../models/data-discovery.model';
+import {
+ NgbPopoverModule,
+ NgbTypeaheadModule
+} from '@ng-bootstrap/ng-bootstrap';
+import { ReactiveFormsModule } from '@angular/forms';
+import { HttpClientTestingModule } from '@angular/common/http/testing';
+import { BehaviorSubject } from 'rxjs';
+import { GermplasmSearchCriteria } from '../../models/gnpis.model';
+import { ComponentTester } from 'ngx-speculoos';
+import { SwitchButtonComponent } from '../switch-button/switch-button.component';
+
+
+describe('LargeFacetsComponent', () => {
+ let component: LargeFacetsComponent;
+ let fixture: ComponentFixture<LargeFacetsComponent>;
+
+ class LargeFacetsComponentTester extends ComponentTester<LargeFacetsComponent> {
+ constructor() {
+ super(LargeFacetsComponent);
+ }
+
+ get facetTitle() {
+ return this.element('h3');
+ }
+
+ get facetInput() {
+ return this.element('input');
+ }
+ }
+
+ const largeFacet: DataDiscoveryFacet = {
+ field: 'large Facet',
+ terms: [
+ {
+ term: 'source 1',
+ label: 'SOURCE 1',
+ count: 10
+ }, {
+ term: 'source 2',
+ label: 'SOURCE 2',
+ count: 20
+ }, {
+ term: 'Germplasm',
+ label: 'GERMPLASM',
+ count: 10
+ }, {
+ term: 'Traditional cultivar/landrace',
+ label: 'Traditional cultivar/landrace',
+ count: 74
+ }, {
+ term: 'Wild',
+ label: 'Wild',
+ count: 7095
+ }, {
+ term: 'Hybrid',
+ label: 'Hybrid',
+ count: 478
+ }, {
+ term: 'INRA',
+ label: 'INRA',
+ count: 74
+ }, {
+ term: 'INRA-ONF',
+ label: 'INRA-ONF',
+ count: 8282
+ }, {
+ term: 'USDA',
+ label: 'USDA',
+ count: 3871
+ }, {
+ term: 'IPK',
+ label: 'IPK',
+ count: 2606
+ }, {
+ term: 'INRA, CNRS',
+ label: 'INRA, CNRS',
+ count: 2170
+ }
+ ]
+ };
+
+ beforeEach(async(() => {
+ TestBed.configureTestingModule({
+ imports: [NgbTypeaheadModule, ReactiveFormsModule, HttpClientTestingModule, NgbPopoverModule],
+ declarations: [LargeFacetsComponent, SwitchButtonComponent]
+ })
+ .compileComponents();
+
+ fixture = TestBed.createComponent(LargeFacetsComponent);
+ component = fixture.componentInstance;
+
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
+ component.germplasmSearchCriteria$ = new BehaviorSubject<GermplasmSearchCriteria>(DataDiscoveryCriteriaUtils
+ .emptyGermplasmSearchCriteria());
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+ component.facet = largeFacet;
+ fixture.detectChanges();
+ }));
+
+ it('should create', () => {
+ expect(component).toBeTruthy();
+ });
+
+ it ('should display search box', () => {
+ const tester = new LargeFacetsComponentTester();
+ component = tester.componentInstance;
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+ component.facet = largeFacet;
+ tester.detectChanges();
+
+ expect(tester.facetTitle.textContent).toEqual('Large Facet');
+ expect(tester.facetInput).toBeTruthy();
+
+ });
+});
diff --git a/frontend/src/app/facets/large-facets/large-facets.component.ts b/frontend/src/app/facets/large-facets/large-facets.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..8170e0b80b9397b63242b2a7c8e81ac227171006
--- /dev/null
+++ b/frontend/src/app/facets/large-facets/large-facets.component.ts
@@ -0,0 +1,199 @@
+import { Component, ElementRef, Input, OnInit, ViewChild } from '@angular/core';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils,
+ DataDiscoveryFacet,
+ DataDiscoverySource
+} from '../../models/data-discovery.model';
+import { BehaviorSubject, merge, Observable, Subject } from 'rxjs';
+import { distinctUntilChanged, filter, map } from 'rxjs/operators';
+import { FormControl } from '@angular/forms';
+import { NgbTypeaheadSelectItemEvent } from '@ng-bootstrap/ng-bootstrap';
+import { GermplasmSearchCriteria } from '../../models/gnpis.model';
+import { GnpisService } from '../../gnpis.service';
+import { formatFacets } from '../facets.component';
+
+export type FacetTermOrRefine = {
+ term: string;
+ label: string;
+ count: number;
+} | 'REFINE';
+const maxResultsDisplayed = 8;
+
+@Component({
+ selector: 'faidare-large-facets',
+ templateUrl: './large-facets.component.html',
+ styleUrls: ['./large-facets.component.scss']
+})
+export class LargeFacetsComponent implements OnInit {
+
+ @Input() facet: DataDiscoveryFacet;
+ @Input() criteria$: BehaviorSubject<DataDiscoveryCriteria>;
+ @Input() germplasmSearchCriteria$: BehaviorSubject<GermplasmSearchCriteria>;
+ @Input() displayGermplasmResult$: BehaviorSubject<boolean>;
+
+ @ViewChild('typeahead') typeahead: ElementRef<HTMLInputElement>;
+ formatFacets = formatFacets;
+
+ localCriteria: DataDiscoveryCriteria;
+ germplasmLocalCriteria: GermplasmSearchCriteria;
+ focus$ = new Subject<string>();
+ selectedTerms: { [key: string]: string[]; } = {};
+ criterion = new FormControl('');
+ sources: DataDiscoverySource[];
+ criteriaIsEmpty = true;
+ germplasmDisplayCurrentState = false;
+
+ constructor(private gnpisService: GnpisService) {
+ }
+
+ ngOnInit(): void {
+
+ this.gnpisService.sources$.subscribe(sources => {
+ this.sources = sources;
+ });
+
+ this.displayGermplasmResult$.subscribe(status => {
+ this.germplasmDisplayCurrentState = status;
+ });
+
+ if (this.criteria$) {
+ this.criteria$.pipe(filter(c => c !== this.localCriteria))
+ .subscribe(criteria => {
+ this.localCriteria = { ...criteria };
+ this.selectedTerms[this.facet.field] = criteria[this.facet.field] || [];
+ this.criteriaIsEmpty = DataDiscoveryCriteriaUtils.checkCriteriaIsEmpty(criteria);
+ });
+ }
+
+ if (this.germplasmSearchCriteria$ && this.germplasmDisplayCurrentState) {
+ this.germplasmSearchCriteria$.pipe(filter(c => c !== this.germplasmLocalCriteria))
+ .subscribe(germplasmCriteria => {
+ this.germplasmLocalCriteria = germplasmCriteria;
+ this.selectedTerms[this.facet.field] = germplasmCriteria[this.facet.field] || [];
+ this.criteriaIsEmpty = DataDiscoveryCriteriaUtils.checkCriteriaIsEmpty(germplasmCriteria);
+ });
+ }
+ }
+
+ search = (text$: Observable<string>): Observable<Array<FacetTermOrRefine>> => {
+ const inputFocus$ = this.focus$;
+ const merged$ = merge(text$, inputFocus$)
+ .pipe(
+ distinctUntilChanged(),
+ map(searchTerm => {
+ const allMatchingBuckets = this.facet.terms
+ // returns values not already selected
+ .filter(terms => !this.selectedTerms[this.facet.field].includes(terms.term)
+ // and that contains the term, ignoring the case
+ && this.displayableKey(terms.label).toLowerCase().includes(searchTerm.toString().toLowerCase()));
+
+ // return the first N results
+ const result: Array<FacetTermOrRefine> = allMatchingBuckets.slice(0, maxResultsDisplayed);
+
+ // if more results exist, add a fake refine bucket
+ if (allMatchingBuckets.length > maxResultsDisplayed) {
+ result.push('REFINE');
+ }
+
+ return result;
+ }));
+ return merged$;
+ };
+
+ displayableKey(key: string): string {
+ return key === 'NULL' ? 'None' : key;
+ }
+
+ displaySourceName(sourceId: string) {
+ for (const source of this.sources) {
+ if (source['@id'] === sourceId) {
+ return source['schema:name'];
+ }
+ }
+ return sourceId;
+ }
+
+ selectKey(event: NgbTypeaheadSelectItemEvent) {
+ event.preventDefault();
+ const selected: FacetTermOrRefine = event.item;
+ if (selected !== 'REFINE') {
+ // the item field of the event contains the facet term
+ // we push the selected key to our collection of keys
+ if (this.criteria$) {
+ if (this.localCriteria[this.facet.field]) {
+ this.localCriteria[this.facet.field].push(event.item.term);
+ } else {
+ this.localCriteria[this.facet.field] = [event.item.term];
+ }
+ }
+ if (this.germplasmSearchCriteria$ && this.germplasmDisplayCurrentState) {
+
+ if (event.item.term !== 'Germplasm' && this.facet.field === 'types') {
+ if (this.localCriteria[this.facet.field]) {
+ this.localCriteria[this.facet.field].push(event.item.term);
+ } else {
+ this.localCriteria[this.facet.field] = [event.item.term];
+ }
+ this.switchGermplasmResult();
+ }
+ if (!this.germplasmLocalCriteria[this.facet.field]) {
+ this.germplasmLocalCriteria[this.facet.field] = [event.item.term];
+ } else {
+ this.germplasmLocalCriteria[this.facet.field].push(event.item.term);
+ }
+ }
+ this.emitChanges();
+ }
+ this.typeahead.nativeElement.blur();
+ }
+
+ emitChanges() {
+ if (this.criteria$) {
+ this.criteria$.next(this.localCriteria);
+ }
+ if (this.germplasmSearchCriteria$ && this.germplasmDisplayCurrentState) {
+ this.germplasmSearchCriteria$.next(this.germplasmLocalCriteria);
+ }
+ }
+
+ removeKey(key: string) {
+ this.selectedTerms[this.facet.field] =
+ this.removeFromList(this.selectedTerms[this.facet.field], key);
+ if (this.criteria$ && !this.germplasmDisplayCurrentState) {
+ this.localCriteria[this.facet.field] =
+ this.removeFromList(this.localCriteria[this.facet.field], key);
+ }
+ if (this.germplasmSearchCriteria$ && this.germplasmDisplayCurrentState) {
+ if (key === 'Germplasm') {
+ this.switchGermplasmResult();
+ }
+ this.germplasmLocalCriteria[this.facet.field] =
+ this.removeFromList(this.germplasmLocalCriteria[this.facet.field], key);
+ }
+ this.emitChanges();
+ }
+
+ removeFromList(list: string[], elem: string) {
+ const index = list.indexOf(elem);
+ return [
+ ...list.slice(0, index),
+ ...list.slice(index + 1)];
+ }
+
+ switchGermplasmResult() {
+ if (!this.germplasmDisplayCurrentState) {
+ this.localCriteria = {
+ ...this.localCriteria,
+ facetFields: ['types']
+ };
+ } else {
+ this.localCriteria = {
+ ...this.localCriteria,
+ facetFields: ['types', 'sources']
+ };
+ }
+ this.criteria$.next(this.localCriteria);
+ this.displayGermplasmResult$.next(!this.germplasmDisplayCurrentState);
+ }
+}
diff --git a/frontend/src/app/facets/small-facets/small-facets.component.html b/frontend/src/app/facets/small-facets/small-facets.component.html
new file mode 100644
index 0000000000000000000000000000000000000000..c14fa0278731851618ba27647b08c8f14f825124
--- /dev/null
+++ b/frontend/src/app/facets/small-facets/small-facets.component.html
@@ -0,0 +1,38 @@
+<ng-template #germplasmDetailsPopup>
+ <div class="card ngb-popover-window ">
+ <br>
+ This is a button to view more information about the germplasm that are return by your search.<br>
+ You can also download the results in standard format.
+ </div>
+</ng-template>
+
+
+<div class="card mb-1" *ngIf="facet.terms.length && facet.terms.length <= 8">
+ <div class="card-body">
+ <h3
+ class="card-title">{{ formatFacets[facet.field] ? (formatFacets[facet.field] | titlecase) : facet.field | titlecase }}</h3>
+
+ <form [formGroup]="checkBoxes" class="card-text">
+ <div class="form-check" *ngFor="let term of facet.terms">
+ <input class="form-check-input"
+ type="checkbox"
+ id="{{ term.term }}"
+ [formControlName]="term.term"
+ />
+ <label class="form-check-label" for="{{ term.term }}">
+ {{ term.label }} ({{ term.count | number }})
+ </label>
+
+ <faidare-switch-button
+ style="margin-top: 5px"
+ *ngIf="term.term == 'Germplasm' && !criteriaIsEmpty"
+ [criteria$]=criteria$
+ [germplasmSearchCriteria$]="germplasmSearchCriteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$"
+ [facetFiled]="facet.field"
+ [switchTitle]="'Details'">
+ </faidare-switch-button>
+ </div>
+ </form>
+ </div>
+</div>
diff --git a/frontend/src/app/facets/small-facets/small-facets.component.scss b/frontend/src/app/facets/small-facets/small-facets.component.scss
new file mode 100644
index 0000000000000000000000000000000000000000..0fd05582424850d221bbf6d200d344ad9f319360
--- /dev/null
+++ b/frontend/src/app/facets/small-facets/small-facets.component.scss
@@ -0,0 +1,80 @@
+
+
+.card * {
+ font-size: 1em;
+}
+
+.card h3 {
+ font-weight: bold;
+}
+.popovers{
+ cursor: pointer;
+}
+
+#switchTitle {
+ cursor: pointer;
+}
+
+/* The switch - the box around the slider */
+
+.switch {
+ position: relative;
+ display: inline-block;
+ width: 30px;
+ height: 17px;
+}
+
+/* Hide default HTML checkbox */
+.switch input {
+ opacity: 0;
+ width: 0;
+ height: 0;
+}
+/* The slider */
+.slider {
+ position: absolute;
+ cursor: pointer;
+ top: 0;
+ left: 0;
+ right: 0;
+ bottom: 0;
+ background-color: #ccc;
+ -webkit-transition: .4s;
+ transition: .4s;
+}
+
+.slider:before {
+ position: absolute;
+ content: "";
+ height: 13px;
+ width: 13px;
+ left: 2px;
+ bottom: 2px;
+ background-color: white;
+ -webkit-transition: .4s;
+ transition: .4s;
+}
+
+input:checked + .slider {
+ background-color: #2196F3;
+}
+
+input:focus + .slider {
+ box-shadow: 0 0 1px #2196F3;
+}
+
+input:checked + .slider:before {
+ -webkit-transform: translateX(15px);
+ -ms-transform: translateX(15px);
+ transform: translateX(15px);
+}
+
+/* Rounded sliders */
+.slider.round {
+ border-radius: 17px;
+}
+
+.slider.round:before {
+ border-radius: 50%;
+}
+
diff --git a/frontend/src/app/facets/small-facets/small-facets.component.spec.ts b/frontend/src/app/facets/small-facets/small-facets.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..491899470af2d5824ab51dfc2ff350e5c886ccba
--- /dev/null
+++ b/frontend/src/app/facets/small-facets/small-facets.component.spec.ts
@@ -0,0 +1,180 @@
+import { TestBed } from '@angular/core/testing';
+
+import { SmallFacetsComponent } from './small-facets.component';
+import { ReactiveFormsModule } from '@angular/forms';
+import { ComponentTester, speculoosMatchers } from 'ngx-speculoos';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils,
+ DataDiscoveryFacet
+} from '../../models/data-discovery.model';
+import { BehaviorSubject } from 'rxjs';
+import { take } from 'rxjs/operators';
+import { NO_ERRORS_SCHEMA } from '@angular/core';
+import { GermplasmSearchCriteria } from '../../models/gnpis.model';
+import { SwitchButtonComponent } from '../switch-button/switch-button.component';
+
+describe('SmallFacetsComponent', () => {
+ class FacetsComponentTester extends ComponentTester<SmallFacetsComponent> {
+ constructor() {
+ super(SmallFacetsComponent);
+ }
+
+ get title() {
+ return this.element('h3.card-title');
+ }
+
+ get terms() {
+ return this.elements('label');
+ }
+
+ get checkboxes() {
+ return this.elements('input');
+ }
+
+ get switchButton() {
+ return this.elements('label#switchTitle');
+ }
+
+ }
+
+ const exampleFacet1: DataDiscoveryFacet = {
+ field: 'sources',
+ terms: [
+ {
+ term: 'source 1',
+ label: 'SOURCE 1',
+ count: 10
+ }, {
+ term: 'source 2',
+ label: 'SOURCE 2',
+ count: 20
+ }
+ ]
+ };
+
+ const exampleFacet2: DataDiscoveryFacet = {
+ field: 'types',
+ terms: [
+ {
+ term: 'Germplasm',
+ label: 'GERMPLASM',
+ count: 10
+ }
+ ]
+ };
+
+ beforeEach(() => TestBed.configureTestingModule({
+ imports: [ReactiveFormsModule],
+ declarations: [SmallFacetsComponent, SwitchButtonComponent],
+ schemas: [NO_ERRORS_SCHEMA]
+ }));
+
+ beforeEach(() => jasmine.addMatchers(speculoosMatchers));
+
+ it('should display facet', () => {
+ const tester = new FacetsComponentTester();
+
+ const component = tester.componentInstance;
+ component.facet = exampleFacet1;
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
+ component.germplasmSearchCriteria$ = new BehaviorSubject<GermplasmSearchCriteria>(DataDiscoveryCriteriaUtils
+ .emptyGermplasmSearchCriteria());
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+ tester.detectChanges();
+
+ expect(tester.title).toContainText('Sources');
+
+ expect(tester.terms[0]).toContainText('SOURCE 1 (10)');
+ expect(tester.terms[0].attr('for')).toBe('source 1');
+ expect(tester.checkboxes[0].attr('id')).toBe('source 1');
+
+ expect(tester.terms[1]).toContainText('SOURCE 2 (20)');
+ expect(tester.terms[1].attr('for')).toBe('source 2');
+ expect(tester.checkboxes[1].attr('id')).toBe('source 2');
+ });
+
+ it('should initialize with criteria', () => {
+ const tester = new FacetsComponentTester();
+
+ const component = tester.componentInstance;
+ component.facet = exampleFacet1;
+
+ const criteria = {
+ ...DataDiscoveryCriteriaUtils.emptyCriteria(),
+ sources: ['source 2']
+ };
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(criteria);
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+
+ tester.detectChanges();
+
+
+ expect(tester.checkboxes[0].nativeElement['checked']).toBe(false);
+ expect(tester.checkboxes[1].nativeElement['checked']).toBe(true);
+ });
+
+ it('should change criteria on checkbox selection change', () => {
+ const tester = new FacetsComponentTester();
+
+ const component = tester.componentInstance;
+ component.facet = exampleFacet1;
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
+ component.germplasmSearchCriteria$ = new BehaviorSubject<GermplasmSearchCriteria>(DataDiscoveryCriteriaUtils
+ .emptyGermplasmSearchCriteria());
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+ tester.detectChanges();
+
+ // No sources selected in criteria
+ component.criteria$.pipe(take(1)).subscribe(criteria => {
+ expect(criteria.sources).toEqual(null);
+ });
+
+ // Click on checkbox
+ // @ts-ignore
+ tester.checkboxes[1].nativeElement.click();
+ expect(tester.checkboxes[1].nativeElement['checked']).toBe(true);
+
+ // Source 2 selected
+ component.criteria$.subscribe(criteria => {
+ expect(criteria.sources).toEqual(['source 2']);
+ });
+ });
+
+ it('should display advance search button for germplasm', () => {
+ const tester = new FacetsComponentTester();
+
+ const component = tester.componentInstance;
+ const criteria = {
+ ...DataDiscoveryCriteriaUtils.emptyCriteria(),
+ types: ['Germplasm']
+ };
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(criteria);
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(true);
+ component.facet = exampleFacet2;
+ tester.detectChanges();
+
+ expect(tester.switchButton.length).toEqual(1);
+ expect(tester.switchButton[0]).toContainText('Details');
+
+ });
+
+ it('should not display advance search button for germplasm', () => {
+ const tester = new FacetsComponentTester();
+
+ const component = tester.componentInstance;
+ const criteria = {
+ ...DataDiscoveryCriteriaUtils.emptyCriteria(),
+ types: ['Germplasm', 'Phenotyping Study']
+ };
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
+ component.germplasmSearchCriteria$ = new BehaviorSubject<GermplasmSearchCriteria>(DataDiscoveryCriteriaUtils
+ .emptyGermplasmSearchCriteria());
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+ component.facet = exampleFacet2;
+ tester.detectChanges();
+
+ expect(tester.switchButton).toEqual([]);
+
+ });
+});
diff --git a/frontend/src/app/facets/small-facets/small-facets.component.ts b/frontend/src/app/facets/small-facets/small-facets.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4d978e46e8f69942cef2fcad0f78d2043a68468c
--- /dev/null
+++ b/frontend/src/app/facets/small-facets/small-facets.component.ts
@@ -0,0 +1,116 @@
+import { Component, EventEmitter, Input, OnInit, Output } from '@angular/core';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils,
+ DataDiscoveryFacet
+} from '../../models/data-discovery.model';
+import { FormControl, FormGroup } from '@angular/forms';
+import { BehaviorSubject } from 'rxjs';
+import { filter } from 'rxjs/operators';
+import { Params } from '@angular/router';
+import { GermplasmSearchCriteria } from '../../models/gnpis.model';
+import { formatFacets } from '../facets.component';
+
+@Component({
+ selector: 'faidare-small-facets',
+ templateUrl: './small-facets.component.html',
+ styleUrls: ['./small-facets.component.scss']
+})
+export class SmallFacetsComponent implements OnInit {
+
+ @Input() facet: DataDiscoveryFacet;
+ @Input() criteria$: BehaviorSubject<DataDiscoveryCriteria>;
+ @Input() germplasmSearchCriteria$: BehaviorSubject<GermplasmSearchCriteria>;
+ @Input() displayGermplasmResult$: BehaviorSubject<boolean>;
+
+ @Output() changed = new EventEmitter<boolean>();
+ formatFacets = formatFacets;
+
+
+ localCriteria: DataDiscoveryCriteria;
+ germplasmLocalCriteria: GermplasmSearchCriteria;
+ criteriaIsEmpty = true;
+ queryParams: Params;
+ checkBoxes: FormGroup = new FormGroup({});
+ germplasmDisplayCurrentState = false;
+
+ constructor() {
+ }
+
+ ngOnInit(): void {
+ for (const term of this.facet.terms) {
+ const control = new FormControl(false);
+ this.checkBoxes.addControl(term.term, control);
+ }
+ if (this.facet.field === 'types') {
+ const switchControl = new FormControl(false);
+ this.checkBoxes.addControl('selectSwitchButton', switchControl);
+ }
+
+ this.displayGermplasmResult$.subscribe(value => {
+ this.germplasmDisplayCurrentState = value;
+ });
+
+ if (this.criteria$) {
+ this.criteria$.pipe(filter(c => c !== this.localCriteria))
+ .subscribe(criteria => {
+ this.localCriteria = criteria;
+ this.getSelectedTerms(criteria);
+
+ this.criteriaIsEmpty = DataDiscoveryCriteriaUtils.checkCriteriaIsEmpty(criteria);
+ });
+ }
+
+ if (this.germplasmSearchCriteria$ && this.germplasmDisplayCurrentState) {
+ this.germplasmSearchCriteria$.pipe(filter(c => c !== this.germplasmLocalCriteria))
+ .subscribe(germplasmCriteria => {
+ this.germplasmLocalCriteria = germplasmCriteria;
+ if (this.germplasmDisplayCurrentState) {
+ this.getSelectedTerms(germplasmCriteria);
+ }
+ });
+ }
+
+ this.checkBoxes.valueChanges.subscribe(checkBoxesValue => {
+ const selectedTerms = Object.keys(checkBoxesValue).filter(key => checkBoxesValue[key]);
+ const multiSelection = Object.keys(checkBoxesValue).filter(key => checkBoxesValue[key] && key !== 'Germplasm');
+ const unselectGermplasm = Object.keys(checkBoxesValue).filter(key => key === 'Germplasm' && !checkBoxesValue[key]);
+
+ if ((multiSelection.length > 0 && this.facet.field === 'types') || unselectGermplasm.length > 0) {
+ this.localCriteria = {
+ ...this.localCriteria,
+ facetFields: ['types', 'sources'],
+ [this.facet.field]: selectedTerms
+ };
+ this.criteria$.next(this.localCriteria);
+ this.displayGermplasmResult$.next(false);
+ }
+
+ if (this.criteria$) {
+ this.localCriteria = {
+ ...this.localCriteria,
+ [this.facet.field]: selectedTerms
+ };
+ this.criteria$.next(this.localCriteria);
+ }
+ if (this.germplasmSearchCriteria$ && this.germplasmDisplayCurrentState) {
+ this.germplasmLocalCriteria = {
+ ...this.germplasmLocalCriteria,
+ [this.facet.field]: selectedTerms
+ };
+ this.germplasmSearchCriteria$.next(this.germplasmLocalCriteria);
+ }
+ });
+ }
+
+ getSelectedTerms(criteria) {
+ const selectedTerms = criteria[this.facet.field] || [];
+
+ for (const [key, control] of Object.entries(this.checkBoxes.controls)) {
+ const isSelected = selectedTerms.indexOf(key) >= 0;
+ control.setValue(isSelected, { emitEvent: false });
+ }
+
+ this.criteriaIsEmpty = DataDiscoveryCriteriaUtils.checkCriteriaIsEmpty(criteria);
+ }
+}
diff --git a/frontend/src/app/facets/switch-button/switch-button.component.html b/frontend/src/app/facets/switch-button/switch-button.component.html
new file mode 100644
index 0000000000000000000000000000000000000000..1b865ae51c239039d8636352c9ddf0fe3f9bd4e1
--- /dev/null
+++ b/frontend/src/app/facets/switch-button/switch-button.component.html
@@ -0,0 +1,33 @@
+<div id="germplasmSearch"
+ title=""
+ *ngIf="facetFiled == 'types'">
+ <label for="selectSwitchButton" style="margin-right: 5px"
+ id="switchTitle">
+ {{ switchTitle }}
+ </label>
+ <label class="switch" id="switchButton">
+ <input type="checkbox" id="selectSwitchButton"
+ [checked]="germplasmDisplayCurrentState"
+ (change)="switchGermplasmResult()">
+ <span class="slider round"></span>
+ </label>
+ <a class="btn popovers" data-boundary="window" placement="auto"
+ [autoClose]="'outside'"
+ [ngbPopover]="germplasmDetailsPopup"
+ [popoverTitle]="'Details button\'s help.'" container="body">
+
+ <img src="assets/faidare/images/question-mark.png" alt="help"
+ title="This is a button to view more information about the germplasm that are return by your search.
+ You can also download the results in standard format."
+ height="20px" style="margin-top: -10px; margin-left: 10px"/>
+ </a>
+</div>
+
+
+<ng-template #germplasmDetailsPopup>
+ <div class="card ngb-popover-window ">
+ <br>
+ This is a button to view more information about the germplasm that are return by your search.<br>
+ You can also download the results in standard format.
+ </div>
+</ng-template>
diff --git a/frontend/src/app/facets/switch-button/switch-button.component.scss b/frontend/src/app/facets/switch-button/switch-button.component.scss
new file mode 100644
index 0000000000000000000000000000000000000000..9e31a5a9c2ebbda9d5e3cadebe188c34a9666f59
--- /dev/null
+++ b/frontend/src/app/facets/switch-button/switch-button.component.scss
@@ -0,0 +1,71 @@
+
+.popovers{
+ cursor: pointer;
+}
+
+#switchTitle {
+ cursor: pointer;
+}
+
+/* The switch - the box around the slider */
+
+.switch {
+ position: relative;
+ display: inline-block;
+ width: 30px;
+ height: 17px;
+}
+
+/* Hide default HTML checkbox */
+.switch input {
+ opacity: 0;
+ width: 0;
+ height: 0;
+}
+/* The slider */
+.slider {
+ position: absolute;
+ cursor: pointer;
+ top: 0;
+ left: 0;
+ right: 0;
+ bottom: 0;
+ background-color: #ccc;
+ -webkit-transition: .4s;
+ transition: .4s;
+}
+
+.slider:before {
+ position: absolute;
+ content: "";
+ height: 13px;
+ width: 13px;
+ left: 2px;
+ bottom: 2px;
+ background-color: white;
+ -webkit-transition: .4s;
+ transition: .4s;
+}
+
+input:checked + .slider {
+ background-color: #2196F3;
+}
+
+input:focus + .slider {
+ box-shadow: 0 0 1px #2196F3;
+}
+
+input:checked + .slider:before {
+ -webkit-transform: translateX(15px);
+ -ms-transform: translateX(15px);
+ transform: translateX(15px);
+}
+
+/* Rounded sliders */
+.slider.round {
+ border-radius: 17px;
+}
+
+.slider.round:before {
+ border-radius: 50%;
+}
diff --git a/frontend/src/app/facets/switch-button/switch-button.component.spec.ts b/frontend/src/app/facets/switch-button/switch-button.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..927fd40c350c6244d97ade9fc12e22505675b074
--- /dev/null
+++ b/frontend/src/app/facets/switch-button/switch-button.component.spec.ts
@@ -0,0 +1,31 @@
+import { async, ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { SwitchButtonComponent } from './switch-button.component';
+import { NgbPopoverModule } from '@ng-bootstrap/ng-bootstrap';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils
+} from '../../models/data-discovery.model';
+import { BehaviorSubject } from 'rxjs';
+
+describe('SwitchButtonComponent', () => {
+ let component: SwitchButtonComponent;
+ let fixture: ComponentFixture<SwitchButtonComponent>;
+
+ beforeEach(async(() => {
+ TestBed.configureTestingModule({
+ imports: [NgbPopoverModule],
+ declarations: [SwitchButtonComponent]
+ })
+ .compileComponents();
+ }));
+
+ it('should create', () => {
+ fixture = TestBed.createComponent(SwitchButtonComponent);
+ component = fixture.componentInstance;
+ component.displayGermplasmResult$ = new BehaviorSubject<boolean>(false);
+ component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
+ fixture.detectChanges();
+ expect(component).toBeTruthy();
+ });
+});
diff --git a/frontend/src/app/facets/switch-button/switch-button.component.ts b/frontend/src/app/facets/switch-button/switch-button.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..ecdb42fadaa8b073080fb4d21f398bf9e2466b73
--- /dev/null
+++ b/frontend/src/app/facets/switch-button/switch-button.component.ts
@@ -0,0 +1,65 @@
+import { Component, Input, OnInit } from '@angular/core';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils,
+ DataDiscoverySource
+} from '../../models/data-discovery.model';
+import { BehaviorSubject } from 'rxjs';
+import { GermplasmSearchCriteria } from '../../models/gnpis.model';
+
+@Component({
+ selector: 'faidare-switch-button',
+ templateUrl: './switch-button.component.html',
+ styleUrls: ['./switch-button.component.scss']
+})
+export class SwitchButtonComponent implements OnInit {
+
+
+ @Input() criteria$: BehaviorSubject<DataDiscoveryCriteria>;
+ @Input() germplasmSearchCriteria$: BehaviorSubject<GermplasmSearchCriteria>;
+ @Input() displayGermplasmResult$: BehaviorSubject<boolean>;
+ @Input() facetFiled: string;
+ @Input() switchTitle: string;
+
+ localCriteria: DataDiscoveryCriteria;
+ sources: DataDiscoverySource[];
+ criteriaIsEmpty = true;
+ germplasmDisplayCurrentState = false;
+
+ constructor() {
+ }
+
+ ngOnInit() {
+
+ this.displayGermplasmResult$.subscribe(value => {
+ this.germplasmDisplayCurrentState = value;
+ });
+
+ if (this.criteria$) {
+ this.criteria$.subscribe(criteria => {
+ this.localCriteria = criteria;
+ this.criteriaIsEmpty = DataDiscoveryCriteriaUtils.checkCriteriaIsEmpty(criteria);
+ });
+ }
+ }
+
+ switchGermplasmResult() {
+
+ this.displayGermplasmResult$.next(!this.germplasmDisplayCurrentState);
+ if (this.germplasmDisplayCurrentState) {
+ this.localCriteria = {
+ ...this.localCriteria,
+ facetFields: ['types'],
+ germplasmLists: null,
+ types: this.localCriteria.types ? this.localCriteria.types : ['Germplasm']
+ };
+ } else {
+ this.localCriteria = {
+ ...this.localCriteria,
+ facetFields: ['types', 'sources'],
+ };
+ this.germplasmSearchCriteria$.next(DataDiscoveryCriteriaUtils.emptyGermplasmSearchCriteria());
+ }
+ this.criteria$.next(this.localCriteria);
+ }
+}
diff --git a/frontend/src/app/form/form.component.html b/frontend/src/app/form/form.component.html
index d699f8bc0279d3ade9b98a2113baaed42e7a4450..ca5638c7b236200f01bc5cbb3450b5f5c13fc8cb 100644
--- a/frontend/src/app/form/form.component.html
+++ b/frontend/src/app/form/form.component.html
@@ -6,7 +6,8 @@
{{ tabs.GERMPLASM }}
</a>
</li>
- <li class="nav-item">
+ <li class="nav-item"
+ *ngIf="!displayGermplasmResult">
<a tabindex="1"
class="nav-link trait {{ getNavClass(tabs.TRAIT) }}"
(click)="activeTab=tabs.TRAIT">
@@ -30,12 +31,14 @@
inputId="crops"
criteriaField="crops"
[criteria$]="criteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$"
placeholder="Search crops">
</faidare-suggestion-field>
</div>
</div>
<!-- Input for the germplasmList field -->
- <div class="form-group row">
+ <div class="form-group row"
+ *ngIf="!displayGermplasmResult">
<label for="germplasmList" class="col-sm-4">
<span>Germplasm list</span>
<small class="small text-muted">
@@ -47,6 +50,7 @@
inputId="germplasmList"
criteriaField="germplasmLists"
[criteria$]="criteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$"
placeholder="Search germplasm lists">
</faidare-suggestion-field>
</div>
@@ -64,6 +68,7 @@
inputId="accessions"
criteriaField="accessions"
[criteria$]="criteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$"
placeholder="Search germplasm accession">
</faidare-suggestion-field>
</div>
diff --git a/frontend/src/app/form/form.component.spec.ts b/frontend/src/app/form/form.component.spec.ts
index b6ef6e077a0053e6f7956dce8152facd6dc35686..1a950eed51ada86bce37eef1b50e2ecb47a1ec46 100644
--- a/frontend/src/app/form/form.component.spec.ts
+++ b/frontend/src/app/form/form.component.spec.ts
@@ -4,6 +4,7 @@ import { FormComponent } from './form.component';
import { MockComponents } from 'ng-mocks';
import { SuggestionFieldComponent } from './suggestion-field/suggestion-field.component';
import { TraitOntologyWidgetComponent } from './trait-ontology-widget/trait-ontology-widget.component';
+import { BehaviorSubject } from 'rxjs';
describe('FormComponent', () => {
@@ -18,6 +19,8 @@ describe('FormComponent', () => {
it('should switch tabs', async(() => {
const fixture = TestBed.createComponent(FormComponent);
+ const component = fixture.componentInstance;
+ component.displayGermplasmResult$ = new BehaviorSubject(false);
fixture.detectChanges();
const element: HTMLElement = fixture.nativeElement;
diff --git a/frontend/src/app/form/form.component.ts b/frontend/src/app/form/form.component.ts
index fe09236ad2c431ba72886a527eb471f1a99cb02f..836ed4b8d5ac8604fadf5b06866adcb47bb54fb5 100644
--- a/frontend/src/app/form/form.component.ts
+++ b/frontend/src/app/form/form.component.ts
@@ -1,4 +1,4 @@
-import { Component, EventEmitter, Input, Output } from '@angular/core';
+import { Component, EventEmitter, Input, OnInit, Output } from '@angular/core';
import { DataDiscoveryCriteria } from '../models/data-discovery.model';
import { BehaviorSubject } from 'rxjs';
@@ -12,8 +12,9 @@ enum Tabs {
templateUrl: './form.component.html',
styleUrls: ['./form.component.scss']
})
-export class FormComponent {
+export class FormComponent implements OnInit {
@Input() criteria$: BehaviorSubject<DataDiscoveryCriteria>;
+ @Input() displayGermplasmResult$: BehaviorSubject<boolean>;
@Output() traitWidgetInitialized = new EventEmitter();
// Default active tab
@@ -21,6 +22,7 @@ export class FormComponent {
// to give access in HTML template
tabs = Tabs;
+ displayGermplasmResult: boolean;
getNavClass(tab: Tabs) {
return this.activeTab === tab ? 'active' : '';
@@ -29,4 +31,12 @@ export class FormComponent {
getTabClass(tab: Tabs) {
return this.activeTab === tab ? 'visible' : 'd-none';
}
+ ngOnInit(): void {
+ this.displayGermplasmResult$.subscribe(displayStatus => {
+ this.displayGermplasmResult = displayStatus;
+ if (this.displayGermplasmResult) {
+ this.activeTab = Tabs.GERMPLASM;
+ }
+ });
+ }
}
diff --git a/frontend/src/app/form/suggestion-field/suggestion-field.component.ts b/frontend/src/app/form/suggestion-field/suggestion-field.component.ts
index bbac52ab39b25cac5ee8dd7c59afcc839606187b..5b43b56d27a4de67e28cc9005889cafbadd0d75f 100644
--- a/frontend/src/app/form/suggestion-field/suggestion-field.component.ts
+++ b/frontend/src/app/form/suggestion-field/suggestion-field.component.ts
@@ -1,7 +1,10 @@
import { Component, ElementRef, Input, OnInit, ViewChild } from '@angular/core';
-import { BehaviorSubject, merge, Observable, of, Subject } from 'rxjs';
+import { BehaviorSubject, merge, Observable, Subject } from 'rxjs';
import { FormControl } from '@angular/forms';
-import { NgbTypeahead, NgbTypeaheadSelectItemEvent } from '@ng-bootstrap/ng-bootstrap';
+import {
+ NgbTypeahead,
+ NgbTypeaheadSelectItemEvent
+} from '@ng-bootstrap/ng-bootstrap';
import { GnpisService } from '../../gnpis.service';
import { debounceTime, filter, map, switchMap } from 'rxjs/operators';
import { DataDiscoveryCriteria } from '../../models/data-discovery.model';
@@ -16,6 +19,7 @@ export class SuggestionFieldComponent implements OnInit {
@Input() criteriaField: string;
@Input() inputId: string;
@Input() criteria$: BehaviorSubject<DataDiscoveryCriteria>;
+ @Input() displayGermplasmResult$: BehaviorSubject<boolean>;
@Input() placeholder: string;
selectedKeys: string[] = [];
@@ -25,7 +29,6 @@ export class SuggestionFieldComponent implements OnInit {
input = new FormControl();
@ViewChild('inputElement') inputElement: ElementRef;
-
@ViewChild('typeahead') typeahead: NgbTypeahead;
private localCriteria: DataDiscoveryCriteria = null;
@@ -60,18 +63,18 @@ export class SuggestionFieldComponent implements OnInit {
const clicksWithClosedPopup$ = this.click$.pipe(
filter(() => !this.typeahead.isPopupOpen())
);
- const text2$ = text$.pipe(
+ /*const text2$ = text$.pipe(
filter(term => term.length >= 2)
- );
+ );*/
// When new text or focus or click with popup closed
- return merge(text2$, clicksWithClosedPopup$).pipe(
+ return merge(text$, clicksWithClosedPopup$).pipe(
debounceTime(250),
switchMap((term: string) => {
- if (!term) {
+ /*if (!term) {
// No term to search
return of([]);
- }
+ }*/
// Otherwise, we fetch new suggestions
return this.fetchSuggestion(term);
@@ -145,5 +148,10 @@ export class SuggestionFieldComponent implements OnInit {
[this.criteriaField]: [...this.selectedKeys]
};
this.criteria$.next(this.localCriteria);
+ let displayGermplasmResult = false;
+ this.displayGermplasmResult$.subscribe(germplasmResultState => {
+ displayGermplasmResult = germplasmResultState;
+ });
+ this.displayGermplasmResult$.next(displayGermplasmResult);
}
}
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 04735dd58837edcf96893a5e715e28fa7161b3fe..b0fa68a891c1b0ab425b895723bec06825e81f2a 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.spec.ts
@@ -40,14 +40,6 @@ describe('GermplasmCardComponent', () => {
}
}
- const gnpisSite: Site = {
- latitude: null,
- longitude: null,
- siteId: null,
- siteName: null,
- siteType: null
- };
-
const brapiSibling: BrapiSibling = {
germplasmDbId: 'frere1',
defaultDisplayName: 'frere1'
diff --git a/frontend/src/app/germplasm-card/germplasm-card.component.ts b/frontend/src/app/germplasm-card/germplasm-card.component.ts
index 73616b708099f586416ee142f59d19e149e3fabc..6c8d91088dc726cf22f485fa4d9198ab5cf07313 100644
--- a/frontend/src/app/germplasm-card/germplasm-card.component.ts
+++ b/frontend/src/app/germplasm-card/germplasm-card.component.ts
@@ -2,7 +2,12 @@ import { Component, OnInit } from '@angular/core';
import { ActivatedRoute } from '@angular/router';
import { BrapiService } from '../brapi.service';
import { GnpisService } from '../gnpis.service';
-import { BrapiAttributeData, BrapiGermplasmPedigree, BrapiLocation, BrapiTaxonIds } from '../models/brapi.model';
+import {
+ BrapiAttributeData,
+ BrapiGermplasmPedigree,
+ BrapiLocation,
+ BrapiTaxonIds
+} from '../models/brapi.model';
import { Children, Germplasm, Site } from '../models/gnpis.model';
import { environment } from '../../environments/environment';
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
new file mode 100644
index 0000000000000000000000000000000000000000..01f2ff47114210bb06c852bde5865b7b3ab71f94
--- /dev/null
+++ b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.html
@@ -0,0 +1,124 @@
+<ng-container *ngIf="germplasms && germplasms.length>0">
+
+ <div class="container mb-3">
+ <div class="row result align-content-center">
+ <span class="col mt-2 bolder">
+ Results:
+ </span>
+ <div class="row align-content-center">
+ <span *ngIf="pagination.totalResult" style="margin-right: 5px"
+ class="col align-self-end small text-muted mt-3">
+ From {{ pagination.startResult | number }}
+ to {{ pagination.endResult | number }}
+ over {{ pagination.totalResult | number }} documents
+ <span *ngIf="pagination.totalResult > pagination.maxResults">
+ (limited to {{ pagination.maxResults | number }})
+ </span>
+ </span>
+ </div>
+ </div>
+ </div>
+
+ <button type="button" class="btn btn-outline-success mb-2"
+ (click)="exportPlantMaterial(localCriteria)">
+
+ <span class="iconify" data-icon="fa-solid:file-csv" data-inline="false"></span>
+ Export Plant Material list
+ </button>
+
+ <!-- Loading spinner-->
+ <div class="text-center">
+ <faidare-loading-spinner [loading]="loading"></faidare-loading-spinner>
+ </div>
+
+ <faidare-card-section
+ class="col-12 col-lg"
+ header="Germplasm data: "
+ [test]="germplasms">
+ <ng-template>
+ <div class="table-responsive table-card-body">
+ <table class="table table-sm table-striped">
+ <thead>
+ <tr>
+ <th id="germplasmResultThead"
+ *ngFor="let header of headers" scope="col">
+ <label id="tabHeader"
+ (click)="getTabField(header)">{{ formatHeaders[header] }}
+ <i *ngIf="!fieldSortState[header]" class="fa fa-sort"
+ aria-hidden="true"></i>
+ <i *ngIf="fieldSortState[header] =='desc'"
+ class="fa fa-sort-desc"
+ aria-hidden="true"></i>
+ <i *ngIf="fieldSortState[header] == 'asc'"
+ class="fa fa-sort-asc"
+ aria-hidden="true"></i>
+ </label>
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+ <ng-container *ngFor="let germplasm of germplasms">
+ <tr>
+ <td>
+ <a [routerLink]="['/germplasm']"
+ [queryParams]="{id: germplasm.germplasmDbId}"
+ target="_blank">
+ {{ germplasm.germplasmName }}
+ </a>
+ </td>
+ <td>{{ germplasm.accessionNumber }}</td>
+ <td>{{ germplasm.genusSpecies }}</td>
+ <td>{{ germplasm.instituteName }}</td>
+ <td>{{ germplasm.biologicalStatusOfAccessionCode }}</td>
+ <td>{{ germplasm.countryOfOriginCode }}</td>
+ </tr>
+ </ng-container>
+ </tbody>
+ </table>
+ </div>
+ </ng-template>
+ </faidare-card-section>
+
+ <div class="container text-right"
+ style="margin-top: -30px"
+ *ngIf="germplasms">
+ <div ngbDropdown class="dropdown-container">
+ <button class="btn btn-outline-secondary btn-sm"
+ ngbDropdownToggle>Results per page : {{ pagination.pageSize }}
+ </button>
+ <div ngbDropdownMenu class="dropdown-menu" id="pageSizes">
+ <div *ngFor="let pageSize of elementPerPage">
+ <button type="button"
+ class="btn btn-light"
+ (click)="changeNbElementPerPage(pageSize)"
+ style="width: 160px;" ngbDropdownItem>{{ pageSize }}
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div class="d-flex justify-content-center mt-2 mb-5"
+ *ngIf="pagination.totalPages > 1">
+ <!-- we add 1 to the page because ngb-pagination is 1 based -->
+ <ngb-pagination [page]="pagination.currentPage + 1"
+ (pageChange)="changePage($event)"
+ [collectionSize]="resultCount()"
+ [pageSize]="pagination.pageSize"
+ [maxSize]="5"
+ [boundaryLinks]="true"
+ [ellipses]="false"
+ size="sm">
+ </ngb-pagination>
+ </div>
+
+</ng-container>
+
+
+<div *ngIf="germplasms && germplasms.length == 0"
+ id="no-results" class="text-center">
+ <div class="no-result-icon">
+ <span class="fa fa-meh-o"></span>
+ </div>
+ No results.
+</div>
diff --git a/frontend/src/app/germplasm-result-page/germplasm-result-page.component.scss b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.scss
new file mode 100644
index 0000000000000000000000000000000000000000..7579016a3ec6d8f426d3ffd20228f766480dcd43
--- /dev/null
+++ b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.scss
@@ -0,0 +1,47 @@
+@import "theme";
+@import '../../styles.scss';
+
+
+#tabHeader {
+ cursor: pointer;
+}
+
+#germplasmResultThead {
+ margin-top: 26px;
+ border-bottom-width: 3px;
+ border-bottom-color: #d0d8e1;
+}
+
+
+.result {
+ border-top: 4.5px solid #c2c2c2;
+ border-bottom: 1px solid #c2c2c2;
+}
+
+.no-result-icon {
+ font-size: 8rem;
+ color: $gray-300;
+}
+
+.bolder {
+ font-size: 1.2rem;
+ font-weight: bold;
+}
+
+thead th {
+ position: sticky;
+ top: 0;
+ background-color: white;
+}
+
+label {
+ span {
+ font-weight: bold;
+ display: block;
+ }
+}
+
+
+.iconify {
+ width: 35px;
+ height: 35px; }
diff --git a/frontend/src/app/germplasm-result-page/germplasm-result-page.component.spec.ts b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..786c51b78ca6d746b9bd81248d02a2a1e1ae693b
--- /dev/null
+++ b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.spec.ts
@@ -0,0 +1,302 @@
+import { async, ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { GermplasmResultPageComponent } from './germplasm-result-page.component';
+import { RouterTestingModule } from '@angular/router/testing';
+import { LoadingSpinnerComponent } from '../loading-spinner/loading-spinner.component';
+import { GnpisService } from '../gnpis.service';
+import { GermplasmResults } from '../models/brapi.model';
+import { CardSectionComponent } from '../card-section/card-section.component';
+import { NO_ERRORS_SCHEMA } from '@angular/core';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils,
+ DataDiscoveryFacet,
+ DEFAULT_PAGE_SIZE,
+ MAX_RESULTS
+} from '../models/data-discovery.model';
+import { Germplasm, GermplasmSearchCriteria } from '../models/gnpis.model';
+import { BehaviorSubject, of } from 'rxjs';
+
+
+describe('GermplasmResultPageComponent', () => {
+ let component: GermplasmResultPageComponent;
+ let fixture: ComponentFixture<GermplasmResultPageComponent>;
+
+ const pagination = {
+ startResult: 1,
+ endResult: DEFAULT_PAGE_SIZE,
+ totalResult: 2,
+ currentPage: 0,
+ pageSize: DEFAULT_PAGE_SIZE,
+ totalPages: 1,
+ totalCount: 2,
+ maxResults: MAX_RESULTS
+ };
+
+ const facets: DataDiscoveryFacet[] = [
+ {
+ field: 'holdingInstitute',
+ terms: [
+ {
+ term: 'INRA',
+ label: 'INRA',
+ count: 74
+ },
+ {
+ term: 'INRA-ONF',
+ label: 'INRA-ONF',
+ count: 8282
+ },
+ {
+ term: 'USDA',
+ label: 'USDA',
+ count: 3871
+ },
+ {
+ term: 'IPK',
+ label: 'IPK',
+ count: 2606
+ },
+ {
+ term: 'INRA, CNRS',
+ label: 'INRA, CNRS',
+ count: 2170
+ }
+ ]
+ },
+ {
+ field: 'biologicalStatus',
+ terms: [
+ {
+ term: 'Traditional cultivar/landrace',
+ label: 'Traditional cultivar/landrace',
+ count: 74
+ },
+ {
+ term: 'Wild',
+ label: 'Wild',
+ count: 7095
+ },
+ {
+ term: 'Hybrid',
+ label: 'Hybrid',
+ count: 478
+ }
+ ]
+ }
+ ];
+
+ const germplasmSearchResult: GermplasmResults<Germplasm> = {
+ metadata: {
+ pagination: pagination
+ },
+ facets: facets,
+ result: {
+ data: [{
+ germplasmDbId: 'g1',
+ defaultDisplayName: 'germplam1',
+ accessionNumber: 'G_10',
+ germplasmName: 'germplam1',
+ germplasmPUI: 'urn_g1',
+ pedigree: null,
+ seedSource: 'Versaille Institute',
+ synonyms: null,
+ commonCropName: 'cheery',
+ instituteCode: '78',
+ instituteName: 'Versaille Institute',
+ biologicalStatusOfAccessionCode: null,
+ countryOfOriginCode: 'FR',
+ typeOfGermplasmStorageCode: null,
+ taxonIds: null,
+ genus: 'Populus',
+ species: 'x generosa',
+ speciesAuthority: 'Pop',
+ subtaxa: 'subsp',
+ subtaxaAuthority: '',
+ donors: null,
+ acquisitionDate: 'yesterday',
+
+
+ genusSpecies: null,
+ genusSpeciesSubtaxa: null,
+ taxonSynonyms: null,
+ taxonCommonNames: null,
+ taxonComment: null,
+ geneticNature: null,
+ comment: null,
+ photo: null,
+ holdingInstitute: null,
+ holdingGenbank: null,
+ presenceStatus: null,
+ children: null,
+ originSite: null,
+ collectingSite: null,
+ evaluationSites: null,
+ collector: null,
+ breeder: null,
+ distributors: null,
+ panel: null,
+ collection: null,
+ population: null,
+ 'schema:includedInDataCatalog': null
+ }, {
+ germplasmDbId: 'g2',
+ defaultDisplayName: 'germplam2',
+ accessionNumber: 'G_20',
+ germplasmName: 'germplam2',
+ germplasmPUI: 'urn_g2',
+ pedigree: null,
+ seedSource: 'Versaille Institute',
+ synonyms: null,
+ commonCropName: 'cheery',
+ instituteCode: '78',
+ instituteName: 'Versaille Institute',
+ biologicalStatusOfAccessionCode: null,
+ countryOfOriginCode: 'FR',
+ typeOfGermplasmStorageCode: null,
+ taxonIds: null,
+ genus: 'Triticum',
+ species: 'aestivum',
+ speciesAuthority: 'Trit',
+ subtaxa: 'subsp',
+ subtaxaAuthority: '',
+ donors: null,
+ acquisitionDate: 'today',
+
+
+ genusSpecies: null,
+ genusSpeciesSubtaxa: null,
+ taxonSynonyms: null,
+ taxonCommonNames: null,
+ taxonComment: null,
+ geneticNature: null,
+ comment: null,
+ photo: null,
+ holdingInstitute: null,
+ holdingGenbank: null,
+ presenceStatus: null,
+ children: null,
+ originSite: null,
+ collectingSite: null,
+ evaluationSites: null,
+ collector: null,
+ breeder: null,
+ distributors: null,
+ panel: null,
+ collection: null,
+ population: null,
+ 'schema:includedInDataCatalog': null
+
+ }],
+ }
+ };
+
+
+
+
+
+
+ const criteria: GermplasmSearchCriteria = {
+ accessionNumbers: ['G_20'],
+ germplasmDbIds: null,
+ germplasmGenus: null,
+ germplasmNames: ['germplam1'],
+ germplasmPUIs: null,
+ germplasmSpecies: null,
+
+ synonyms: null,
+ panel: null,
+ collection: null,
+ population: null,
+ commonCropName: null,
+ species: null,
+ genusSpecies: null,
+ subtaxa: null,
+ genusSpeciesSubtaxa: null,
+ taxonSynonyms: null,
+ taxonCommonNames: null,
+ biologicalStatus: null,
+ geneticNature: null,
+ holdingInstitute: null,
+ sources: null,
+ types: null,
+
+ facetFields: null,
+ sortBy: 'germplasmName',
+ sortOrder: null,
+ page: 1,
+ pageSize: 10,
+ };
+
+ const dataDiscoveryCriteria: DataDiscoveryCriteria = {
+ accessions: ['G_10', 'incisa', 'G_20'],
+ crops: ['cheery', 'prunus'],
+ facetFields: null,
+ germplasmLists: null,
+ observationVariableIds: null,
+ sources: ['URGI'],
+ types: null,
+ topSelectedTraitOntologyIds: null,
+
+ page: 1,
+ pageSize: 10
+ };
+
+
+ const gnpisService = jasmine.createSpyObj(
+ 'GnpisService', [
+ 'germplasmSearch'
+ ]
+ );
+ gnpisService.germplasmSearch.and.returnValue(of(germplasmSearchResult));
+
+
+ beforeEach(async(() => {
+ TestBed.configureTestingModule({
+ imports: [RouterTestingModule],
+ declarations: [GermplasmResultPageComponent, CardSectionComponent, LoadingSpinnerComponent],
+ providers: [
+ { provide: GnpisService, useValue: gnpisService }
+ ],
+ schemas: [NO_ERRORS_SCHEMA],
+ })
+ .compileComponents();
+
+ fixture = TestBed.createComponent(GermplasmResultPageComponent);
+ component = fixture.componentInstance;
+ component.criteriaFromForm$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils
+ .emptyCriteria());
+ component.germplasmSearchCriteria$ = new BehaviorSubject<GermplasmSearchCriteria>(DataDiscoveryCriteriaUtils
+ .emptyGermplasmSearchCriteria());
+
+ component.germplasmFacets$ = new BehaviorSubject<DataDiscoveryFacet[]>(facets);
+ fixture.detectChanges();
+ }));
+
+ it('should create', () => {
+ expect(component).toBeTruthy();
+ });
+
+ it('should fecth the germplasm', () => {
+ component.germplasmSearchCriteria$.next(criteria);
+ expect(component.localCriteria).toEqual(criteria);
+ expect(gnpisService.germplasmSearch).toHaveBeenCalledWith(criteria);
+ expect(component.germplasms).toEqual(germplasmSearchResult.result.data);
+
+ });
+
+ it('should get criteria information from data discovery criteria', () => {
+ component.criteriaFromForm$.next(dataDiscoveryCriteria);
+ fixture.detectChanges();
+
+ expect(component.localCriteria.commonCropName).toContain('cheery');
+ expect(component.localCriteria.commonCropName).toContain('prunus');
+ expect(component.localCriteria.commonCropName).toContain('cheery');
+ expect(component.localCriteria.genusSpecies).toContain('prunus');
+ expect(component.localCriteria.genusSpeciesSubtaxa).toContain('prunus');
+
+ expect(component.localCriteria.germplasmNames).toContain('G_10');
+ expect(component.localCriteria.accessionNumbers).toContain('incisa');
+ expect(component.localCriteria.synonyms).toContain('G_20');
+ });
+});
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
new file mode 100644
index 0000000000000000000000000000000000000000..8118524d06c3516b2a1297eccffb8fc688b778ac
--- /dev/null
+++ b/frontend/src/app/germplasm-result-page/germplasm-result-page.component.ts
@@ -0,0 +1,193 @@
+import { Component, Input, OnInit } from '@angular/core';
+import { GnpisService } from '../gnpis.service';
+import { Germplasm, GermplasmSearchCriteria } from '../models/gnpis.model';
+
+
+import { saveAs } from 'file-saver';
+import { ActivatedRoute } from '@angular/router';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoveryCriteriaUtils,
+ DataDiscoveryFacet,
+ DEFAULT_PAGE_SIZE,
+ MAX_RESULTS
+} from '../models/data-discovery.model';
+import { asArray } from '../utils';
+import { BehaviorSubject } from 'rxjs';
+
+@Component({
+ selector: 'faidare-germplasm-result-page',
+ templateUrl: './germplasm-result-page.component.html',
+ styleUrls: ['./germplasm-result-page.component.scss']
+})
+export class GermplasmResultPageComponent implements OnInit {
+
+
+ germplasms: Germplasm[];
+ localCriteria: GermplasmSearchCriteria = DataDiscoveryCriteriaUtils.emptyGermplasmSearchCriteria();
+
+ @Input() criteriaFromForm$: BehaviorSubject<DataDiscoveryCriteria>;
+ @Input() germplasmSearchCriteria$: BehaviorSubject<GermplasmSearchCriteria>;
+ @Input() germplasmFacets$: BehaviorSubject<DataDiscoveryFacet[]>;
+
+ headers: string[] = [
+ 'germplasmName',
+ 'accessionNumber',
+ 'genusSpecies',
+ 'instituteName',
+ 'biologicalStatusOfAccessionCode',
+ 'countryOfOriginCode'];
+ elementPerPage: number[] = [15, 20, 25];
+ loading: boolean;
+ fieldSortState: object = {
+ germplasmName: null,
+ accessionNumber: null,
+ genusSpecies: null,
+ instituteName: null,
+ biologicalStatusOfAccessionCode: null
+ };
+
+ formatHeaders: { [key: string]: string } = {
+ 'germplasmName': 'Germplasm name',
+ 'accessionNumber': 'Accession number',
+ 'genusSpecies': 'Genus species',
+ 'instituteName': 'Institute name',
+ 'biologicalStatusOfAccessionCode': 'Biological status',
+ 'countryOfOriginCode': 'Country of origin'
+ };
+
+ pagination = {
+ startResult: 1,
+ endResult: DEFAULT_PAGE_SIZE,
+ totalResult: null,
+ currentPage: 0,
+ pageSize: DEFAULT_PAGE_SIZE,
+ totalPages: null,
+ maxResults: MAX_RESULTS
+ };
+
+ constructor(public service: GnpisService, private route: ActivatedRoute) {
+ }
+
+ ngOnInit() {
+
+ const queryParams = this.route.snapshot.queryParams;
+ this.reassignCriteriaFieldFromDataDiscoveryFields(queryParams);
+
+ this.criteriaFromForm$.subscribe(criteria => {
+ this.reassignCriteriaFieldFromDataDiscoveryFields(criteria);
+ this.germplasmSearchCriteria$.next(this.localCriteria);
+ });
+
+ this.germplasmSearchCriteria$
+ .subscribe(criteria => {
+ this.localCriteria = criteria;
+ this.searchGermplasm(this.localCriteria);
+ });
+
+ }
+
+ searchGermplasm(criteria: GermplasmSearchCriteria) {
+ this.service.germplasmSearch(criteria)
+ .subscribe(({ metadata, facets, result }) => {
+ this.germplasms = result.data;
+ this.germplasmFacets$.next(facets);
+ DataDiscoveryCriteriaUtils.updatePagination(this.pagination, metadata.pagination);
+ });
+ }
+
+
+ reassignCriteriaFieldFromDataDiscoveryFields(criteria) {
+
+ this.localCriteria = {
+ ...this.localCriteria,
+ commonCropName: asArray(criteria.crops),
+ species: asArray(criteria.crops),
+ germplasmGenus: asArray(criteria.crops),
+ genusSpecies: asArray(criteria.crops),
+ subtaxa: asArray(criteria.crops),
+ genusSpeciesSubtaxa: asArray(criteria.crops),
+ taxonSynonyms: asArray(criteria.crops),
+ taxonCommonNames: asArray(criteria.crops),
+
+ panel: asArray(criteria.germplasmLists),
+ collection: asArray(criteria.germplasmLists),
+ population: asArray(criteria.germplasmLists),
+
+ germplasmNames: asArray(criteria.accessions),
+ accessionNumbers: asArray(criteria.accessions),
+ synonyms: asArray(criteria.accessions),
+
+ sources: asArray(criteria.sources)
+ };
+
+ }
+
+ exportPlantMaterial(criteria: GermplasmSearchCriteria) {
+ this.loading = true;
+ this.service.plantMaterialExport(criteria).subscribe(
+ result => {
+ const blob = new Blob([result], { type: 'text/plain;charset=utf-8' });
+ saveAs(blob, 'germplasm.gnpis.csv');
+ this.loading = false;
+ },
+ error => {
+ console.log(error);
+ });
+ }
+
+ getTabField(tabField) {
+
+ this.switchSortOrder(tabField);
+ this.resetOtherFieldSort(tabField);
+
+ this.localCriteria.sortOrder = this.fieldSortState[tabField];
+
+ this.germplasmSearchCriteria$.next(this.localCriteria);
+
+ return tabField;
+ }
+
+ switchSortOrder(tabField) {
+ if (this.fieldSortState[tabField] === 'asc') {
+ this.localCriteria.sortBy = null;
+ return this.fieldSortState[tabField] = null;
+ }
+ if (this.fieldSortState[tabField] === 'desc') {
+ this.localCriteria.sortBy = tabField;
+ return this.fieldSortState[tabField] = 'asc';
+ }
+ if (!this.fieldSortState[tabField]) {
+ this.localCriteria.sortBy = tabField;
+ return this.fieldSortState[tabField] = 'desc';
+ }
+ }
+
+ resetOtherFieldSort(tabField) {
+ const otherHeaders = this.headers.filter(header => header !== tabField);
+ for (const header of otherHeaders) {
+ this.fieldSortState[header] = null;
+ }
+ }
+
+ resultCount() {
+ return Math.min(
+ this.pagination.totalResult,
+ MAX_RESULTS - DEFAULT_PAGE_SIZE
+ );
+ }
+
+ changePage(page: number) {
+ this.localCriteria.page = page - 1;
+ this.germplasmSearchCriteria$.next(this.localCriteria);
+ }
+
+ changeNbElementPerPage(pageSize: number) {
+ this.pagination.pageSize = pageSize;
+ this.elementPerPage = [10, 15, 20, 25];
+ this.elementPerPage = this.elementPerPage
+ .filter(otherPageSize => otherPageSize !== pageSize);
+ this.localCriteria.pageSize = pageSize;
+ this.germplasmSearchCriteria$.next(this.localCriteria);
+ }
+}
diff --git a/frontend/src/app/gnpis.service.spec.ts b/frontend/src/app/gnpis.service.spec.ts
index 6032743909d25675bdeb69c29754bea427aa1101..6f82603c7dbd7595f0acaf3a4de3a29a9b6ca157 100644
--- a/frontend/src/app/gnpis.service.spec.ts
+++ b/frontend/src/app/gnpis.service.spec.ts
@@ -1,9 +1,23 @@
import { BASE_URL, GnpisService } from './gnpis.service';
import { BrapiMetaData, BrapiResults } from './models/brapi.model';
-import { DataDiscoveryCriteria, DataDiscoverySource } from './models/data-discovery.model';
-import { HttpClientTestingModule, HttpTestingController } from '@angular/common/http/testing';
+import {
+ DataDiscoveryCriteria,
+ DataDiscoverySource
+} from './models/data-discovery.model';
+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,
+ GermplasmSearchCriteria,
+ GermplasmSet,
+ Institute,
+ Site
+} from './models/gnpis.model';
describe('GnpisService', () => {
@@ -112,9 +126,53 @@ describe('GnpisService', () => {
distributors: [germplasmInstitute],
panel: [germplasmSet],
collection: [germplasmSet],
- population: [germplasmSet]
+ population: [germplasmSet],
+ 'schema:includedInDataCatalog': null
};
+ const germplasmExportCriteria: GermplasmSearchCriteria = {
+ accessionNumbers: ['VCR010'],
+ germplasmDbIds: [],
+ germplasmGenus: [],
+ germplasmNames: [],
+ germplasmPUIs: [],
+ germplasmSpecies: [],
+
+ synonyms: null,
+ panel: null,
+ collection: null,
+ population: null,
+ commonCropName: null,
+ species: null,
+ genusSpecies: null,
+ subtaxa: null,
+ genusSpeciesSubtaxa: null,
+ taxonSynonyms: null,
+ taxonCommonNames: null,
+ biologicalStatus: null,
+ geneticNature: null,
+ holdingInstitute: null,
+ sources: null,
+ types: ['Germplasm'],
+
+ facetFields: null,
+ sortBy: null,
+ sortOrder: null,
+ page: 1,
+ pageSize: 10
+ };
+
+ const exportFile: string = '"DOI";"AccessionNumber";' +
+ '"AccessionName";"TaxonGroup";' +
+ '"HoldingInstitution";"LotName";' +
+ '"LotSynonym";' +
+ '"CollectionName";' +
+ '"CollectionType";' +
+ '"PanelName";' +
+ '"PanelSize"\n' +
+ '"https://germplasmdoi";"germplasm01";GermplasmTest;Pea;INRA-URGI;;;;;;';
+
+
let gnpisService: GnpisService;
let http: HttpTestingController;
beforeEach(() => {
@@ -228,5 +286,18 @@ describe('GnpisService', () => {
});
});
});
+
+ it('should export germplasm as PlantMaterial', () => {
+ gnpisService.plantMaterialExport(germplasmExportCriteria).subscribe(
+ plantMaterialExport => {
+ expect(plantMaterialExport).toEqual(exportFile);
+ }
+ );
+ const req = http.expectOne({
+ url: `${BASE_URL}/germplasm/germplasm-list-csv`,
+ method: 'POST'
+ });
+ req.flush(exportFile);
+ });
})
;
diff --git a/frontend/src/app/gnpis.service.ts b/frontend/src/app/gnpis.service.ts
index 5146ebdb82204c700e93ed483b3132bc76e3b31f..aff0fac08c66ab0120543e85f9791eca1a2e5281 100644
--- a/frontend/src/app/gnpis.service.ts
+++ b/frontend/src/app/gnpis.service.ts
@@ -7,9 +7,13 @@ import {
DataDiscoveryResults,
DataDiscoverySource
} from './models/data-discovery.model';
-import { BrapiResults } from './models/brapi.model';
+import {
+ BrapiResults,
+ GermplasmCriteria,
+ GermplasmResults
+} from './models/brapi.model';
import { map } from 'rxjs/operators';
-import { Germplasm } from './models/gnpis.model';
+import { Germplasm, GermplasmSearchCriteria } from './models/gnpis.model';
import { XrefResponse } from './models/xref.model';
import { removeNullUndefined } from './utils';
@@ -23,6 +27,7 @@ export class GnpisService {
static URGI_SOURCE_URI = 'https://urgi.versailles.inra.fr';
sourceByURI$ = new ReplaySubject<Record<string, DataDiscoverySource>>(1);
+ sources$ = new ReplaySubject<DataDiscoverySource[]>(1);
constructor(private http: HttpClient) {
// Get data sources
@@ -34,6 +39,7 @@ export class GnpisService {
for (const dataSource of dataSources) {
sourceByURI[dataSource['@id']] = dataSource;
}
+ this.sources$.next(dataSources);
this.sourceByURI$.next(sourceByURI);
});
}
@@ -66,12 +72,17 @@ export class GnpisService {
search(
criteria: DataDiscoveryCriteria
): Observable<DataDiscoveryResults> {
- return zip(
+ return this.mapSources( zip(
// Get source by URI
this.sourceByURI$,
// Get documents by criteria
this.http.post<any>(`${BASE_URL}/datadiscovery/search`, criteria)
- ).pipe(map(([sourceByURI, response]) => {
+ ));
+ }
+
+
+ mapSources(httpResponse: Observable<any>) {
+ return httpResponse.pipe(map(([sourceByURI, response]) => {
// Extract BrAPI documents from result
const documents = response.result.data;
@@ -82,22 +93,16 @@ export class GnpisService {
return document;
});
if (response.facets) {
- response.facets = response.facets.map((facet: DataDiscoveryFacet) => {
- facet.terms = facet.terms.map(term => {
- if (facet.field === 'sources') {
- term.label = sourceByURI[term.term]['schema:name'];
- } else {
- term.label = term.term;
- }
- return term;
- });
- return facet;
- });
+ this.getSourcesName(sourceByURI, response);
}
return response;
}));
+
}
+
+
+
/**
* Get germplasm by ID or PUI with data source (present in JSON-LD response)
* @param params containing Id or PUI
@@ -112,6 +117,17 @@ export class GnpisService {
);
}
+ germplasmSearch(criteria: GermplasmCriteria): Observable<GermplasmResults<Germplasm>> {
+
+ return this.mapSources(zip(
+ // Get source by URI
+ this.sourceByURI$,
+ // Get documents by criteria
+ this.http.post<GermplasmResults<Germplasm>>(`${BASE_URL}/germplasm/search`,
+ criteria,
+ { headers: { 'Accept': 'application/ld+json,application/json' } })));
+ }
+
/**
* Get data source by URI
*/
@@ -123,4 +139,30 @@ export class GnpisService {
return this.http.get<XrefResponse>(`${BASE_URL}/xref/documentbyfulltextid?linkedRessourcesID=${xrefId}`);
}
+ plantMaterialExport(criteria: GermplasmSearchCriteria): Observable<any> {
+ const requestOptions: Object = {
+ /* other options here */
+ responseType: 'text'
+ };
+ return this.http.post<any>(
+ `${BASE_URL}/germplasm/germplasm-list-csv`,
+ criteria,
+ requestOptions
+ );
+ }
+
+ getSourcesName(sourceByURI, response) {
+ response.facets = response.facets.map((facet: DataDiscoveryFacet) => {
+ facet.terms = facet.terms.map(term => {
+ if (facet.field === 'sources') {
+ term.label = sourceByURI[term.term]['schema:name'];
+ } else {
+ term.label = term.term;
+ }
+ return term;
+ });
+ return facet;
+ });
+ }
+
}
diff --git a/frontend/src/app/models/brapi.model.ts b/frontend/src/app/models/brapi.model.ts
index c758338cc3c3792cfc1e2085e5ef7ce9f0d7c85c..f8630ff08b968c324a9e842a9707c1aa9ae5c64d 100644
--- a/frontend/src/app/models/brapi.model.ts
+++ b/frontend/src/app/models/brapi.model.ts
@@ -1,4 +1,33 @@
import * as schema from './schema.org.model';
+import { DataDiscoveryFacet } from './data-discovery.model';
+
+export interface GermplasmCriteria {
+ accessionNumbers: string[];
+ germplasmDbIds: string[];
+ germplasmGenus: string[];
+ germplasmNames: string[];
+ germplasmPUIs: string[];
+ germplasmSpecies: string[];
+ page: number;
+ pageSize: number;
+}
+
+export const DEFAULT_PAGE_SIZE = 10;
+
+export class BrapiCriteriaUtils {
+ static emptyCriteria(): GermplasmCriteria {
+ return {
+ accessionNumbers: null,
+ germplasmDbIds: null,
+ germplasmGenus: null,
+ germplasmNames: null,
+ germplasmPUIs: null,
+ germplasmSpecies: null,
+ page: 0,
+ pageSize: DEFAULT_PAGE_SIZE
+ };
+ }
+}
export interface BrapiMetaData {
pagination: {
@@ -17,6 +46,12 @@ export interface BrapiResult<T> {
result: T;
}
+export interface GermplasmResult<T> {
+ metadata: BrapiMetaData;
+ facets: DataDiscoveryFacet[];
+ result: T;
+}
+
/**
* BrAPI list response
*/
@@ -24,6 +59,10 @@ export type BrapiResults<T> = BrapiResult<{
data: T[];
}>;
+export type GermplasmResults<T> = GermplasmResult<{
+ data: T[];
+}>;
+
interface BrapiHasDocumentationURL {
documentationURL?: string;
@@ -84,7 +123,7 @@ export interface BrapiAdditionalInfo {
}
-export interface BrapiObservationVariable extends BrapiHasDocumentationURL {
+export interface BrapiObservationVariable extends BrapiHasDocumentationURL {
observationVariableDbId: string;
contextOfUse: string[];
institution: string;
@@ -192,7 +231,7 @@ export interface BrapiGermplasmAttributes {
data: BrapiAttributeData[];
}
-export interface BrapiAttributeData {
+export interface BrapiAttributeData {
attributeDbId: string;
attributeName: string;
attributeCode: string;
diff --git a/frontend/src/app/models/data-discovery.model.ts b/frontend/src/app/models/data-discovery.model.ts
index d8682915c745547d9387218e39ed2420aad53e92..63958fcc13fe2cd1d6719239767fe13e0803baa6 100644
--- a/frontend/src/app/models/data-discovery.model.ts
+++ b/frontend/src/app/models/data-discovery.model.ts
@@ -2,6 +2,7 @@ import { BrapiResults } from './brapi.model';
import { Params } from '@angular/router';
import { asArray } from '../utils';
import * as schema from './schema.org.model';
+import { GermplasmSearchCriteria } from './gnpis.model';
export const MAX_RESULTS = 10000;
@@ -30,7 +31,7 @@ export class DataDiscoveryCriteriaUtils {
return {
accessions: null,
crops: null,
- facetFields: ['sources', 'types'],
+ facetFields: ['types', 'sources'],
germplasmLists: null,
observationVariableIds: null,
topSelectedTraitOntologyIds: null,
@@ -42,6 +43,54 @@ export class DataDiscoveryCriteriaUtils {
};
}
+ static emptyGermplasmSearchCriteria(): GermplasmSearchCriteria {
+ return {
+ accessionNumbers: null,
+ germplasmDbIds: null,
+ germplasmGenus: null,
+ germplasmNames: null,
+ germplasmPUIs: null,
+ germplasmSpecies: null,
+ holdingInstitute: null,
+ synonyms: null,
+ panel: null,
+ collection: null,
+ population: null,
+ commonCropName: null,
+ species: null,
+ genusSpecies: null,
+ subtaxa: null,
+ genusSpeciesSubtaxa: null,
+ taxonSynonyms: null,
+ taxonCommonNames: null,
+ biologicalStatus: null,
+ geneticNature: null,
+ sources: null,
+ types: ['Germplasm'],
+
+ facetFields: ['sources', 'holdingInstitute',
+ 'biologicalStatus', 'geneticNature', 'country'],
+ sortBy: null,
+ sortOrder: null,
+ page: 0,
+ pageSize: 10,
+ };
+ }
+
+ static checkCriteriaIsEmpty(criteria): boolean {
+ for (const field of Object.keys(criteria)) {
+ if (field === 'facetFields') {
+ // Ignore facet fields criteria
+ continue;
+ }
+ if (criteria[field] && criteria[field].length) {
+ return false;
+ }
+
+ }
+ return true;
+ }
+
static fromQueryParams(queryParams: Params): DataDiscoveryCriteria {
return {
...DataDiscoveryCriteriaUtils.emptyCriteria(),
@@ -73,6 +122,15 @@ export class DataDiscoveryCriteriaUtils {
page: newCriteria.page + 1
};
}
+
+ static updatePagination(previousPagination, { currentPage, pageSize, totalCount, totalPages }) {
+ previousPagination.currentPage = currentPage;
+ previousPagination.pageSize = pageSize;
+ previousPagination.totalPages = totalPages;
+ previousPagination.startResult = pageSize * currentPage + 1;
+ previousPagination.endResult = previousPagination.startResult + pageSize - 1;
+ previousPagination.totalResult = totalCount;
+ }
}
export type DataDiscoverySource = schema.DataCatalog;
diff --git a/frontend/src/app/models/gnpis.model.ts b/frontend/src/app/models/gnpis.model.ts
index edee6ddf7211609bc3009ecf1f15df4f404590da..93760346383a76dcc5e9d8ee4e46cd4a8dd40d01 100644
--- a/frontend/src/app/models/gnpis.model.ts
+++ b/frontend/src/app/models/gnpis.model.ts
@@ -1,5 +1,39 @@
import { BrapiDonor, BrapiGermplasm } from './brapi.model';
+
+export interface GermplasmSearchCriteria {
+ accessionNumbers: string[];
+ germplasmDbIds: string[];
+ germplasmGenus: string[];
+ germplasmNames: string[];
+ germplasmPUIs: string[];
+ germplasmSpecies: string[];
+
+ synonyms: string[];
+ panel: string[];
+ collection: string[];
+ population: string[];
+ commonCropName: string[];
+ species: string[];
+ genusSpecies: string[];
+ subtaxa: string[];
+ genusSpeciesSubtaxa: string[];
+ taxonSynonyms: string[];
+ taxonCommonNames: string[];
+ biologicalStatus: string[];
+ geneticNature: string[];
+ holdingInstitute: string[];
+ sources: string[];
+ types: string[];
+
+ facetFields: string[];
+ sortBy: string;
+ sortOrder: string;
+ page: number;
+ pageSize: number;
+}
+
+
export interface Germplasm extends BrapiGermplasm {
genusSpecies: string;
genusSpeciesSubtaxa: string;
@@ -23,6 +57,7 @@ export interface Germplasm extends BrapiGermplasm {
panel: GermplasmSet[];
collection: GermplasmSet[];
population: GermplasmSet[];
+ 'schema:includedInDataCatalog': any;
}
export interface Site {
diff --git a/frontend/src/app/result-page/facets/facets.component.html b/frontend/src/app/result-page/facets/facets.component.html
deleted file mode 100644
index 88998bf31da45a7b741d183c64def74912655b29..0000000000000000000000000000000000000000
--- a/frontend/src/app/result-page/facets/facets.component.html
+++ /dev/null
@@ -1,18 +0,0 @@
-<div class="card mb-1">
- <div class="card-body">
- <h3 class="card-title">{{ facet.field | titlecase }}</h3>
-
- <form [formGroup]="checkBoxes" class="card-text">
- <div class="form-check" *ngFor="let term of facet.terms">
- <input class="form-check-input"
- type="checkbox"
- id="{{ term.term }}"
- [formControlName]="term.term"
- />
- <label class="form-check-label" for="{{ term.term }}">
- {{ term.label }} ({{ term.count | number }})
- </label>
- </div>
- </form>
- </div>
-</div>
diff --git a/frontend/src/app/result-page/facets/facets.component.scss b/frontend/src/app/result-page/facets/facets.component.scss
deleted file mode 100644
index b5e79bd7d6ac1690ef30fcadef7945dc2a70b696..0000000000000000000000000000000000000000
--- a/frontend/src/app/result-page/facets/facets.component.scss
+++ /dev/null
@@ -1,9 +0,0 @@
-
-
-.card * {
- font-size: 0.98em;
-}
-
-.card h3 {
- font-weight: bold;
-}
diff --git a/frontend/src/app/result-page/facets/facets.component.spec.ts b/frontend/src/app/result-page/facets/facets.component.spec.ts
deleted file mode 100644
index b00fa981b5676c9a48bb15705c682a9cfeca32c4..0000000000000000000000000000000000000000
--- a/frontend/src/app/result-page/facets/facets.component.spec.ts
+++ /dev/null
@@ -1,114 +0,0 @@
-import { TestBed } from '@angular/core/testing';
-
-import { FacetsComponent } from './facets.component';
-import { ReactiveFormsModule } from '@angular/forms';
-import { ComponentTester, speculoosMatchers } from 'ngx-speculoos';
-import { DataDiscoveryCriteria, DataDiscoveryCriteriaUtils, DataDiscoveryFacet } from '../../models/data-discovery.model';
-import { BehaviorSubject } from 'rxjs';
-import { take } from 'rxjs/operators';
-
-describe('FacetsComponent', () => {
-
- class FacetsComponentTester extends ComponentTester<FacetsComponent> {
- constructor() {
- super(FacetsComponent);
- }
-
- get title() {
- return this.element('h3.card-title');
- }
-
- get terms() {
- return this.elements('label');
- }
-
- get checkboxes() {
- return this.elements('input');
- }
-
- }
-
- const exampleFacet: DataDiscoveryFacet = {
- field: 'sources',
- terms: [
- {
- term: 'source 1',
- label: 'SOURCE 1',
- count: 10
- }, {
- term: 'source 2',
- label: 'SOURCE 2',
- count: 20
- }
- ]
- };
-
- beforeEach(() => TestBed.configureTestingModule({
- imports: [ReactiveFormsModule],
- declarations: [FacetsComponent]
- }));
-
- beforeEach(() => jasmine.addMatchers(speculoosMatchers));
-
- it('should display facet', () => {
- const tester = new FacetsComponentTester();
-
- const component = tester.componentInstance;
- component.facet = exampleFacet;
- component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
- tester.detectChanges();
-
- expect(tester.title).toContainText('Sources');
-
- expect(tester.terms[0]).toContainText('SOURCE 1 (10)');
- expect(tester.terms[0].attr('for')).toBe('source 1');
- expect(tester.checkboxes[0].attr('id')).toBe('source 1');
-
- expect(tester.terms[1]).toContainText('SOURCE 2 (20)');
- expect(tester.terms[1].attr('for')).toBe('source 2');
- expect(tester.checkboxes[1].attr('id')).toBe('source 2');
- });
-
- it('should initialize with criteria', () => {
- const tester = new FacetsComponentTester();
-
- const component = tester.componentInstance;
- component.facet = exampleFacet;
-
- const criteria = {
- ...DataDiscoveryCriteriaUtils.emptyCriteria(),
- sources: ['source 2']
- };
- component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(criteria);
-
- tester.detectChanges();
-
-
- expect(tester.checkboxes[0].nativeElement['checked']).toBe(false);
- expect(tester.checkboxes[1].nativeElement['checked']).toBe(true);
- });
-
- it('should change criteria on checkbox selection change', () => {
- const tester = new FacetsComponentTester();
-
- const component = tester.componentInstance;
- component.facet = exampleFacet;
- component.criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
- tester.detectChanges();
-
- // No sources selected in criteria
- component.criteria$.pipe(take(1)).subscribe(criteria => {
- expect(criteria.sources).toEqual(null);
- });
-
- // Click on checkbox
- // @ts-ignore
- tester.checkboxes[1].nativeElement.click();
- expect(tester.checkboxes[1].nativeElement['checked']).toBe(true);
-
- // Source 2 selected
- component.criteria$.subscribe(criteria => {
- expect(criteria.sources).toEqual(['source 2']);
- });
- });
-});
diff --git a/frontend/src/app/result-page/facets/facets.component.ts b/frontend/src/app/result-page/facets/facets.component.ts
deleted file mode 100644
index d78745ed208c44e7324567907ca11f863d8cacc9..0000000000000000000000000000000000000000
--- a/frontend/src/app/result-page/facets/facets.component.ts
+++ /dev/null
@@ -1,52 +0,0 @@
-import { Component, Input, OnInit } from '@angular/core';
-import { DataDiscoveryCriteria, DataDiscoveryFacet } from '../../models/data-discovery.model';
-import { FormControl, FormGroup } from '@angular/forms';
-import { BehaviorSubject } from 'rxjs';
-import { filter } from 'rxjs/operators';
-
-@Component({
- selector: 'faidare-facets',
- templateUrl: './facets.component.html',
- styleUrls: ['./facets.component.scss']
-})
-export class FacetsComponent implements OnInit {
-
- @Input() facet: DataDiscoveryFacet;
- @Input() criteria$: BehaviorSubject<DataDiscoveryCriteria>;
-
-
- localCriteria: DataDiscoveryCriteria;
- checkBoxes: FormGroup = new FormGroup({});
-
- constructor() {
- }
-
- ngOnInit(): void {
- for (const term of this.facet.terms) {
- const control = new FormControl(false);
- this.checkBoxes.addControl(term.term, control);
- }
-
- this.criteria$.pipe(filter(c => c !== this.localCriteria))
- .subscribe(criteria => {
- this.localCriteria = criteria;
- const selectedTerms = criteria[this.facet.field] || [];
-
- for (const [key, control] of Object.entries(this.checkBoxes.controls)) {
- const isSelected = selectedTerms.indexOf(key) >= 0;
- control.setValue(isSelected, { emitEvent: false });
- }
- });
-
- this.checkBoxes.valueChanges.subscribe(values => {
- const selectedTerms = Object.keys(values).filter(key => values[key]);
- this.localCriteria = {
- ...this.localCriteria,
- [this.facet.field]: selectedTerms
- };
- this.criteria$.next(this.localCriteria);
- });
- }
-
-
-}
diff --git a/frontend/src/app/result-page/result-page.component.html b/frontend/src/app/result-page/result-page.component.html
index 234ba4a45b64bdc3f04f441581975e60165b4d8e..265a7e381762287c121d4b281eed9b6b52c34b84 100644
--- a/frontend/src/app/result-page/result-page.component.html
+++ b/frontend/src/app/result-page/result-page.component.html
@@ -1,107 +1,141 @@
<h3 align="center" class="mb-4">{{ appTitle }}</h3>
-<div class="row justify-content-end">
- <!-- Column for form -->
- <div class="col-lg-9">
- <!-- Reset all button -->
- <div class="text-right reset-all-div">
- <button type="button" class="btn btn-sm btn-danger mt-1" (click)="resetAll()">
- Reset all
- </button>
- </div>
- <!-- Form -->
- <faidare-form
- #form
- [criteria$]="criteria$">
- </faidare-form>
- </div>
+<!-- Reset all button -->
+<div class="text-right">
+ <button type="button" class="btn btn-sm btn-danger mt-1"
+ (click)="resetAll()">
+ Reset all
+ </button>
+</div>
+
+<div class="row">
<!-- Column for facets -->
- <div class="col-lg-3 order-lg-first">
- <div class="row">
- <faidare-facets
- class="col-12 col-lg-12 col-sm-6"
- *ngFor="let facet of facets"
- [criteria$]="criteria$"
- [facet]="facet">
- </faidare-facets>
- </div>
+ <div class="col-3">
+ <faidare-facets
+ [criteria$]="criteria$"
+ [facets]="facets"
+ [displayGermplasmResult$]="displayGermplasmResult$"
+ [germplasmSearchCriteria$]="germplasmSearchCriteria$">
+ </faidare-facets>
+ <faidare-facets
+ *ngIf="displayGermplasmResult && germplasmfacets.length"
+ [facets]="germplasmfacets"
+ [criteria$]="criteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$"
+ [germplasmSearchCriteria$]="germplasmSearchCriteria$">
+ </faidare-facets>
</div>
- <!-- Column for result -->
- <div class="col-lg-9">
- <!-- Loading spinner-->
- <div class="text-center">
- <faidare-loading-spinner [loading]="loading"></faidare-loading-spinner>
- </div>
- <!-- No criteria selected -->
- <div *ngIf="criteriaIsEmpty && !loading" class="text-center text-muted mt-5 bolder">
- Select criteria to get results.
- </div>
+ <!-- Column for form and results -->
+ <div class="col-9">
+ <div class="row">
+
+ <div class="col-12">
+ <!-- Form -->
+ <faidare-form
+ #form
+ [criteria$]="criteria$"
+ [displayGermplasmResult$]="displayGermplasmResult$">
+ </faidare-form>
+ </div>
+
+ <div class="col-12">
+ <!-- Loading spinner-->
+ <div class="text-center">
+ <faidare-loading-spinner
+ [loading]="loading"></faidare-loading-spinner>
+ </div>
+
+ <!-- No criteria selected -->
+ <div *ngIf="criteriaIsEmpty && !loading"
+ class="text-center text-muted mt-5 bolder">
+ Select criteria to get results.
+ </div>
- <!-- Display results when possible -->
- <ng-container *ngIf="documents.length && !criteriaIsEmpty && !loading">
- <!-- Pagination status -->
- <div class="container">
- <div class="row result align-content-center">
+
+ <!-- Display results when possible -->
+ <ng-container
+ *ngIf="documents.length && !criteriaIsEmpty && !loading && !displayGermplasmResult">
+ <!-- Pagination status -->
+ <div class="container">
+ <div class="row result align-content-center">
<span class="col-4 mt-2 bolder">
Results:
</span>
- <span *ngIf="pagination.totalResult" class="col-8 text-right small text-muted mt-3">
- From {{ pagination.startResult | number }} to {{ pagination.endResult | number }}
- over {{ pagination.totalResult | number }} documents
+ <span *ngIf="pagination.totalResult"
+ class="col-8 text-right small text-muted mt-3">
+ From {{ pagination.startResult | number }}
+ to {{ pagination.endResult | number }}
+ over {{ pagination.totalResult | number }} documents
<span *ngIf="pagination.totalResult > pagination.maxResults">
(limited to {{ pagination.maxResults | number }})
</span>
</span>
- </div>
- </div>
+ </div>
+ </div>
- <!--Top page navigator-->
- <div class="d-flex justify-content-center mt-3" *ngIf="pagination.totalPages > 1">
- <!-- we add 1 to the page because ngb-pagination is 1 based -->
- <ngb-pagination [page]="pagination.currentPage + 1"
- (pageChange)="changePage($event)"
- [collectionSize]="resultCount()"
- [pageSize]="pagination.pageSize"
- [maxSize]="5"
- [boundaryLinks]="true"
- [ellipses]="false"
- size="sm">
- </ngb-pagination>
- </div>
+ <!--Top page navigator-->
+ <div class="d-flex justify-content-center mt-3"
+ *ngIf="pagination.totalPages > 1">
+ <!-- we add 1 to the page because ngb-pagination is 1 based -->
+ <ngb-pagination [page]="pagination.currentPage + 1"
+ (pageChange)="changePage($event)"
+ [collectionSize]="resultCount()"
+ [pageSize]="pagination.pageSize"
+ [maxSize]="5"
+ [boundaryLinks]="true"
+ [ellipses]="false"
+ size="sm">
+ </ngb-pagination>
+ </div>
- <!-- Result document -->
- <faidare-document
- *ngFor="let document of documents"
- [document]="document">
- </faidare-document>
-
- <!-- Pagination -->
- <!--Bottom page navigator-->
- <div class="d-flex justify-content-center mt-4 mb-5" *ngIf="pagination.totalPages > 1">
- <!-- we add 1 to the page because ngb-pagination is 1 based -->
- <ngb-pagination [page]="pagination.currentPage + 1"
- (pageChange)="changePage($event)"
- [collectionSize]="resultCount()"
- [pageSize]="pagination.pageSize"
- [maxSize]="5"
- [boundaryLinks]="true"
- [ellipses]="false"
- size="sm">
- </ngb-pagination>
- </div>
- </ng-container>
+ <!-- Result document -->
+ <faidare-document
+ *ngFor="let document of documents"
+ [document]="document">
+ </faidare-document>
+
+ <!-- Pagination -->
+ <!--Bottom page navigator-->
+ <div class="d-flex justify-content-center mt-4 mb-5"
+ *ngIf="pagination.totalPages > 1">
+ <!-- we add 1 to the page because ngb-pagination is 1 based -->
+ <ngb-pagination [page]="pagination.currentPage + 1"
+ (pageChange)="changePage($event)"
+ [collectionSize]="resultCount()"
+ [pageSize]="pagination.pageSize"
+ [maxSize]="5"
+ [boundaryLinks]="true"
+ [ellipses]="false"
+ size="sm">
+ </ngb-pagination>
+ </div>
+ </ng-container>
+
+ <!-- Display the table of the germplasm-result-page -->
+ <ng-container *ngIf="displayGermplasmResult">
+ <faidare-germplasm-result-page
+ [criteriaFromForm$]=criteria$
+ [germplasmSearchCriteria$]="germplasmSearchCriteria$"
+ [germplasmFacets$]="germplasmfacets$">
+ </faidare-germplasm-result-page>
+ </ng-container>
+
+ <!-- Else we display a simple message when no result found -->
+ <div *ngIf="pagination.totalResult == 0 && !loading
+ && (!criteriaIsEmpty && !displayGermplasmResult)"
+ id="no-results" class="text-center">
+ <div class="no-result-icon">
+ <span class="fa fa-meh-o"></span>
+ </div>
+ No results.
+ </div>
- <!-- Else we display a simple message when no result found -->
- <div *ngIf="pagination.totalResult == 0 && !loading && !criteriaIsEmpty" id="no-results" class="text-center">
- <div class="no-result-icon">
- <span class="fa fa-meh-o"></span>
</div>
- No results.
</div>
</div>
</div>
diff --git a/frontend/src/app/result-page/result-page.component.scss b/frontend/src/app/result-page/result-page.component.scss
index 334361d5d04fc9cce7ed3d02d40c62fde75de967..7e5e103787017f47102f6aa78d82359266ee9f52 100644
--- a/frontend/src/app/result-page/result-page.component.scss
+++ b/frontend/src/app/result-page/result-page.component.scss
@@ -15,10 +15,6 @@
font-weight: bold;
}
-.reset-all-div {
- height: 0;
-}
-
// Loading spinner
.lds-spinner {
$scale: 0.75;
diff --git a/frontend/src/app/result-page/result-page.component.ts b/frontend/src/app/result-page/result-page.component.ts
index 9f9d7dbd66ecdff5ee8ba7c2d5a598898a35220a..1005b86317455cb1d8d825bbd4bffb194da12416 100644
--- a/frontend/src/app/result-page/result-page.component.ts
+++ b/frontend/src/app/result-page/result-page.component.ts
@@ -1,5 +1,5 @@
import { Component, OnInit, ViewChild } from '@angular/core';
-import { ActivatedRoute, Router } from '@angular/router';
+import { ActivatedRoute, NavigationStart, Router } from '@angular/router';
import {
DataDiscoveryCriteria,
DataDiscoveryCriteriaUtils,
@@ -13,6 +13,7 @@ import { GnpisService } from '../gnpis.service';
import { filter } from 'rxjs/operators';
import { FormComponent } from '../form/form.component';
import { environment } from '../../environments/environment';
+import { GermplasmSearchCriteria } from '../models/gnpis.model';
@Component({
@@ -28,6 +29,9 @@ export class ResultPageComponent implements OnInit {
criteria$ = new BehaviorSubject<DataDiscoveryCriteria>(DataDiscoveryCriteriaUtils.emptyCriteria());
documents: DataDiscoveryDocument[] = [];
facets: DataDiscoveryFacet[] = [];
+ germplasmSearchCriteria$ = new BehaviorSubject<GermplasmSearchCriteria>(DataDiscoveryCriteriaUtils.emptyGermplasmSearchCriteria());
+ germplasmfacets$ = new BehaviorSubject<DataDiscoveryFacet[]>([]);
+ germplasmfacets: DataDiscoveryFacet[] = [];
pagination = {
startResult: 1,
endResult: DEFAULT_PAGE_SIZE,
@@ -39,6 +43,8 @@ export class ResultPageComponent implements OnInit {
};
criteriaIsEmpty = true;
+ displayGermplasmResult$ = new BehaviorSubject(false);
+ displayGermplasmResult = false;
loading = true;
constructor(private route: ActivatedRoute,
@@ -54,46 +60,35 @@ export class ResultPageComponent implements OnInit {
.subscribe(({ metadata, result, facets }) => {
this.loading = false;
this.documents = result.data;
- this.updatePagination(metadata.pagination);
+ DataDiscoveryCriteriaUtils.updatePagination(this.pagination, metadata.pagination);
this.facets = facets;
});
}
- private updatePagination({ currentPage, pageSize, totalCount, totalPages }) {
- this.pagination.currentPage = currentPage;
- this.pagination.pageSize = pageSize;
- this.pagination.totalPages = totalPages;
- this.pagination.startResult = pageSize * currentPage + 1;
- this.pagination.endResult = this.pagination.startResult + pageSize - 1;
- this.pagination.totalResult = totalCount;
- }
-
ngOnInit(): void {
const queryParams = this.route.snapshot.queryParams;
+ this.router.events.subscribe((event) => {
+ if (event instanceof NavigationStart) {
+ this.displayGermplasmResult = false;
+ }
+ });
// Parse criteria from URL query params
const initialCriteria = DataDiscoveryCriteriaUtils.fromQueryParams(queryParams);
this.criteria$.next(initialCriteria);
- this.criteria$.subscribe(criteria => {
- this.criteriaIsEmpty = true;
- for (const field of Object.keys(criteria)) {
- if (field === 'facetFields') {
- // Ignore facet fields criteria
- continue;
- }
+ this.criteriaIsEmpty = DataDiscoveryCriteriaUtils.checkCriteriaIsEmpty(initialCriteria);
- if (criteria[field] && criteria[field].length) {
- this.criteriaIsEmpty = false;
- break;
- }
- }
- });
this.form.traitWidgetInitialized.subscribe(() => {
this.fetchDocumentsAndFacets();
});
+ this.displayGermplasmResult$.subscribe(value => {
+ this.displayGermplasmResult = value;
+ });
+ this.displayGermplasmResult$.next(this.displayGermplasmResult);
+
this.criteria$
.pipe(filter(c => c !== initialCriteria))
.subscribe(newCriteria => {
@@ -101,13 +96,20 @@ export class ResultPageComponent implements OnInit {
newCriteria.page = 0;
// Fetch documents and facets
this.fetchDocumentsAndFacets();
-
- // Update URL query params
- this.router.navigate(['.'], {
- relativeTo: this.route,
- queryParams: DataDiscoveryCriteriaUtils.toQueryParams(newCriteria)
- });
+ this.criteriaIsEmpty = DataDiscoveryCriteriaUtils.checkCriteriaIsEmpty(newCriteria);
+
+ if (!this.displayGermplasmResult) {
+ // Update URL query params
+ this.router.navigate(['.'], {
+ relativeTo: this.route,
+ queryParams: DataDiscoveryCriteriaUtils.toQueryParams(newCriteria)
+ });
+ }
});
+
+ this.germplasmfacets$.subscribe(facets => {
+ this.germplasmfacets = facets;
+ });
}
resultCount() {
@@ -124,6 +126,7 @@ export class ResultPageComponent implements OnInit {
// Use of empty param to force re-parse of URL in ngOnInit
queryParams: { empty: [] }
});
+ this.displayGermplasmResult$.next(false);
this.criteria$.next(DataDiscoveryCriteriaUtils.emptyCriteria());
}
diff --git a/frontend/src/assets/faidare/images/question-mark.png b/frontend/src/assets/faidare/images/question-mark.png
new file mode 100644
index 0000000000000000000000000000000000000000..87fbdf4294ddba32291fdcae056a7c0f9cef793c
Binary files /dev/null and b/frontend/src/assets/faidare/images/question-mark.png differ
diff --git a/frontend/src/index.html b/frontend/src/index.html
index de174438eef6b693ddff3f9eeb7d06c846f1dedb..4f9431d72739dbc532c81dd2f49e81732cd1688b 100644
--- a/frontend/src/index.html
+++ b/frontend/src/index.html
@@ -7,6 +7,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="icon" type="image/x-icon" href="assets/favicon.ico">
+ <script src="https://code.iconify.design/1/1.0.7/iconify.min.js"></script>
</head>
<body>
<faidare-root></faidare-root>
diff --git a/frontend/src/styles.scss b/frontend/src/styles.scss
index a86efa94111eb75fb5fb8f8beaa1e2dcb28b1a0d..a0804b179bb02466f0d46db3ceac691b7cbcc46c 100644
--- a/frontend/src/styles.scss
+++ b/frontend/src/styles.scss
@@ -61,21 +61,21 @@ $fa-font-path: '~font-awesome/fonts';
.popover {
width: 100%;
- max-width:500px;
+ max-width: 500px;
}
-.mt-custom{
+.mt-custom {
margin-top: 75px;
}
-h1{
+h1 {
border-bottom: solid;
font-weight: bold;
color: #0f6191;
margin-bottom: 20px;
}
-h2{
+h2 {
border-bottom: solid;
color: #0f6191;
margin-bottom: 16px;
@@ -86,7 +86,7 @@ h3 {
color: #0f6191;
}
-blockquote{
+blockquote {
border-left-style: solid;
border-left-width: 3px;
color: grey;
diff --git a/frontend/src/tslint.json b/frontend/src/tslint.json
index 97be2aaf26914218cc66d277eb23e054d01e66b9..f1b7fa4d97ff90740e26ab98216f16247f26ed77 100644
--- a/frontend/src/tslint.json
+++ b/frontend/src/tslint.json
@@ -15,7 +15,7 @@
],
"template-cyclomatic-complexity": [
true,
- 11
+ 12
]
}
}