diff --git a/.secrets.baseline b/.secrets.baseline
index d3ef77762f5b265ef889ac52eb82c0c51f4bb108..98da8f09266a811eeab2c2b78d06eb1d5d8d197d 100644
--- a/.secrets.baseline
+++ b/.secrets.baseline
@@ -2552,6 +2552,22 @@
"type": "Base64 High Entropy String"
}
],
+ "gradle.properties": [
+ {
+ "hashed_secret": "93220646d2e029229894cf6f9e5d170c8fc59dbb",
+ "is_secret": true,
+ "is_verified": false,
+ "line_number": 5,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "93220646d2e029229894cf6f9e5d170c8fc59dbb",
+ "is_secret": true,
+ "is_verified": false,
+ "line_number": 5,
+ "type": "Hex High Entropy String"
+ }
+ ],
"scripts/harvest.sh": [
{
"hashed_secret": "9b4ea0964706f977148ec989e7373d9622613547",
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/XRefDocumentController.java b/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/XRefDocumentController.java
index 14b8f046089a6df7d267700a8c00f784c94081b0..09c5c25d93cce30a19f6ddc52586ca990c60863c 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/XRefDocumentController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/XRefDocumentController.java
@@ -31,12 +31,12 @@ public class XRefDocumentController {
@ApiOperation("Find xref documents")
@GetMapping(value = "/faidare/v1/xref/documentbyfulltextid")
public PaginatedList<XRefDocumentVO> documentByFullTextId(
- @RequestParam(required = false, value = "entry_type") String entryType,
- @RequestParam(required = false) List<String> linkedRessourcesID
+ @RequestParam(required = false, value = "entryType") String entryType,
+ @RequestParam(required = false) List<String> linkedResourcesID
) {
XRefDocumentSearchCriteria criteria = new XRefDocumentSearchCriteria();
criteria.setEntryType(entryType);
- criteria.setLinkedRessourcesID(linkedRessourcesID);
+ criteria.setLinkedResourcesID(linkedResourcesID);
return repository.find(criteria);
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/DocumentFields.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/DocumentFields.java
index af7420a01082796fdd1d467fdec2cca8d3efdccf..5a43e4d68a5522e54a328ae8fae803297da68eef 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/DocumentFields.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/DocumentFields.java
@@ -5,7 +5,7 @@ package fr.inra.urgi.faidare.domain.xref;
*/
public enum DocumentFields {
- ENTRY_TYPE("entry_type"), LINKEDRESSOURCESID("linkedRessourcesID");
+ ENTRY_TYPE("entryType"), LINKED_RESOURCES_ID("linkedResourcesID");
private String field;
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentSearchCriteria.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentSearchCriteria.java
index 7ca7b26afe0f212fa6c997315c92214409f74b88..44c426279fca61d852c183b81bf52d8974215bdb 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentSearchCriteria.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentSearchCriteria.java
@@ -12,11 +12,11 @@ import java.util.List;
@CriteriaForDocument(XRefDocumentVO.class)
public class XRefDocumentSearchCriteria extends PaginationCriteriaImpl {
- @DocumentPath("entry_type")
+ @DocumentPath("entryType")
private String entryType;
- @DocumentPath("linkedRessourcesID")
- private List<String> linkedRessourcesID;
+ @DocumentPath("linkedResourcesID") // pragma: allowlist secret
+ private List<String> linkedResourcesID;
public String getEntryType() {
return entryType;
@@ -26,11 +26,11 @@ public class XRefDocumentSearchCriteria extends PaginationCriteriaImpl {
this.entryType = entryType;
}
- public List<String> getLinkedRessourcesID() {
- return linkedRessourcesID;
+ public List<String> getLinkedResourcesID() {
+ return linkedResourcesID;
}
- public void setLinkedRessourcesID(List<String> linkedRessourcesID) {
- this.linkedRessourcesID = linkedRessourcesID;
+ public void setLinkedResourcesID(List<String> linkedResourcesID) {
+ this.linkedResourcesID = linkedResourcesID;
}
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentVO.java
index b6ae340faf0b51cffd5914df39958e687bd09ca5..0cc7e84fbcf7822596b938d142e8e48fc1649ed0 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentVO.java
@@ -11,23 +11,20 @@ import java.util.List;
*
* @author fphilippe
*/
-@Document(type = "transplant")
+@Document(type = "xref")
public class XRefDocumentVO {
- @JsonProperty("group_id")
+ @JsonProperty("groupId")
private String groupId;
- @JsonProperty("entry_type")
+ @JsonProperty("entryType")
private String entryType;
- @JsonProperty("database_name")
+ @JsonProperty("databaseName")
private String databaseName;
- @JsonProperty("db_id")
- private String dbId;
-
- @JsonProperty("db_version")
- private String dbVersion;
+ @JsonProperty("identifier")
+ private String identifier;
@JsonProperty("name")
private String name;
@@ -41,58 +38,7 @@ public class XRefDocumentVO {
@JsonProperty("species")
private String species;
- @JsonProperty("xref")
- private String xref;
-
- @JsonProperty("feature_type")
- private String featureType;
-
- @JsonProperty("sequence_id")
- private String sequenceId;
-
- @JsonProperty("sequence_version")
- private String sequence_version;
-
- @JsonProperty("start_position")
- private String startPosition;
-
- @JsonProperty("end_position")
- private String endPosition;
-
- @JsonProperty("map")
- private String map;
-
- @JsonProperty("map_position")
- private String mapPosition;
-
- @JsonProperty("authority")
- private String authority;
-
- @JsonProperty("trait")
- private String trait;
-
- @JsonProperty("trait_id")
- private String traitId;
-
- @JsonProperty("environment")
- private String environment;
-
- @JsonProperty("environment_id")
- private String environmentId;
-
- @JsonProperty("statistic")
- private String statistic;
-
- @JsonProperty("unit")
- private String unit;
-
- @JsonProperty("genotype")
- private String genotype;
-
- @JsonProperty("experiment_type")
- private String experimentType;
-
- private List<String> linkedRessourcesID;
+ private List<String> linkedResourcesID;
public String getGroupId() {
return groupId;
@@ -118,20 +64,12 @@ public class XRefDocumentVO {
this.databaseName = databaseName;
}
- public String getDbId() {
- return dbId;
+ public String getIdentifier() {
+ return identifier;
}
- public void setDbId(String dbId) {
- this.dbId = dbId;
- }
-
- public String getDbVersion() {
- return dbVersion;
- }
-
- public void setDbVersion(String dbVersion) {
- this.dbVersion = dbVersion;
+ public void setIdentifier(String identifier) {
+ this.identifier = identifier;
}
public String getName() {
@@ -166,148 +104,12 @@ public class XRefDocumentVO {
this.species = species;
}
- public String getXref() {
- return xref;
- }
-
- public void setXref(String xref) {
- this.xref = xref;
- }
-
- public String getFeatureType() {
- return featureType;
- }
-
- public void setFeatureType(String featureType) {
- this.featureType = featureType;
- }
-
- public String getSequenceId() {
- return sequenceId;
- }
-
- public void setSequenceId(String sequenceId) {
- this.sequenceId = sequenceId;
- }
-
- public String getSequence_version() {
- return sequence_version;
- }
-
- public void setSequence_version(String sequence_version) {
- this.sequence_version = sequence_version;
- }
-
- public String getStartPosition() {
- return startPosition;
- }
-
- public void setStartPosition(String startPosition) {
- this.startPosition = startPosition;
- }
-
- public String getEndPosition() {
- return endPosition;
- }
-
- public void setEndPosition(String endPosition) {
- this.endPosition = endPosition;
- }
-
- public String getMap() {
- return map;
- }
-
- public void setMap(String map) {
- this.map = map;
- }
-
- public String getMapPosition() {
- return mapPosition;
- }
-
- public void setMapPosition(String mapPosition) {
- this.mapPosition = mapPosition;
- }
-
- public String getAuthority() {
- return authority;
- }
-
- public void setAuthority(String authority) {
- this.authority = authority;
- }
-
- public String getTrait() {
- return trait;
- }
-
- public void setTrait(String trait) {
- this.trait = trait;
- }
-
- public String getTraitId() {
- return traitId;
- }
-
- public void setTraitId(String traitId) {
- this.traitId = traitId;
- }
-
- public String getEnvironment() {
- return environment;
- }
-
- public void setEnvironment(String environment) {
- this.environment = environment;
- }
-
- public String getEnvironmentId() {
- return environmentId;
- }
-
- public void setEnvironmentId(String environmentId) {
- this.environmentId = environmentId;
- }
-
- public String getStatistic() {
- return statistic;
- }
-
- public void setStatistic(String statistic) {
- this.statistic = statistic;
- }
-
- public String getUnit() {
- return unit;
- }
-
- public void setUnit(String unit) {
- this.unit = unit;
- }
-
- public String getGenotype() {
- return genotype;
- }
-
- public void setGenotype(String genotype) {
- this.genotype = genotype;
- }
-
- public String getExperimentType() {
- return experimentType;
- }
-
- public void setExperimentType(String experimentType) {
- this.experimentType = experimentType;
- }
-
- public List<String> getLinkedRessourcesID() {
- return linkedRessourcesID;
+ public List<String> getLinkedResourcesID() {
+ return linkedResourcesID;
}
- public void setLinkedRessourcesID(List<String> linkedRessourcesID) {
- this.linkedRessourcesID = linkedRessourcesID;
+ public void setLinkedResourcesID(List<String> linkedResourcesID) {
+ this.linkedResourcesID = linkedResourcesID;
}
}
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/XRefDocumentRepositoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/XRefDocumentRepositoryTest.java
index 8d488134985ba82d9197472b2b0a349873dd0343..19b8fde5434ab4106718a6da9fa863687679d364 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/XRefDocumentRepositoryTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/XRefDocumentRepositoryTest.java
@@ -61,13 +61,13 @@ class XRefDocumentRepositoryTest {
@Test
void should_Find_By_Linked_Id() {
- String id = "ID2";
- List<String> linkedRessourcesID = Collections.singletonList(id);
+ String id = "ID2";
+ List<String> linkedResourcesID = Collections.singletonList(id);
XRefDocumentSearchCriteria criteria = new XRefDocumentSearchCriteria();
- criteria.setLinkedRessourcesID(linkedRessourcesID);
+ criteria.setLinkedResourcesID(linkedResourcesID);
PaginatedList<XRefDocumentVO> documents = repository.find(criteria);
assertThat(documents).isNotNull().hasSize(2)
- .flatExtracting("linkedRessourcesID")
+ .flatExtracting("linkedResourcesID")
.contains(id);
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/urgi_xref_test-group0.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/urgi_xref_test-group0.json
index 05809a8ce030a613e8cb4cc1d2649afe33e08063..a91de2ba3d914716f9b07eec2bef2d7e549b6b36 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/urgi_xref_test-group0.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/urgi_xref_test-group0.json
@@ -1,46 +1,28 @@
[
{
- "linkedRessourcesID": [
+ "linkedResourcesID": [
"ID2"
],
- "group_id": "0",
- "entry_type": "Accession",
- "database_name": "GnpIS",
- "db_id": "ID1",
- "db_version": "ACCESSION_https://doi.org/10.15454/KFQTFL_1",
+ "groupId": "0",
+ "entryType": "Accession",
+ "databaseName": "GnpIS",
+ "identifier": "ID1",
"name": "355",
"description": "Lorem ipsum....",
"url": "https://urgi.versailles.inra.fr/gnpis-core/#accessionCard/id=aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L0tGUVRGTA==",
- "species": "Quercus petraea",
- "xref": "",
- "feature_type": "",
- "sequence_id": "",
- "sequence_version": "",
- "start_position": "",
- "end_position": "",
- "map": "",
- "map_position": "",
- "authority": "INRA-UMR1202-BIOGECO (Biodiversité Gènes et Communauté)",
- "trait": "",
- "trait_id": "",
- "environment": "",
- "environment_id": "",
- "statistic": "",
- "unit": "",
- "genotype": "",
- "experiment_type": ""
+ "species": "Quercus petraea"
},
{
- "linkedRessourcesID": [
+ "linkedResourcesID": [
"ID3"
],
- "entry_type": "Site"
+ "entryType": "Site"
},
{
- "linkedRessourcesID": [
+ "linkedResourcesID": [
"ID2",
"ID3"
],
- "entry_type": "Site"
+ "entryType": "Site"
}
]
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/transplant_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/xref_mapping.json
similarity index 62%
rename from backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/transplant_mapping.json
rename to backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/xref_mapping.json
index 5aec114caea1a5828d00461d3ce98b73ce4921e0..afe94b2fccdcf593c1e6afb0e098ce5a4fbc1703 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/transplant_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/xref_mapping.json
@@ -1,11 +1,11 @@
{
- "transplant": {
+ "xref": {
"dynamic": "true",
"properties": {
- "entry_type": {
+ "entryType": {
"type": "keyword"
},
- "linkedRessourcesID": {
+ "linkedResourcesID": {
"type": "keyword"
}
}
diff --git a/frontend/src/app/gnpis.service.ts b/frontend/src/app/gnpis.service.ts
index 32e43a0ae23c348f0a8e19bd8f0881e4d1972a3e..1dc8d672c41dc9d947338222ef92cca2ad5d9d66 100644
--- a/frontend/src/app/gnpis.service.ts
+++ b/frontend/src/app/gnpis.service.ts
@@ -24,7 +24,7 @@ export const BASE_URL = 'faidare/v1';
providedIn: 'root'
})
export class GnpisService {
- static URGI_SOURCE_URI = 'https://urgi.versailles.inra.fr';
+ static URGI_SOURCE_URI = 'https://urgi.versailles.inrae.fr';
sourceByURI$ = new ReplaySubject<Record<string, DataDiscoverySource>>(1);
sources$ = new ReplaySubject<DataDiscoverySource[]>(1);
@@ -136,7 +136,7 @@ export class GnpisService {
}
xref(xrefId: string): Observable<XrefResponse> {
- return this.http.get<XrefResponse>(`${BASE_URL}/xref/documentbyfulltextid?linkedRessourcesID=${xrefId}`);
+ return this.http.get<XrefResponse>(`${BASE_URL}/xref/documentbyfulltextid?linkedResourcesID=${xrefId}`);
}
// TODO Change the service's response to return an object with the number of results and handle here if the number is over the limit
diff --git a/frontend/src/app/models/xref.model.ts b/frontend/src/app/models/xref.model.ts
index c204f787c40384df66d385d62c03eaa5bfdfa4ee..011b222b42b7b2ca79ae2cb739859f0482dfe326 100644
--- a/frontend/src/app/models/xref.model.ts
+++ b/frontend/src/app/models/xref.model.ts
@@ -2,9 +2,9 @@ export interface XrefModel {
url: string;
description: string;
- database_name: string;
- entry_type: string;
- db_version: string;
+ databaseName: string;
+ entryType: string;
+ identifier: string;
name: string;
}
diff --git a/frontend/src/app/xrefs/xrefs.component.html b/frontend/src/app/xrefs/xrefs.component.html
index a6bdbff8e7b0e37d2e6b26d0fbfe7df44369a036..e0b4ded030e60a3d7f2e697cf2c066563a0b6f21 100644
--- a/frontend/src/app/xrefs/xrefs.component.html
+++ b/frontend/src/app/xrefs/xrefs.component.html
@@ -13,8 +13,8 @@
<ng-template let-crossRef>
<tr>
<td><a [href]="crossRef.url" target="_blank">{{ crossRef.name }}</a></td>
- <td>{{ crossRef.database_name }}</td>
- <td>{{ crossRef.entry_type }}</td>
+ <td>{{ crossRef.databaseName }}</td>
+ <td>{{ crossRef.entryType }}</td>
<td>{{ crossRef.description | slice:0:120 }}...</td>
</tr>
</ng-template>
diff --git a/frontend/src/app/xrefs/xrefs.component.spec.ts b/frontend/src/app/xrefs/xrefs.component.spec.ts
index f09708ac219d67fcabfdd62ae1f5e20a92fd7f1b..470dfda4520885db2aa1b0f9aac2fd392c392eb1 100644
--- a/frontend/src/app/xrefs/xrefs.component.spec.ts
+++ b/frontend/src/app/xrefs/xrefs.component.spec.ts
@@ -35,9 +35,9 @@ describe('XrefsComponent', () => {
url: 'https://urgi.versailles.inra.fr/association/association/viewer.do#results/analysisIds=1808038',
description: 'Col-Fa-b*_MLM+Q+K is a GWASd anté paneCol-Fa-b*_MLM+Q+K is aGAS anlysis involving CC_Qualité' +
'djs dsqdsq djsqpodsjqodsqdsqkpdqpdWOLOLOLOOOOOOOsqpkdsqkdsqkdsqdsdsqdsqdsqddsqffjùsodfusjùfsfsd',
- database_name: 'GnpIS',
- entry_type: 'GWAS analysis',
- db_version: 'GWAS_ANALYSIS_1808038_1',
+ databaseName: 'GnpIS',
+ entryType: 'GWAS analysis',
+ identifier: 'GWAS_ANALYSIS_1808038_1',
name: 'Col-Fa-b*_MLM+Q+K'
}];
@@ -64,8 +64,8 @@ describe('XrefsComponent', () => {
expect(tester.cardHeader).toContainText('Cross References');
expect(tester.columns[0]).toContainText(xref[0].name);
- expect(tester.columns[1]).toContainText(xref[0].database_name);
- expect(tester.columns[2]).toContainText(xref[0].entry_type);
+ expect(tester.columns[1]).toContainText(xref[0].databaseName);
+ expect(tester.columns[2]).toContainText(xref[0].entryType);
expect(tester.columns[3].textContent.length).toBeLessThanOrEqual(124);
}));