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 733d1da9794950b689b43cd95ae465823f45778c..616a33d7e6083e9f1abc027f590b692a9a17573e 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
@@ -121,7 +121,7 @@ public class GermplasmRepositoryImpl implements GermplasmRepository {
@Override
public Iterator<GermplasmMcpdVO> scrollGermplasmMcpdsByIds(Set<String> ids, int fetchSize) {
- QueryBuilder query = QueryBuilders.idsQuery().addIds(ids.toArray(new String[0]));
+ QueryBuilder query = QueryBuilders.termsQuery("germplasmDbId", ids);
return new ESScrollIterator<>(client, requestFactory, parser, GermplasmMcpdVO.class, query, fetchSize);
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
index 84da94f897426a8b78c7bc6a3dc2c62b74d4a4c3..ec4ed09ba66253fc5662fbd9a60076c6c0153694 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
@@ -76,15 +76,17 @@ public class GermplasmController {
@GetMapping("/{germplasmId}")
public ModelAndView get(@PathVariable("germplasmId") String germplasmId) {
- // GermplasmVO germplasm = germplasmRepository.getById(germplasmId);
-
- // TODO replace this block by the above commented one
- GermplasmVO germplasm = createGermplasm();
+ GermplasmVO germplasm = germplasmRepository.getById(germplasmId);
if (germplasm == null) {
throw new NotFoundException("Germplasm with ID " + germplasmId + " not found");
}
+ // TODO remove this, which is used to display all the sections on a specific germplasm
+ if (germplasm.getGermplasmDbId().equals("dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUwxOFJJTDJ3YXlfX185Ng==")) {
+ germplasm = createGermplasm();
+ }
+
return toModelAndView(germplasm);
}
@@ -132,17 +134,19 @@ public class GermplasmController {
}
private ModelAndView toModelAndView(GermplasmVO germplasm) {
- // List<BrapiGermplasmAttributeValue> attributes = getAttributes(germplasm);
- // PedigreeVO pedigree = getPedigree(germplasm);
+ List<BrapiGermplasmAttributeValue> attributes = getAttributes(germplasm);
+ PedigreeVO pedigree = getPedigree(germplasm);
+
+ // TODO remove this
+ if (germplasm.getGermplasmDbId().equals("dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUwxOFJJTDJ3YXlfX185Ng==")) {
+ attributes = Arrays.asList(createAttribute());
+ pedigree = createPedigree();
+ }
+
// List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
// XRefDocumentSearchCriteria.forXRefId(germplasm.getGermplasmDbId())
// );
-
// TODO replace this block by the above commented one
- List<BrapiGermplasmAttributeValue> attributes = Arrays.asList(
- createAttribute()
- );
- PedigreeVO pedigree = createPedigree();
List<XRefDocumentVO> crossReferences = Arrays.asList(
createXref("foobar"),
createXref("bazbing")
@@ -224,7 +228,7 @@ public class GermplasmController {
private GermplasmVO createGermplasm() {
GermplasmVO result = new GermplasmVO();
-
+ result.setGermplasmDbId("dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUwxOFJJTDJ3YXlfX185Ng==");
result.setGermplasmName("BLE BARBU DU ROUSSILLON");
result.setAccessionNumber("1408");
result.setSynonyms(Arrays.asList("BLE DU ROUSSILLON", "FRA051:1699", "ROUSSILLON"));
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
index c28705adcb4ebeb98a2bcb3c1afc0dec9ae9e61c..cf17c73ddddca7b2d20e9ac263c93edc3c59beef 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
@@ -50,6 +50,11 @@ public class SiteController {
public ModelAndView get(@PathVariable("siteId") String siteId) {
LocationVO site = locationRepository.getById(siteId);
+ if (site == null) {
+ throw new NotFoundException("Site with ID " + siteId + " not found");
+ }
+
+ // TODO uncomment this and remove the hard-coded xrefs
// List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
// XRefDocumentSearchCriteria.forXRefId(site.getLocationDbId()));
List<XRefDocumentVO> crossReferences = Arrays.asList(
@@ -57,13 +62,6 @@ public class SiteController {
createXref("bazbing")
);
- // LocationVO site = createSite();
-
- if (site == null) {
- throw new NotFoundException("Site with ID " + siteId + " not found");
- }
-
-
return new ModelAndView("site",
"model",
new SiteModel(
@@ -93,24 +91,6 @@ public class SiteController {
return ResponseEntity.ok().contentType(MediaType.TEXT_PLAIN).body(body);
}
- private LocationVO createSite() {
- LocationVO site = new LocationVO();
- site.setLocationName("France");
- site.setSourceUri("https://urgi.versailles.inrae.fr/gnpis");
- site.setUri("Test URI");
- site.setUrl("https://google.com");
- site.setLatitude(45.65);
- site.setLongitude(1.34);
- BrapiAdditionalInfo additionalInfo = new BrapiAdditionalInfo();
- additionalInfo.addProperty("Slope", 4.32);
- additionalInfo.addProperty("Distance to city", "3 km");
- additionalInfo.addProperty("foo", "bar");
- additionalInfo.addProperty("baz", "zing");
- additionalInfo.addProperty("blob", null);
- site.setAdditionalInfo(additionalInfo);
- return site;
- }
-
private XRefDocumentVO createXref(String name) {
XRefDocumentVO xref = new XRefDocumentVO();
xref.setName(name);
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
index 11ea51f7f956ea7793c7b0afc5810a2e901b04c0..626df842e50b8fe1eaab7f6492e70fb064da9b3d 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
@@ -75,6 +75,10 @@ public class StudyController {
public ModelAndView get(@PathVariable("studyId") String studyId) {
StudyDetailVO study = studyRepository.getById(studyId);
+ if (study == null) {
+ throw new NotFoundException("Study with ID " + studyId + " not found");
+ }
+
// TODO uncomment this
// List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
// XRefDocumentSearchCriteria.forXRefId(study.getStudyDbId()));
@@ -83,19 +87,11 @@ public class StudyController {
createXref("bazbing")
);
- if (study == null) {
- throw new NotFoundException("Study with ID " + studyId + " not found");
- }
-
List<GermplasmVO> germplasms = getGermplasms(study);
List<ObservationVariableVO> variables = getVariables(study);
List<TrialVO> trials = getTrials(study);
LocationVO location = getLocation(study);
- // TODO remove this
- location.setLatitude(34.0);
- location.setLongitude(14.0);
-
return new ModelAndView("study",
"model",
new StudyModel(
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java
index 9ba16d342d94e9097e720c5b3ad2e370d564fe6d..342c41655def0bdee5eb87df5055dde98c986a79 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java
@@ -2,9 +2,11 @@ package fr.inra.urgi.faidare.web.thymeleaf;
import java.nio.charset.StandardCharsets;
import java.text.DecimalFormat;
+import java.util.Arrays;
import java.util.Base64;
import java.util.Collections;
import java.util.HashMap;
+import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.function.Function;
@@ -24,7 +26,9 @@ public class FaidareExpressions {
private static final Map<String, Function<String, String>> TAXON_ID_URL_FACTORIES_BY_SOURCE_NAME =
createTaxonIdUrlFactories();
- private static final ObjectMapper objectMapper = new ObjectMapper();
+
+ private static final List<NavbarEntry> NAVBAR_ENTRIES =
+ createNavbarEntries();
private static Map<String, Function<String, String>> createTaxonIdUrlFactories() {
Map<String, Function<String, String>> result = new HashMap<>();
@@ -35,6 +39,23 @@ public class FaidareExpressions {
return Collections.unmodifiableMap(result);
}
+ private static List<NavbarEntry> createNavbarEntries() {
+ return Arrays.asList(
+ NavbarEntry.menu("URGI", Arrays.asList(
+ NavbarEntry.link("Home", "https://urgi.versailles.inra.fr"),
+ NavbarEntry.link("News", "https://urgi.versailles.inra.fr/About-us/News"),
+ NavbarEntry.link("About us", "https://urgi.versailles.inra.fr/About-us")
+ )),
+ NavbarEntry.menu("More...", Arrays.asList(
+ NavbarEntry.link("About", "https://urgi.versailles.inrae.fr/faidare/about"),
+ NavbarEntry.link("Join us", "https://urgi.versailles.inra.fr/faidare/join"),
+ NavbarEntry.link("Terms of use", "https://urgi.versailles.inra.fr/faidare/legal"),
+ NavbarEntry.link("Help", "https://urgi.versailles.inra.fr/faidare/help"),
+ NavbarEntry.link("News/Perspectives", "https://urgi.versailles.inra.fr/faidare/news")
+ ))
+ );
+ }
+
private final Locale locale;
public FaidareExpressions(Locale locale) {
@@ -59,13 +80,8 @@ public class FaidareExpressions {
return urlFactory != null ? urlFactory.apply(taxonSource.getTaxonId()) : null;
}
- public String toJson(Object value) {
- try {
- return objectMapper.writeValueAsString(value);
- }
- catch (JsonProcessingException e) {
- throw new IllegalArgumentException(e);
- }
+ public List<NavbarEntry> navbarEntries() {
+ return NAVBAR_ENTRIES;
}
private String collPopTitle(CollPopVO collPopVO, Function<String, String> nameTransformer) {
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/NavbarEntry.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/NavbarEntry.java
new file mode 100644
index 0000000000000000000000000000000000000000..8925aec060762927cf87328c2e40164e5bb7e589
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/NavbarEntry.java
@@ -0,0 +1,40 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * A navbar link
+ * @author JB Nizet
+ */
+public final class NavbarEntry {
+ private final String label;
+ private final String url;
+ private final List<NavbarEntry> subMenu;
+
+ private NavbarEntry(String label, String url, List<NavbarEntry> subMenu) {
+ this.label = label;
+ this.url = url;
+ this.subMenu = subMenu;
+ }
+
+ public static NavbarEntry link(String label, String url) {
+ return new NavbarEntry(label, url, Collections.emptyList());
+ }
+
+ public static NavbarEntry menu(String label, List<NavbarEntry> subMenu) {
+ return new NavbarEntry(label, null, subMenu);
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public String getUrl() {
+ return url;
+ }
+
+ public List<NavbarEntry> getSubMenu() {
+ return subMenu;
+ }
+}
diff --git a/backend/src/main/resources/templates/layout/main.html b/backend/src/main/resources/templates/layout/main.html
index 8097134fddb189f6c038ba29aceb29f14eee972f..0ceb3ebf650b4ce83e8fc1371d175841769ee0da 100644
--- a/backend/src/main/resources/templates/layout/main.html
+++ b/backend/src/main/resources/templates/layout/main.html
@@ -14,7 +14,7 @@
<link
rel="shortcut icon"
- th:href="@{/static/assets/images/favicon.ico}"
+ th:href="@{/assets/images/favicon.ico}"
type="image/x-icon"
/>
</head>
@@ -22,9 +22,63 @@
<body>
<nav class="navbar navbar-expand-lg navbar-light bg-light">
<div class="container">
- <span class="navbar-brand py-0">
+ <a
+ class="navbar-brand py-0"
+ href="https://urgi.versailles.inrae.fr/faidare"
+ >
<img th:src="@{/assets/images/logo.png}" style="height: 40px" />
- </span>
+ </a>
+ <button
+ class="navbar-toggler"
+ type="button"
+ data-bs-toggle="collapse"
+ data-bs-target="#navbarContent"
+ aria-controls="navbarContent"
+ aria-expanded="false"
+ aria-label="Toggle navigation"
+ >
+ <span class="navbar-toggler-icon"></span>
+ </button>
+ <div class="collapse navbar-collapse" id="navbarContent">
+ <ul class="navbar-nav me-auto">
+ <th:block th:each="topEntry : ${#faidare.navbarEntries}">
+ <li class="nav-item" th:if="${#lists.isEmpty(topEntry.subMenu)}">
+ <a
+ class="nav-link"
+ th:href="${topEntry.url}"
+ th:text="${topEntry.label}"
+ ></a>
+ </li>
+ <li
+ class="nav-item dropdown"
+ th:if="${not #lists.isEmpty(topEntry.subMenu)}"
+ >
+ <a
+ class="nav-link dropdown-toggle"
+ th:id="${'navbar-dropdown-' + topEntry.label}"
+ href="#"
+ role="button"
+ data-bs-toggle="dropdown"
+ aria-expanded="false"
+ th:text="${topEntry.label}"
+ >
+ </a>
+ <ul
+ class="dropdown-menu bg-light"
+ th:aria-labelledby="${'navbar-dropdown-' + topEntry.label}"
+ >
+ <li th:each="subEntry : ${topEntry.subMenu}" class="bg-light">
+ <a
+ class="dropdown-item"
+ th:href="${subEntry.url}"
+ th:text="${subEntry.label}"
+ ></a>
+ </li>
+ </ul>
+ </li>
+ </th:block>
+ </ul>
+ </div>
</div>
</nav>
<div class="container mt-3">
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java
index 930cbbe92bf6f58456bacae4109f42ef5ce2c931..7ec9bb8e27fa23dbdb2a84b87e5c116334fae20c 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryTest.java
@@ -52,7 +52,6 @@ class GermplasmRepositoryTest {
esSetUp.initialize(ProgenyVO.class, 0L);
esSetUp.initialize(PedigreeVO.class, 0L);
esSetUp.initialize(GermplasmMcpdVO.class, 0L);
-
}
@Autowired
@@ -137,6 +136,22 @@ class GermplasmRepositoryTest {
.allMatch(vo -> !vo.getGermplasmDbId().isEmpty());
}
+ @Test
+ void shouldScrollGermplasmMcpdsByIds() {
+ Iterator<GermplasmMcpdVO> list = repository.scrollGermplasmMcpdsByIds(Collections.singleton("13705"), 1000);
+ assertThat(list).toIterable()
+ .isNotEmpty()
+ .allMatch(vo -> !vo.getGermplasmDbId().isEmpty());
+
+ list = repository.scrollGermplasmMcpdsByIds(Collections.singleton("1370"), 1000);
+ assertThat(list).toIterable()
+ .isEmpty();
+
+ list = repository.scrollGermplasmMcpdsByIds(Collections.singleton("Prunus"), 1000);
+ assertThat(list).toIterable()
+ .isEmpty();
+ }
+
@Test
void should_Scroll_By_accessionNumber() {
GermplasmPOSTSearchCriteria criteria = new GermplasmPOSTSearchCriteria();
diff --git a/web/package.json b/web/package.json
index 3efc776bb3c7da2b2537fa6e7aaaebd295d57509..d4dae567299cac36ee27d7aa43752435a21589ae 100644
--- a/web/package.json
+++ b/web/package.json
@@ -16,7 +16,7 @@
"license": "MIT",
"dependencies": {
"@types/leaflet": "1.7.5",
- "bootstrap": "5.1.0",
+ "bootstrap": "5.1.1",
"leaflet": "1.7.1"
},
"devDependencies": {
diff --git a/web/src/bootstrap/popovers.ts b/web/src/bootstrap/popovers.ts
index b19e5e75dedc37274b3a863bd1f18e448af43bdf..4e6baa5bbdd271604c328bd0167729290c6b0f97 100644
--- a/web/src/bootstrap/popovers.ts
+++ b/web/src/bootstrap/popovers.ts
@@ -1,4 +1,4 @@
-import { Popover } from 'bootstrap';
+import Popover from 'bootstrap/js/dist/popover';
export function initializePopovers() {
const popoverTriggerList: Array<HTMLElement> = [].slice.call(document.querySelectorAll('[data-bs-toggle="popover"]'));
diff --git a/web/src/index.ts b/web/src/index.ts
index 060cf75d6a996a175e6d4b29c8fa1b067cf0610e..18fd98fd9580fd50269bf100a160d93660172a7e 100644
--- a/web/src/index.ts
+++ b/web/src/index.ts
@@ -1,5 +1,7 @@
import { initializePopovers } from './bootstrap/popovers';
import { initializeMap } from './map/map';
+import 'bootstrap/js/dist/dropdown';
+import 'bootstrap/js/dist/collapse';
(window as any).faidare = {
initializePopovers,
diff --git a/web/yarn.lock b/web/yarn.lock
index 006da818ecb29a7986970a0c18274d4648db5611..877a23dac04a277365934d2a8f391bfbfa49b98e 100644
--- a/web/yarn.lock
+++ b/web/yarn.lock
@@ -372,10 +372,10 @@ boolbase@^1.0.0:
resolved "https://registry.yarnpkg.com/boolbase/-/boolbase-1.0.0.tgz#68dff5fbe60c51eb37725ea9e3ed310dcc1e776e"
integrity sha1-aN/1++YMUes3cl6p4+0xDcwed24=
-bootstrap@5.1.0:
- version "5.1.0"
- resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-5.1.0.tgz#543ef8f44f4b9af67b0230f19508542fec38ef55"
- integrity sha512-bs74WNI9BgBo3cEovmdMHikSKoXnDgA6VQjJ7TyTotU6L7d41ZyCEEelPwkYEzsG/Zjv3ie9IE3EMAje0W9Xew==
+bootstrap@5.1.1:
+ version "5.1.1"
+ resolved "https://registry.yarnpkg.com/bootstrap/-/bootstrap-5.1.1.tgz#9d6eed81e08feaccedf3adaca51fe4b73a2871df"
+ integrity sha512-/jUa4sSuDZWlDLQ1gwQQR8uoYSvLJzDd8m5o6bPKh3asLAMYVZKdRCjb1joUd5WXf0WwCNzd2EjwQQhupou0dA==
brace-expansion@^1.1.7:
version "1.1.11"