diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index eccc3a3761667f6457fcea42c9dd1242b307347a..b4b066c01226690a8073165dde5353aabd998886 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -154,7 +154,6 @@ deploy-to-beta:
only:
refs:
- branches
- when: always
deploy-to-staging:
stage: deploy-staging
diff --git a/.secrets.baseline b/.secrets.baseline
index 41a7ef088e1359fff04c2bf6e985920a1333708b..025ba64c81a262fad3164e15701657092736e32d 100644
--- a/.secrets.baseline
+++ b/.secrets.baseline
@@ -71,6 +71,15 @@
"type": "Base64 High Entropy String"
}
],
+ ".idea/misc.xml": [
+ {
+ "hashed_secret": "a7174bf8908cdbd4fb5c32aa36b487ac0a6f1160",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 3,
+ "type": "Base64 High Entropy String"
+ }
+ ],
".idea/modules.xml": [
{
"hashed_secret": "e214f6735f68ae8b517a0fb7ea1bcf5999a96cb3",
@@ -205,6 +214,13 @@
"is_verified": false,
"line_number": 28,
"type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "91166050949814b7f312b785b4c8b6417134b547",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 105,
+ "type": "Base64 High Entropy String"
}
],
"backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/XRefDocumentController.java": [
@@ -234,6 +250,29 @@
"type": "Base64 High Entropy String"
}
],
+ "backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/FaidareGermplasmPOSTShearchCriteria.java": [
+ {
+ "hashed_secret": "084c833a01fb1d770f994aaec6a07f282e41827a",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 44,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "ce74e278f4bd61efdd35fcdce522284654db7762",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 59,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "a577a4f5f8dab94eff3f257aec15319f14a8037a",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 65,
+ "type": "Base64 High Entropy String"
+ }
+ ],
"backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/GermplasmAttributeCriteria.java": [
{
"hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
@@ -375,6 +414,22 @@
"type": "Base64 High Entropy String"
}
],
+ "backend/src/main/java/fr/inra/urgi/faidare/elasticsearch/query/impl/ESGenericQueryFactory.java": [
+ {
+ "hashed_secret": "084c833a01fb1d770f994aaec6a07f282e41827a",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 379,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "38d9070c435d5fc2e1186bf2c4ff4ddd39dc60c7",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 380,
+ "type": "Base64 High Entropy String"
+ }
+ ],
"backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java": [
{
"hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
@@ -787,6 +842,29 @@
"type": "Base64 High Entropy String"
}
],
+ "backend/src/test/resources/fr/inra/urgi/faidare/elasticsearch/query/impl/expected/query8.json": [
+ {
+ "hashed_secret": "084c833a01fb1d770f994aaec6a07f282e41827a",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 18,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "ce74e278f4bd61efdd35fcdce522284654db7762",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 79,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "a2aa9fa2bfb92c62d375348f3742857cf8190288",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 86,
+ "type": "Base64 High Entropy String"
+ }
+ ],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/datadiscovery0.json": [
{
"hashed_secret": "5b8be2878e5e88bbede6815df7f3d95af70f4c7c",
@@ -1689,6 +1767,83 @@
"type": "Base64 High Entropy String"
}
],
+ "frontend/src/app/facets/large-facets/large-facets.component.spec.ts": [
+ {
+ "hashed_secret": "83f7b470406d6cbca92e194913cdbdc5ea1b85c9",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 20,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/facets/small-facets/small-facets.component.html": [
+ {
+ "hashed_secret": "afb93ee4477b9a6582c902606428278a05da3618",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 17,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/facets/small-facets/small-facets.component.spec.ts": [
+ {
+ "hashed_secret": "81288bf2844b17e3c97050a47cb6c3babcbc92da",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 17,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/facets/small-facets/small-facets.component.ts": [
+ {
+ "hashed_secret": "3a31f524452919142fbdd3d62c8eed1512d3eb4b",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 47,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/facets/switch-button/switch-button.component.html": [
+ {
+ "hashed_secret": "3a31f524452919142fbdd3d62c8eed1512d3eb4b",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 4,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "2169579b2d46b57be73fd0962c07b1da063fd563",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 10,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "ea699843f43129a8e7e19b5f49f0a75ef04c1219",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 16,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/facets/switch-button/switch-button.component.spec.ts": [
+ {
+ "hashed_secret": "f29e999f75ca9fefd4d2120152d457e18534c23c",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 11,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/facets/switch-button/switch-button.component.ts": [
+ {
+ "hashed_secret": "383b10964f8ad1adbc337eba49c2caa3a70f8e76",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 11,
+ "type": "Base64 High Entropy String"
+ }
+ ],
"frontend/src/app/form/suggestion-field/suggestion-field.component.spec.ts": [
{
"hashed_secret": "409bbacccbf11c0ad835f1c018f011c2a28df4a2",
@@ -1828,6 +1983,54 @@
"line_number": 10,
"type": "Base64 High Entropy String"
}
+ ],
+ "frontend/src/app/germplasm-result-page/germplasm-result-page.component.spec.ts": [
+ {
+ "hashed_secret": "fe8321f237ba8e8dd0cd47ace880133faca88569",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 21,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/germplasm-result-page/germplasm-result-page.component.ts": [
+ {
+ "hashed_secret": "984a29d9e1e162a89ea0f9a74cac732fd7ae613c",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 19,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "38d9070c435d5fc2e1186bf2c4ff4ddd39dc60c7",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 52,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "ce74e278f4bd61efdd35fcdce522284654db7762",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 55,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "a577a4f5f8dab94eff3f257aec15319f14a8037a",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 56,
+ "type": "Base64 High Entropy String"
+ }
+ ],
+ "frontend/src/app/gnpis.service.spec.ts": [
+ {
+ "hashed_secret": "1d140def038cb8ed1fc9dcf662d2851a64fa277f",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 165,
+ "type": "Base64 High Entropy String"
+ }
],
"frontend/src/app/loading-spinner/loading-spinner.component.ts": [
{
@@ -2333,6 +2536,22 @@
"type": "Base64 High Entropy String"
}
],
+ "gradle.properties": [
+ {
+ "hashed_secret": "93220646d2e029229894cf6f9e5d170c8fc59dbb",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 5,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "93220646d2e029229894cf6f9e5d170c8fc59dbb",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 5,
+ "type": "Hex High Entropy String"
+ }
+ ],
"scripts/harvest.sh": [
{
"hashed_secret": "9b4ea0964706f977148ec989e7373d9622613547",
diff --git a/frontend/src/app/app-routing.module.ts b/frontend/src/app/app-routing.module.ts
index 01ef7b6a7388a041723ef7463758aacd5e1f25dc..809524fdd7281afc03409746a315b2475dfe59c1 100644
--- a/frontend/src/app/app-routing.module.ts
+++ b/frontend/src/app/app-routing.module.ts
@@ -18,7 +18,8 @@ export const routes: Routes = [
{ path: 'join', component: MarkdownPageComponent, data: { mdFile: environment.joinUsMdFile } },
{ path: 'legal', component: MarkdownPageComponent, data: { mdFile: environment.legalMentionsMdFile } },
{ path: 'help', component: MarkdownPageComponent, data: { mdFile: environment.helpMdFile } },
- { path: 'HOW-TO-JOIN.md', redirectTo: '/join' },
+ // { path: 'HOW-TO-JOIN.md', redirectTo: 'join', pathMatch: 'full' },
+ { path: 'HOW-TO-JOIN.md', component: MarkdownPageComponent, data: { mdFile: environment.joinUsMdFile } },
];
diff --git a/frontend/src/assets/faidare/ABOUT.md b/frontend/src/assets/faidare/ABOUT.md
index dd96099fbd84cf52d7941189fa8412b3b4c431cb..aabb81698b63757e60d450d95f6394a080b9904e 100644
--- a/frontend/src/assets/faidare/ABOUT.md
+++ b/frontend/src/assets/faidare/ABOUT.md
@@ -3,11 +3,11 @@
The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.
It is based on the [Breeding API (BrAPI)](https://brapi.org/) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface.
-It also provides a standard interface that can be accessed programatically through [web services](https://urgi.versailles.inra.fr/faidare/swagger-ui.html).
+It also provides a standard interface that can be accessed programatically through [web services](https://urgi.versailles.inrae.fr/faidare/swagger-ui.html).
It is an extension of the generic [Data-Discovery portal](https://forgemia.inra.fr/urgi-is/data-discovery), a web portal that allows finding any type of data across several databases through a lightweight keyword based search.
FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
-It has been developed by [INRA-URGI](http://urgi.versailles.inra.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
+It has been developed by [INRA-URGI](http://urgi.versailles.inrae.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
-If you want to join the FAIDARE federation, please read the [HOW TO JOIN guide](HOW-TO-JOIN.md) and [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
+If you want to join the FAIDARE federation, please read the [HOW TO JOIN guide](HOW-TO-JOIN.md) and [contact us](mailto:urgi-data@inrae.fr?subject=%5BFAIDARE%5D).
diff --git a/frontend/src/assets/faidare/HOW-TO-JOIN.md b/frontend/src/assets/faidare/HOW-TO-JOIN.md
index 4c9843e23b05a35cced150e06f38d1260509cb80..34ed23d27eedff6c751a085f84869b73c66ebeac 100644
--- a/frontend/src/assets/faidare/HOW-TO-JOIN.md
+++ b/frontend/src/assets/faidare/HOW-TO-JOIN.md
@@ -1,6 +1,6 @@
# How to join FAIDARE federation?
-If you want your information system to be part of the FAIDARE federation, we invite you to [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D) as soon as possible so that we can follow your progress and assist you if needed.
+If you want your information system to be part of the FAIDARE federation, we invite you to [contact us](mailto:urgi-data@inrae.fr?subject=%5BFAIDARE%5D) as soon as possible so that we can follow your progress and assist you if needed.
You will need to create a new `source` corresponding to your information system.
For this, you will have to set up your own [BrAPI](https://brapi.org/) endpoint and reference it in the sources of [Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).
@@ -52,15 +52,18 @@ Example: [URGI.json](https://github.com/elixir-europe/plant-brapi-etl-data-looku
"brapi": "https://brapi.org/"
},
"@type": "schema:DataCatalog",
- "@id": "https://urgi.versailles.inra.fr/gnpis",
+ "@id": "https://urgi.versailles.inrae.fr/gnpis",
"schema:identifier": "URGI",
"schema:name": "URGI GnpIS",
- "brapi:endpointUrl": "https://urgi.versailles.inra.fr/faidare/brapi/v1/"
+ "brapi:endpointUrl": "https://urgi.versailles.inrae.fr/faidare/brapi/v1/"
}
```
-If you have any question or need help referencing your endpoint, you can [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
+If you have any question or need help referencing your endpoint, you can [contact us](mailto:urgi-data@inrae.fr?subject=%5BFAIDARE%5D).
## Data availability & update
[Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis) extract the metadata available from all declared sources (_i.e._ BrAPI endpoint) and index it into a centralised Elasticsearch cache.
-The sources are reindexed regularly (once a month maximum) but if you want a reindexation following a major update on your side, please [inform us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
+The sources are reindexed regularly (once a month maximum) but if you want a reindexation following a major update on your side, please [inform us](mailto:urgi-data@inrae.fr?subject=%5BFAIDARE%5D).
+
+
+_Figure: data integration in FAIDARE_
diff --git a/frontend/src/assets/faidare/LEGAL-MENTIONS.md b/frontend/src/assets/faidare/LEGAL-MENTIONS.md
index 6710d8b81b583cc5d6b1b7321dbbe6c075873ced..58355695b702bf9b87dd61d42a54a2f2bde4acb8 100644
--- a/frontend/src/assets/faidare/LEGAL-MENTIONS.md
+++ b/frontend/src/assets/faidare/LEGAL-MENTIONS.md
@@ -39,8 +39,8 @@ Visitors can configure their web browsers in order to be informed of the setting
According to the European Regulation on the protection of personal data (EU Regulation 2016/679), you have the right to access, rectify, oppose and delete information about yourself.
If you wish to exercise this right and obtain information about yourself, please contact us:
-- By [email](mailto:urgi-contact@inra.fr?subject=%5BData%20Discovery%5D%20GPDR%20request)
-- Or via any other way available on our [contact form](https://urgi.versailles.inra.fr/Contact-us)
+- By [email](mailto:urgi-contact@inrae.fr?subject=%5BData%20Discovery%5D%20GPDR%20request)
+- Or via any other way available on our [contact form](https://urgi.versailles.inrae.fr/Contact-us)
## Modifications