diff --git a/.gitignore b/.gitignore
index 0648667bdb50f03dbf8151eff52f71c863b4bcf7..ef6f322552824d51d4938c0b1be7ea2d68e4e69f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -95,43 +95,11 @@ local.properties
*.ipr
# User-specific stuff
-.idea/*
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/usage.statistics.xml
-.idea/**/dictionaries
-.idea/**/shelf
-
-# Generated files
-.idea/**/contentModel.xml
-
-# Sensitive or high-churn files
-.idea/**/dataSources/
-.idea/**/dataSources.ids
-.idea/**/dataSources.local.xml
-.idea/**/sqlDataSources.xml
-.idea/**/dynamic.xml
-.idea/**/uiDesigner.xml
-.idea/**/dbnavigator.xml
-
-# Gradle
-.idea/**/gradle.xml
-.idea/**/libraries
-
-# Gradle and Maven with auto-import
-# When using Gradle or Maven with auto-import, you should exclude module files,
-# since they will be recreated, and may cause churn. Uncomment if using
-# auto-import.
-# .idea/modules.xml
-# .idea/*.iml
-# .idea/modules
+.idea
# CMake
cmake-build-*/
-# Mongo Explorer plugin
-.idea/**/mongoSettings.xml
-
# File-based project format
*.iws
@@ -144,21 +112,12 @@ out/
# JIRA plugin
atlassian-ide-plugin.xml
-# Cursive Clojure plugin
-.idea/replstate.xml
-
# Crashlytics plugin (for Android Studio and IntelliJ)
com_crashlytics_export_strings.xml
crashlytics.properties
crashlytics-build.properties
fabric.properties
-# Editor-based Rest Client
-.idea/httpRequests
-
-# Android studio 3.1+ serialized cache file
-.idea/caches/build_file_checksums.ser
-
### Intellij Patch ###
# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
@@ -167,9 +126,6 @@ fabric.properties
# .idea/misc.xml
# *.ipr
-# Sonarlint plugin
-.idea/sonarlint
-
### Kotlin ###
# Compiled class file
*.class
@@ -270,3 +226,4 @@ gradle-app.setting
# End of https://www.gitignore.io/api/gradle,eclipse,intellij,visualstudiocode,kotlin,git,macos,linux
frontend/package-lock.json
+/web/node_modules/
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b5511df7904d649e1cf5dfc50a6bd2c50ad4e3bc..7df3480415c742159af12bd1c3e36c778000c472 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,8 +30,6 @@ cache:
key: "$CI_COMMIT_REF_NAME"
paths:
- ".gradle"
- - "frontend/.gradle/"
- - "frontend/node_modules/"
# PRE-BUILD
@@ -62,20 +60,6 @@ build-loader-docker-image:
# TESTS
-lint:
- stage: test
- tags:
- - openstack
- script: "./gradlew lint"
- cache:
- key: "$CI_COMMIT_REF_NAME"
- policy: pull
- paths:
- - ".gradle"
- - "frontend/.gradle/"
- - "frontend/node_modules/"
-
-
test-and-sonarqube:
stage: test
tags:
@@ -104,20 +88,19 @@ test-and-sonarqube:
policy: pull-push
paths:
- ".gradle"
- - "frontend/.gradle/"
- - "frontend/node_modules/"
- .sonar/cache
script:
- - ./gradlew :frontend:assemble --parallel
- - ./gradlew :backend:test jacocoTestReport --parallel
- - find /tmp/node/*/bin -name node -exec ln -s {} /tmp/node/node \;
- - export PATH="/tmp/node/:$PATH"
- - ./gradlew -s sonarqube -x test
+ - ./gradlew test jacocoTestReport --parallel
+ # disable sonarqube because it apparently needs node, but I don't know why, and it can't find it anymore now that
+ # there is no frontend project anymore, and it takes sooooo much time to complete anyway for results that nobody
+ # will ever look
+ # - find /tmp/node/*/bin -name node -exec ln -s {} /tmp/node/node \;
+ # - export PATH="/tmp/node/:$PATH"
+ # - ./gradlew -s sonarqube -x test
artifacts:
reports:
junit:
- ./backend/build/test-results/test/TEST-*.xml
- # - ./frontend/karma-junit-tests-report/TEST*.xml
only:
refs:
- merge_requests
@@ -144,8 +127,6 @@ build:
policy: pull
paths:
- ".gradle"
- - "frontend/.gradle/"
- - "frontend/node_modules/"
artifacts:
paths:
- "$JAR_PATH"
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
deleted file mode 100644
index ca99a00edbda7ccc394869431fec04f9a5ac33a6..0000000000000000000000000000000000000000
--- a/.idea/compiler.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="CompilerConfiguration">
- <annotationProcessing>
- <profile name="Gradle Imported" enabled="true">
- <outputRelativeToContentRoot value="true" />
- <processorPath useClasspath="false">
- <entry name="$USER_HOME$/.gradle/caches/modules-2/files-2.1/org.springframework.boot/spring-boot-configuration-processor/2.1.2.RELEASE/db9671c321defb942a6700fae8a7700a137a25e/spring-boot-configuration-processor-2.1.2.RELEASE.jar" />
- </processorPath>
- <module name="faidare.backend.main" />
- </profile>
- </annotationProcessing>
- <bytecodeTargetLevel target="1.8" />
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
deleted file mode 100644
index 15a15b218a29e09c9190992732698d646e4d659a..0000000000000000000000000000000000000000
--- a/.idea/encodings.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="Encoding" addBOMForNewFiles="with NO BOM" />
-</project>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index ff8249e49968d1849269b0d8a2fe49a31c72a63f..0000000000000000000000000000000000000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="FrameworkDetectionExcludesConfiguration">
- <file type="web" url="file://$PROJECT_DIR$" />
- </component>
- <component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" default="true" project-jdk-name="1.8" project-jdk-type="JavaSDK">
- <output url="file://$PROJECT_DIR$/out" />
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 3b2a562bc3214c46382cc1761196d85196a94d66..0000000000000000000000000000000000000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectModuleManager">
- <modules>
- <module fileurl="file://$PROJECT_DIR$/.idea/modules/faidare.iml" filepath="$PROJECT_DIR$/.idea/modules/faidare.iml" />
- <module fileurl="file://$PROJECT_DIR$/.idea/modules/backend/faidare.backend.iml" filepath="$PROJECT_DIR$/.idea/modules/backend/faidare.backend.iml" />
- <module fileurl="file://$PROJECT_DIR$/.idea/modules/backend/faidare.backend.main.iml" filepath="$PROJECT_DIR$/.idea/modules/backend/faidare.backend.main.iml" />
- <module fileurl="file://$PROJECT_DIR$/.idea/modules/backend/faidare.backend.test.iml" filepath="$PROJECT_DIR$/.idea/modules/backend/faidare.backend.test.iml" />
- <module fileurl="file://$PROJECT_DIR$/.idea/modules/frontend/faidare.frontend.iml" filepath="$PROJECT_DIR$/.idea/modules/frontend/faidare.frontend.iml" />
- <module fileurl="file://$PROJECT_DIR$/backend/src/main/main.iml" filepath="$PROJECT_DIR$/backend/src/main/main.iml" />
- <module fileurl="file://$PROJECT_DIR$/backend/src/test/test.iml" filepath="$PROJECT_DIR$/backend/src/test/test.iml" />
- </modules>
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 94a25f7f4cb416c083d265558da75d457237d671..0000000000000000000000000000000000000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="VcsDirectoryMappings">
- <mapping directory="$PROJECT_DIR$" vcs="Git" />
- </component>
-</project>
\ No newline at end of file
diff --git a/backend/build.gradle.kts b/backend/build.gradle.kts
index 9ff140544f08a54151ddf9ca56e164de76e37a35..64acb331b41fea7957dcb7ea7c0d7713e561dd43 100644
--- a/backend/build.gradle.kts
+++ b/backend/build.gradle.kts
@@ -1,11 +1,8 @@
import org.gradle.api.tasks.testing.logging.TestExceptionFormat
import org.springframework.boot.gradle.tasks.buildinfo.BuildInfo
-import org.springframework.boot.gradle.tasks.bundling.BootJar
-import org.springframework.boot.gradle.tasks.run.BootRun
buildscript {
repositories {
- mavenLocal()
mavenCentral()
}
}
@@ -20,7 +17,6 @@ plugins {
id("org.owasp.dependencycheck") version "6.0.3"
}
-
java {
sourceCompatibility = JavaVersion.VERSION_1_8
}
@@ -40,7 +36,7 @@ tasks {
options.compilerArgs.add("-parameters")
}
- getByName<Copy>("processResources") {
+ processResources {
inputs.property("app", "gnpis")
filesMatching("bootstrap.yml") {}
@@ -51,25 +47,44 @@ tasks {
// but it's better to do that than using the bootInfo() method of the springBoot closure, because that
// makes the test task out of date, which makes the build much longer.
// See https://github.com/spring-projects/spring-boot/issues/13152
- val buildInfo by creating(BuildInfo::class) {
+ val buildInfo by registering(BuildInfo::class) {
destinationDir = file("$buildDir/buildInfo")
}
- val bootJar by getting(BootJar::class) {
+ bootJar {
archiveName = "${rootProject.name}.jar"
- dependsOn(":frontend:assemble")
dependsOn(buildInfo)
-
- into("BOOT-INF/classes/static") {
- from("${project(":frontend").projectDir}/dist/frontend")
+ dependsOn(":web:assemble")
+
+ // replace the script.js and style.css file names referenced in main.html
+ // by their actual name, containing the content hash
+ filesMatching("**/layout/main.html") {
+ val webAssetsDir = project(":web").file("build/dist/assets/");
+ val scriptFileName = webAssetsDir.list().first { it.startsWith("script") && it.endsWith(".js") }
+ val styleFileName = webAssetsDir.list().first { it.startsWith("style") && it.endsWith(".css") }
+
+ filter { line ->
+ if (line.contains("script.js")) {
+ line.replace("script.js", scriptFileName)
+ }
+ else if (line.contains("style.css")) {
+ line.replace("style.css", styleFileName)
+ } else {
+ line
+ }
+ }
}
+
into("BOOT-INF/classes/META-INF") {
- from(buildInfo.destinationDir)
+ from(buildInfo.map { it.destinationDir })
+ }
+ into("BOOT-INF/classes/static") {
+ from(project(":web").file("build/dist"))
}
launchScript()
}
- val test by getting(Test::class) {
+ test {
useJUnitPlatform()
testLogging {
exceptionFormat = TestExceptionFormat.FULL
@@ -77,7 +92,7 @@ tasks {
outputs.dir(snippetsDir)
}
- val jacocoTestReport by getting(JacocoReport::class) {
+ jacocoTestReport {
reports {
xml.setEnabled(true)
html.setEnabled(true)
@@ -98,6 +113,7 @@ dependencies {
implementation("org.springframework.boot:spring-boot-starter-actuator")
implementation("org.springframework.boot:spring-boot-starter-security")
implementation("org.springframework.cloud:spring-cloud-starter-config")
+ implementation("org.springframework.boot:spring-boot-starter-thymeleaf")
// Elasticsearch
implementation("org.elasticsearch:elasticsearch:6.6.2")
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..6dde515e2d0fa5fedf1d2b36d7d2b30de43dd5f5 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
@@ -4,6 +4,7 @@ import fr.inra.urgi.faidare.domain.criteria.base.PaginationCriteriaImpl;
import fr.inra.urgi.faidare.elasticsearch.criteria.annotation.CriteriaForDocument;
import fr.inra.urgi.faidare.elasticsearch.criteria.annotation.DocumentPath;
+import java.util.Collections;
import java.util.List;
/**
@@ -18,6 +19,12 @@ public class XRefDocumentSearchCriteria extends PaginationCriteriaImpl {
@DocumentPath("linkedRessourcesID")
private List<String> linkedRessourcesID;
+ public static XRefDocumentSearchCriteria forXRefId(String resourceId) {
+ XRefDocumentSearchCriteria criteria = new XRefDocumentSearchCriteria();
+ criteria.setLinkedRessourcesID(Collections.singletonList(resourceId));
+ return criteria;
+ }
+
public String getEntryType() {
return entryType;
}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/filter/AngularRouteFilter.java b/backend/src/main/java/fr/inra/urgi/faidare/filter/AngularRouteFilter.java
deleted file mode 100644
index 81978e5f3bfaca602e70eff0f109477d55e1466a..0000000000000000000000000000000000000000
--- a/backend/src/main/java/fr/inra/urgi/faidare/filter/AngularRouteFilter.java
+++ /dev/null
@@ -1,115 +0,0 @@
-package fr.inra.urgi.faidare.filter;
-
-import com.google.common.base.Charsets;
-import com.google.common.io.ByteSource;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.core.io.ResourceLoader;
-import org.springframework.stereotype.Component;
-
-import javax.servlet.*;
-import javax.servlet.annotation.WebFilter;
-import javax.servlet.http.HttpServletRequest;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Arrays;
-
-/**
- * Filter that intercepts all request to potential Angular routes
- * (ex: /studies/ID) to send back the Angular `index.html` file with a correct
- * base href set to the spring server context path.
- *
- * Potential angular routes are devised by process of elimination:
- * - They should be GET requests
- * - They should not end with common static file suffixes {@link AngularRouteFilter#STATIC_SUFFIXES}
- * - They should not start with API prefixes {@link AngularRouteFilter#API_PREFIXES}
- *
- * <p>
- * Adapted from data-discovery
- *
- * @author gcornut
- */
-@Component
-@WebFilter("/*")
-public class AngularRouteFilter implements Filter {
-
- private static final String[] API_PREFIXES = {
- "/brapi/v1", "/faidare/v1", "/actuator", "/v2/api-docs", "/swagger-resources"
- };
-
- private static final String[] STATIC_SUFFIXES = {
- ".html", ".js", ".css", ".ico", ".png", ".jpg", ".gif", ".eot", ".svg",
- ".woff2", ".ttf", ".woff", ".md"
- };
-
- @Value("${server.servlet.context-path}")
- private String serverContextPath;
-
- private final ResourceLoader resourceLoader;
-
- @Autowired
- public AngularRouteFilter(ResourceLoader resourceLoader) {
- this.resourceLoader = resourceLoader;
- }
-
- @Override
- public void doFilter(
- ServletRequest req,
- ServletResponse response,
- FilterChain chain
- ) throws IOException, ServletException {
- HttpServletRequest request = (HttpServletRequest) req;
-
- if (isAngularRoute(request)) {
- // Angular route
- InputStream inputStream = resourceLoader.getResource("classpath:static/index.html").getInputStream();
-
- ByteSource byteSource = new ByteSource() {
- @Override
- public InputStream openStream() {
- return inputStream;
- }
- };
-
- String content = byteSource.asCharSource(Charsets.UTF_8).read();
- String replacedContent = content.replace(
- "<base href=\"./\">",
- "<base href=\"" + serverContextPath + "/\">"
- );
- response.getWriter().write(replacedContent);
- return;
- }
-
- // Otherwise nothing to do
- chain.doFilter(request, response);
- }
-
- private boolean isAngularRoute(HttpServletRequest request) {
- if (!request.getMethod().equals("GET")) {
- return false;
- }
-
- String fullUri = request.getRequestURI();
- String contextPath = request.getContextPath();
- String uri = fullUri.substring(contextPath.length());
-
- return !isApiOrStaticResource(uri);
- }
-
- private boolean isApiOrStaticResource(String relativePath) {
- // Starts with API prefix
- return Arrays.stream(API_PREFIXES).anyMatch(relativePath::startsWith)
- // or has static file suffix
- || Arrays.stream(STATIC_SUFFIXES).anyMatch(relativePath::endsWith);
- }
-
- @Override
- public void init(FilterConfig filterConfig) {
- // nothing to do
- }
-
- @Override
- public void destroy() {
- // nothing to do
- }
-}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/utils/Sites.java b/backend/src/main/java/fr/inra/urgi/faidare/utils/Sites.java
new file mode 100644
index 0000000000000000000000000000000000000000..67fde44b8117296f13defc599adc6dcd0cd970a3
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/utils/Sites.java
@@ -0,0 +1,14 @@
+package fr.inra.urgi.faidare.utils;
+
+import java.nio.charset.StandardCharsets;
+import java.util.Base64;
+
+/**
+ * Utilities for sites
+ * @author JB Nizet
+ */
+public class Sites {
+ public static String siteIdToLocationId(String siteId) {
+ return Base64.getUrlEncoder().encodeToString(("urn:URGI/location/" + siteId).getBytes(StandardCharsets.US_ASCII));
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/HomeController.java b/backend/src/main/java/fr/inra/urgi/faidare/web/HomeController.java
new file mode 100644
index 0000000000000000000000000000000000000000..6734b6aa97a2ae445af4eb61be86a07883b2a58a
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/HomeController.java
@@ -0,0 +1,19 @@
+package fr.inra.urgi.faidare.web;
+
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.servlet.ModelAndView;
+
+/**
+ * Controller for the home page, which doesn't display much
+ * @author JB Nizet
+ */
+@Controller
+@RequestMapping("")
+public class HomeController {
+ @GetMapping
+ public ModelAndView home() {
+ return new ModelAndView("index");
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..cd24d06dc61698b217db1422c9585ed4b7b97b05
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmController.java
@@ -0,0 +1,412 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import fr.inra.urgi.faidare.api.NotFoundException;
+import fr.inra.urgi.faidare.config.FaidareProperties;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmAttributeValue;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiSibling;
+import fr.inra.urgi.faidare.domain.criteria.GermplasmAttributeCriteria;
+import fr.inra.urgi.faidare.domain.criteria.GermplasmGETSearchCriteria;
+import fr.inra.urgi.faidare.domain.data.germplasm.CollPopVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.DonorVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GenealogyVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmAttributeValueVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmInstituteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.InstituteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.PedigreeVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.PhotoVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.PuiNameValueVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.SiblingVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.SimpleVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.SiteVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.TaxonSourceVO;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+import fr.inra.urgi.faidare.repository.es.GermplasmAttributeRepository;
+import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
+import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.servlet.ModelAndView;
+
+/**
+ * Controller used to display a germplasm card based on its ID.
+ * @author JB Nizet
+ */
+@Controller("webGermplasmController")
+@RequestMapping("/germplasms")
+public class GermplasmController {
+
+ private final GermplasmRepository germplasmRepository;
+ private final FaidareProperties faidareProperties;
+ private final XRefDocumentRepository xRefDocumentRepository;
+ private GermplasmAttributeRepository germplasmAttributeRepository;
+
+ public GermplasmController(GermplasmRepository germplasmRepository,
+ FaidareProperties faidareProperties,
+ XRefDocumentRepository xRefDocumentRepository,
+ GermplasmAttributeRepository germplasmAttributeRepository) {
+ this.germplasmRepository = germplasmRepository;
+ this.faidareProperties = faidareProperties;
+ this.xRefDocumentRepository = xRefDocumentRepository;
+ this.germplasmAttributeRepository = germplasmAttributeRepository;
+ }
+
+ @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();
+
+ if (germplasm == null) {
+ throw new NotFoundException("Germplasm with ID " + germplasmId + " not found");
+ }
+
+ return toModelAndView(germplasm);
+ }
+
+ @GetMapping(params = "pui")
+ public ModelAndView getByPui(@RequestParam("pui") String pui) {
+ GermplasmGETSearchCriteria criteria = new GermplasmGETSearchCriteria();
+ criteria.setGermplasmPUI(Collections.singletonList(pui));
+ List<GermplasmVO> germplasms = germplasmRepository.find(criteria);
+ if (germplasms.size() != 1) {
+ throw new NotFoundException("Germplasm with PUI " + pui + " not found");
+ }
+
+ return toModelAndView(germplasms.get(0));
+ }
+
+ private ModelAndView toModelAndView(GermplasmVO germplasm) {
+ // List<BrapiGermplasmAttributeValue> attributes = getAttributes(germplasm);
+ // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+ // XRefDocumentSearchCriteria.forXRefId(site.getLocationDbId()));
+ // PedigreeVO pedigree = getPedigree(germplasm);
+ // 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")
+ );
+
+ sortDonors(germplasm);
+ sortPopulations(germplasm);
+ sortCollections(germplasm);
+ sortPanels(germplasm);
+ return new ModelAndView("germplasm",
+ "model",
+ new GermplasmModel(
+ germplasm,
+ faidareProperties.getByUri(germplasm.getSourceUri()),
+ attributes,
+ pedigree,
+ crossReferences)
+ );
+ }
+
+ private void sortPopulations(GermplasmVO germplasm) {
+ if (germplasm.getPopulation() != null) {
+ germplasm.setPopulation(germplasm.getPopulation()
+ .stream()
+ .sorted(Comparator.comparing(
+ CollPopVO::getName))
+ .collect(Collectors.toList()));
+ }
+ }
+
+ private void sortCollections(GermplasmVO germplasm) {
+ if (germplasm.getCollection() != null) {
+ germplasm.setCollection(germplasm.getCollection()
+ .stream()
+ .sorted(Comparator.comparing(CollPopVO::getName))
+ .collect(Collectors.toList()));
+ }
+ }
+
+ private void sortPanels(GermplasmVO germplasm) {
+ if (germplasm.getPanel() != null) {
+ germplasm.setPanel(germplasm.getPanel()
+ .stream()
+ .sorted(Comparator.comparing(CollPopVO::getName))
+ .collect(Collectors.toList()));
+ }
+ }
+
+ private void sortDonors(GermplasmVO germplasm) {
+ if (germplasm.getDonors() != null) {
+ germplasm.setDonors(germplasm.getDonors()
+ .stream()
+ .sorted(Comparator.comparing(donor -> donor.getDonorInstitute()
+ .getInstituteName()))
+ .collect(Collectors.toList()));
+ }
+ }
+
+ private List<BrapiGermplasmAttributeValue> getAttributes(GermplasmVO germplasm) {
+ GermplasmAttributeCriteria criteria = new GermplasmAttributeCriteria();
+ criteria.setGermplasmDbId(germplasm.getGermplasmDbId());
+ return germplasmAttributeRepository.find(criteria)
+ .stream()
+ .flatMap(vo -> vo.getData().stream())
+ .sorted(Comparator.comparing(BrapiGermplasmAttributeValue::getAttributeName))
+ .collect(Collectors.toList());
+ }
+
+ private PedigreeVO getPedigree(GermplasmVO germplasm) {
+ return germplasmRepository.findPedigree(germplasm.getGermplasmDbId());
+ }
+
+ private BrapiGermplasmAttributeValue createAttribute() {
+ GermplasmAttributeValueVO result = new GermplasmAttributeValueVO();
+ result.setAttributeName("A1");
+ result.setValue("V1");
+ return result;
+ }
+
+ private GermplasmVO createGermplasm() {
+ GermplasmVO result = new GermplasmVO();
+
+ result.setGermplasmName("BLE BARBU DU ROUSSILLON");
+ result.setAccessionNumber("1408");
+ result.setSynonyms(Arrays.asList("BLE DU ROUSSILLON", "FRA051:1699", "ROUSSILLON"));
+ PhotoVO photo = new PhotoVO();
+ photo.setPhotoName("Blé du roussillon");
+ photo.setCopyright("INRA, Emmanuelle BOULAT/Lionel BARDY 2012");
+ photo.setThumbnailFile("https://urgi.versailles.inrae.fr/files/siregal/images/accession/CEREALS/thumbnails/thumb_1408_R09_S.jpg");
+ photo.setFile("https://urgi.versailles.inrae.fr/files/siregal/images/accession/CEREALS/1408_R09_S.jpg");
+ result.setPhoto(photo);
+
+ InstituteVO holdingGenBank = new InstituteVO();
+ holdingGenBank.setLogo("https://urgi.versailles.inra.fr/files/siregal/images/grc/inra_brc_en.png");
+ holdingGenBank.setInstituteName("INRA BRC");
+ holdingGenBank.setWebSite("http://google.fr");
+ result.setHoldingGenbank(holdingGenBank);
+
+ result.setBiologicalStatusOfAccessionCode("Traditional cultivar/landrace ");
+ result.setPedigree("LV");
+ SiteVO originSite = new SiteVO();
+ originSite.setSiteId("1234");
+ originSite.setSiteName("Le Moulon");
+ originSite.setSiteType("Origin site");
+ originSite.setLatitude(47.0F);
+ originSite.setLongitude(12.0F);
+ result.setOriginSite(originSite);
+
+ List<SiteVO> evaluationSites = new ArrayList<>();
+ for (int i = 0; i < 5; i++) {
+ SiteVO evaluationSite = new SiteVO();
+ evaluationSite.setSiteId(Integer.toString(12347 + i));
+ evaluationSite.setSiteType("Evaluation site");
+ evaluationSite.setSiteName("Site " + i);
+ evaluationSite.setLatitude(46.0F + i);
+ evaluationSite.setLongitude(13.0F + i);
+ evaluationSites.add(evaluationSite);
+ }
+ result.setEvaluationSites(evaluationSites);
+
+ result.setGenus("Genus 1");
+ result.setSpecies("Species 1");
+ result.setSpeciesAuthority("Species Auth");
+ result.setSourceUri("https://urgi.versailles.inrae.fr/gnpis");
+ result.setSubtaxa("Subtaxa 1");
+ result.setGenusSpeciesSubtaxa("Triticum aestivum subsp. aestivum");
+ result.setSubtaxaAuthority("INRAE");
+ result.setTaxonIds(Arrays.asList(createTaxonId(), createTaxonId()));
+ result.setTaxonComment("C'est bon le blé");
+ result.setTaxonCommonNames(Arrays.asList("Blé tendre", "Bread wheat", "Soft wheat"));
+ result.setTaxonSynonyms(Arrays.asList("Blé tendre1", "Bread wheat1", "Soft wheat1"));
+
+ InstituteVO holdingInstitute = new InstituteVO();
+ holdingInstitute.setInstituteName("GDEC - UMR Génétique, Diversité et Ecophysiologie des Céréales");
+ holdingInstitute.setLogo("https://urgi.versailles.inra.fr/files/siregal/images/grc/inra_brc_en.png");
+ holdingInstitute.setWebSite("https://google.fr/q=qsdqsdqsdslqlsdnqlsdqlsdlqskdlqdqlsdqsdqsdqd");
+ holdingInstitute.setInstituteCode("GDEC");
+ holdingInstitute.setInstituteType("Type1");
+ holdingInstitute.setAcronym("G.D.E.C");
+ holdingInstitute.setAddress("Lyon");
+ holdingInstitute.setOrganisation("SAS");
+ result.setHoldingInstitute(holdingInstitute);
+
+ result.setPresenceStatus("Maintained");
+
+ GermplasmInstituteVO collector = new GermplasmInstituteVO();
+ collector.setMaterialType("Fork");
+ collector.setCollectors("Joe, Jack, William, Averell");
+ InstituteVO collectingInstitute = new InstituteVO();
+ collectingInstitute.setInstituteName("Ninja Squad");
+ collector.setInstitute(collectingInstitute);
+ collector.setAccessionNumber("567");
+ result.setCollector(collector);
+
+ SiteVO collectingSite = new SiteVO();
+ collectingSite.setSiteId("1235");
+ collectingSite.setSiteName("St Just");
+ collectingSite.setSiteType("Collecting site");
+ collectingSite.setLatitude(48.0F);
+ collectingSite.setLongitude(13.0F);
+ result.setCollectingSite(collectingSite);
+ result.setAcquisitionDate("In the summer");
+
+ GermplasmInstituteVO breeder = new GermplasmInstituteVO();
+ InstituteVO breedingInstitute = new InstituteVO();
+ breedingInstitute.setInstituteName("Microsoft");
+ breeder.setInstitute(breedingInstitute);
+ breeder.setAccessionCreationDate(2015);
+ breeder.setAccessionNumber("678");
+ breeder.setRegistrationYear(2016);
+ breeder.setDeregistrationYear(2019);
+ result.setBreeder(breeder);
+
+ result.setDonors(Arrays.asList(
+ createDonor()
+ ));
+
+ result.setDistributors(Arrays.asList(
+ createDistributor()
+ ));
+
+ result.setChildren(Arrays.asList(createChild(), createChild()));
+
+ result.setGermplasmPUI("germplasmPUI");
+ result.setPopulation(Arrays.asList(createPopulation1(), createPopulation2(), createPopulation3()));
+
+ result.setCollection(Arrays.asList(createCollection()));
+
+ result.setPanel(Arrays.asList(createPanel()));
+
+ return result;
+ }
+
+ private DonorVO createDonor() {
+ DonorVO result = new DonorVO();
+ result.setDonorGermplasmPUI("PUI1");
+ result.setDonationDate(2017);
+ result.setDonorAccessionNumber("3456");
+ result.setDonorInstituteCode("GD46U");
+ InstituteVO institute = new InstituteVO();
+ institute.setInstituteName("Hello");
+ result.setDonorInstitute(institute);
+ return result;
+ }
+
+ private GermplasmInstituteVO createDistributor() {
+ GermplasmInstituteVO result = new GermplasmInstituteVO();
+ InstituteVO institute = new InstituteVO();
+ institute.setInstituteName("Microsoft");
+ result.setInstitute(institute);
+ result.setAccessionNumber("678");
+ result.setDistributionStatus("OK");
+ return result;
+ }
+
+ private PedigreeVO createPedigree() {
+ PedigreeVO result = new PedigreeVO();
+ result.setPedigree("Pedigree 1");
+ result.setParent1DbId("12345");
+ result.setParent1Name("Parent 1");
+ result.setParent1Type("P1");
+ result.setParent2DbId("12346");
+ result.setParent2Name("Parent 2");
+ result.setParent2Type("P2");
+ result.setCrossingPlan("crossing plan 1");
+ result.setCrossingYear("2012");
+ result.setSiblings(Arrays.asList(createBrapiSibling()));
+ return result;
+ }
+
+ private BrapiSibling createBrapiSibling() {
+ SiblingVO sibling = new SiblingVO();
+ sibling.setGermplasmDbId("5678");
+ sibling.setDefaultDisplayName("Sibling 5678");
+ return sibling;
+ }
+
+ private GenealogyVO createChild() {
+ GenealogyVO result = new GenealogyVO();
+ result.setFirstParentName("CP1");
+ result.setSecondParentName("CP2");
+ result.setSibblings(Arrays.asList(createPuiNameValueVO(), createPuiNameValueVO()));
+ return result;
+ }
+
+ private PuiNameValueVO createPuiNameValueVO() {
+ PuiNameValueVO result = new PuiNameValueVO();
+ result.setName("Child 1");
+ result.setPui("pui1");
+ return result;
+ }
+
+ private CollPopVO createPopulation1() {
+ CollPopVO result = new CollPopVO();
+ result.setName("Population 1");
+ result.setType("Pop Type 1");
+ result.setGermplasmCount(3);
+ result.setGermplasmRef(createPuiNameValueVO());
+ return result;
+ }
+
+ private CollPopVO createPopulation2() {
+ CollPopVO result = new CollPopVO();
+ result.setName("Population 2");
+ result.setGermplasmCount(3);
+ PuiNameValueVO puiNameValueVO = createPuiNameValueVO();
+ puiNameValueVO.setPui("germplasmPUI");
+ result.setGermplasmRef(puiNameValueVO);
+ return result;
+ }
+
+ private CollPopVO createPopulation3() {
+ CollPopVO result = new CollPopVO();
+ result.setName("Population 3");
+ result.setGermplasmCount(5);
+ return result;
+ }
+
+ private CollPopVO createCollection() {
+ CollPopVO result = new CollPopVO();
+ result.setName("Collection 1");
+ result.setGermplasmCount(7);
+ return result;
+ }
+
+ private CollPopVO createPanel() {
+ CollPopVO result = new CollPopVO();
+ result.setName("The_panel_1");
+ result.setGermplasmCount(2);
+ return result;
+ }
+
+ private TaxonSourceVO createTaxonId() {
+ TaxonSourceVO result = new TaxonSourceVO();
+ result.setTaxonId("taxon1");
+ result.setSourceName("ThePlantList");
+ return result;
+ }
+
+ private XRefDocumentVO createXref(String name) {
+ XRefDocumentVO xref = new XRefDocumentVO();
+ xref.setName(name);
+ xref.setDescription("A very large description for the xref " + name + " which has way more than 120 characters bla bla bla bla bla bla bla bla bla bla bla bla");
+ xref.setDatabaseName("db_" + name);
+ xref.setUrl("https://google.com");
+ xref.setEntryType("type " + name);
+ return xref;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
new file mode 100644
index 0000000000000000000000000000000000000000..ffa24336f395b2d00817babacc09b38981318178
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/germplasm/GermplasmModel.java
@@ -0,0 +1,157 @@
+package fr.inra.urgi.faidare.web.germplasm;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiGermplasmAttributeValue;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmInstituteVO;
+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.SiteVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.DataSource;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+import fr.inra.urgi.faidare.web.site.MapLocation;
+import org.apache.logging.log4j.util.Strings;
+
+/**
+ * The model used by the germplasm page
+ * @author JB Nizet
+ */
+public final class GermplasmModel {
+ private final GermplasmVO germplasm;
+ private final DataSource source;
+ private final List<BrapiGermplasmAttributeValue> attributes;
+ private final PedigreeVO pedigree;
+ private final List<XRefDocumentVO> crossReferences;
+
+ public GermplasmModel(GermplasmVO germplasm,
+ DataSource source,
+ List<BrapiGermplasmAttributeValue> attributes,
+ PedigreeVO pedigree,
+ List<XRefDocumentVO> crossReferences) {
+ this.germplasm = germplasm;
+ this.source = source;
+ this.attributes = attributes;
+ this.pedigree = pedigree;
+ this.crossReferences = crossReferences;
+ }
+
+ public GermplasmVO getGermplasm() {
+ return germplasm;
+ }
+
+ public DataSource getSource() {
+ return source;
+ }
+
+ public List<BrapiGermplasmAttributeValue> getAttributes() {
+ return attributes;
+ }
+
+ public PedigreeVO getPedigree() {
+ return pedigree;
+ }
+
+ public List<XRefDocumentVO> getCrossReferences() {
+ return crossReferences;
+ }
+
+ public String getTaxon() {
+ if (Strings.isNotBlank(this.germplasm.getGenusSpeciesSubtaxa())) {
+ return this.germplasm.getGenusSpeciesSubtaxa();
+ } else if (Strings.isNotBlank(this.germplasm.getGenusSpecies())) {
+ return this.germplasm.getGenusSpecies();
+ } else if (Strings.isNotBlank(this.germplasm.getSubtaxa())) {
+ return this.germplasm.getGenus() + " " + this.germplasm.getSpecies() + " " + this.germplasm.getSubtaxa();
+ } else if (Strings.isNotBlank(this.germplasm.getSpecies())) {
+ return this.germplasm.getGenus() + " " + this.germplasm.getSpecies();
+ } else {
+ return this.germplasm.getGenus();
+ }
+ }
+
+ public String getTaxonAuthor() {
+ if (Strings.isNotBlank(this.germplasm.getGenusSpeciesSubtaxa())) {
+ return this.germplasm.getSubtaxaAuthority();
+ } else if (Strings.isNotBlank(this.germplasm.getGenusSpecies())) {
+ return this.germplasm.getSpeciesAuthority();
+ } else if (Strings.isNotBlank(this.germplasm.getSubtaxa())) {
+ return this.germplasm.getSubtaxaAuthority();
+ } else if (Strings.isNotBlank(this.germplasm.getSpecies())) {
+ return this.germplasm.getSpeciesAuthority();
+ } else {
+ return null;
+ }
+ }
+
+ public boolean isCollecting() {
+ return this.isCollectingSitePresent()
+ || this.isCollectorInstitutePresent()
+ || this.isCollectorIntituteFieldPresent();
+ }
+
+ private boolean isCollectingSitePresent() {
+ return this.germplasm.getCollectingSite() != null && Strings.isNotBlank(this.germplasm.getCollectingSite().getSiteName());
+ }
+
+ private boolean isCollectorInstitutePresent() {
+ return this.germplasm.getCollector() != null &&
+ this.germplasm.getCollector().getInstitute() != null &&
+ Strings.isNotBlank(this.germplasm.getCollector().getInstitute().getInstituteName());
+ }
+
+ private boolean isCollectorIntituteFieldPresent() {
+ GermplasmInstituteVO collector = this.germplasm.getCollector();
+ return (collector != null) &&
+ (Strings.isNotBlank(collector.getAccessionNumber())
+ || collector.getAccessionCreationDate() != null
+ || Strings.isNotBlank(collector.getMaterialType())
+ || Strings.isNotBlank(collector.getCollectors())
+ || collector.getRegistrationYear() != null
+ || collector.getDeregistrationYear() != null
+ || Strings.isNotBlank(collector.getDistributionStatus())
+ );
+ }
+
+ public boolean isBreeding() {
+ GermplasmInstituteVO breeder = this.germplasm.getBreeder();
+ return breeder != null &&
+ ((breeder.getInstitute() != null && Strings.isNotBlank(breeder.getInstitute().getInstituteName())) ||
+ breeder.getAccessionCreationDate() != null ||
+ Strings.isNotBlank(breeder.getAccessionNumber()) ||
+ breeder.getRegistrationYear() != null ||
+ breeder.getDeregistrationYear() != null);
+ }
+
+ public boolean isGenealogyPresent() {
+ return isPedigreePresent() || isProgenyPresent();
+ }
+
+ private boolean isProgenyPresent() {
+ return germplasm.getChildren() != null && !germplasm.getChildren().isEmpty();
+ }
+
+ private boolean isPedigreePresent() {
+ return this.pedigree != null &&
+ (Strings.isNotBlank(this.pedigree.getParent1Name())
+ || Strings.isNotBlank(this.pedigree.getParent2Name())
+ || Strings.isNotBlank(this.pedigree.getCrossingPlan())
+ || Strings.isNotBlank(this.pedigree.getCrossingYear())
+ || Strings.isNotBlank(this.pedigree.getFamilyCode()));
+ }
+
+ public List<MapLocation> getMapLocations() {
+ List<SiteVO> sites = new ArrayList<>();
+ if (germplasm.getCollectingSite() != null) {
+ sites.add(germplasm.getCollectingSite());
+ }
+ if (germplasm.getOriginSite() != null) {
+ sites.add(germplasm.getOriginSite());
+ }
+ if (germplasm.getEvaluationSites() != null) {
+ sites.addAll(germplasm.getEvaluationSites());
+ }
+
+ return MapLocation.sitesToDisplayableMapLocations(sites);
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/site/MapLocation.java b/backend/src/main/java/fr/inra/urgi/faidare/web/site/MapLocation.java
new file mode 100644
index 0000000000000000000000000000000000000000..3b096853cfff4a467d7a277f9fb4b41e65b2ad01
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/site/MapLocation.java
@@ -0,0 +1,82 @@
+package fr.inra.urgi.faidare.web.site;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.SiteVO;
+import fr.inra.urgi.faidare.utils.Sites;
+
+/**
+ * An object that can be serialized to JSON to serve as a map marker.
+ * @author JB Nizet
+ */
+public final class MapLocation {
+ private final String locationDbId;
+ private final String locationType;
+ private final String locationName;
+ private final double latitude;
+ private final double longitude;
+
+ public MapLocation(String locationDbId,
+ String locationType,
+ String locationName,
+ double latitude,
+ double longitude) {
+ this.locationDbId = locationDbId;
+ this.locationType = locationType;
+ this.locationName = locationName;
+ this.latitude = latitude;
+ this.longitude = longitude;
+ }
+
+ public MapLocation(LocationVO site) {
+ this(site.getLocationDbId(),
+ site.getLocationType(),
+ site.getLocationName(),
+ site.getLatitude(),
+ site.getLongitude());
+ }
+
+ public MapLocation(SiteVO site) {
+ this(Sites.siteIdToLocationId(site.getSiteId()),
+ site.getSiteType(),
+ site.getSiteName(),
+ site.getLatitude(),
+ site.getLongitude());
+ }
+
+ public static List<MapLocation> locationsToDisplayableMapLocations(List<LocationVO> locations) {
+ return locations.stream()
+ .filter(location -> location.getLatitude() != null && location.getLongitude() != null)
+ .map(MapLocation::new)
+ .collect(Collectors.toList());
+ }
+
+ public static List<MapLocation> sitesToDisplayableMapLocations(List<SiteVO> sites) {
+ return sites.stream()
+ .filter(site -> site.getLatitude() != null && site.getLongitude() != null)
+ .map(MapLocation::new)
+ .collect(Collectors.toList());
+ }
+
+ public String getLocationDbId() {
+ return locationDbId;
+ }
+
+ public String getLocationType() {
+ return locationType;
+ }
+
+ public String getLocationName() {
+ return locationName;
+ }
+
+ public double getLatitude() {
+ return latitude;
+ }
+
+ public double getLongitude() {
+ return longitude;
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..151da527d4393d1f388de8d6098b52d4219d98b2
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteController.java
@@ -0,0 +1,94 @@
+package fr.inra.urgi.faidare.web.site;
+
+import java.util.Arrays;
+import java.util.List;
+
+import fr.inra.urgi.faidare.api.NotFoundException;
+import fr.inra.urgi.faidare.config.FaidareProperties;
+import fr.inra.urgi.faidare.domain.brapi.v1.data.BrapiAdditionalInfo;
+import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+import fr.inra.urgi.faidare.repository.es.LocationRepository;
+import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.servlet.ModelAndView;
+
+/**
+ * Controller used to display a site card based on its ID.
+ * @author JB Nizet
+ */
+@Controller("webSiteController")
+@RequestMapping("/sites")
+public class SiteController {
+
+ private final LocationRepository locationRepository;
+ private final FaidareProperties faidareProperties;
+ private final XRefDocumentRepository xRefDocumentRepository;
+
+ public SiteController(LocationRepository locationRepository,
+ FaidareProperties faidareProperties,
+ XRefDocumentRepository xRefDocumentRepository) {
+ this.locationRepository = locationRepository;
+ this.faidareProperties = faidareProperties;
+ this.xRefDocumentRepository = xRefDocumentRepository;
+ }
+
+ @GetMapping("/{siteId}")
+ public ModelAndView get(@PathVariable("siteId") String siteId) {
+ LocationVO site = locationRepository.getById(siteId);
+
+ // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+ // XRefDocumentSearchCriteria.forXRefId(site.getLocationDbId()));
+ List<XRefDocumentVO> crossReferences = Arrays.asList(
+ createXref("foobar"),
+ createXref("bazbing")
+ );
+
+ // LocationVO site = createSite();
+
+ if (site == null) {
+ throw new NotFoundException("Site with ID " + siteId + " not found");
+ }
+
+
+ return new ModelAndView("site",
+ "model",
+ new SiteModel(
+ site,
+ faidareProperties.getByUri(site.getSourceUri()),
+ crossReferences
+ )
+ );
+ }
+
+ 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);
+ xref.setDescription("A very large description for the xref " + name + " which has way more than 120 characters bla bla bla bla bla bla bla bla bla bla bla bla");
+ xref.setDatabaseName("db_" + name);
+ xref.setUrl("https://google.com");
+ xref.setEntryType("type " + name);
+ return xref;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteModel.java b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteModel.java
new file mode 100644
index 0000000000000000000000000000000000000000..0d7e1c0dcef28b8182a3a5ac8f4aa160f067255c
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/site/SiteModel.java
@@ -0,0 +1,118 @@
+package fr.inra.urgi.faidare.web.site;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.DataSource;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+
+/**
+ * The model used py the site page
+ * @author JB Nizet
+ */
+public final class SiteModel {
+ private static final Set<String> IGNORED_PROPERTIES =
+ new HashSet<>(Arrays.asList("Site status",
+ "Coordinates precision",
+ "Slope",
+ "Exposure",
+ "Geographical location",
+ "Distance to city",
+ "Direction from city",
+ "Environment type",
+ "Topography",
+ "Comment"));
+
+ private final LocationVO site;
+ private final DataSource source;
+ private final Map<String, Object> additionalInfo;
+ private final List<XRefDocumentVO> crossReferences;
+ private final List<Map.Entry<String, Object>> additionalInfoProperties;
+
+ public SiteModel(LocationVO site,
+ DataSource source,
+ List<XRefDocumentVO> crossReferences) {
+ this.site = site;
+ this.source = source;
+ this.additionalInfo = site.getAdditionalInfo() == null ? Collections.emptyMap() : site.getAdditionalInfo().getProperties();
+ this.crossReferences = crossReferences;
+ this.additionalInfoProperties =
+ this.additionalInfo
+ .entrySet()
+ .stream()
+ .filter(entry -> !IGNORED_PROPERTIES.contains(entry.getKey()))
+ .filter(entry -> entry.getValue() != null && !entry.getValue().toString().isEmpty())
+ .sorted(Map.Entry.comparingByKey())
+ .collect(Collectors.toList());
+ }
+
+ public LocationVO getSite() {
+ return site;
+ }
+
+ public DataSource getSource() {
+ return source;
+ }
+
+ public Map<String, Object> getAdditionalInfo() {
+ return this.additionalInfo;
+ }
+
+ public Object getSiteStatus() {
+ return this.additionalInfo.get("Site status");
+ }
+
+ public Object getCoordinatesPrecision() {
+ return this.additionalInfo.get("Coordinates precision");
+ }
+
+ public Object getGeographicalLocation() {
+ return this.additionalInfo.get("Geographical location");
+ }
+
+ public Object getSlope() {
+ return this.additionalInfo.get("Slope");
+ }
+
+ public Object getExposure() {
+ return this.additionalInfo.get("Exposure");
+ }
+
+ public Object getTopography() {
+ return this.additionalInfo.get("Topography");
+ }
+
+ public Object getEnvironmentType() {
+ return this.additionalInfo.get("Environment type");
+ }
+
+ public Object getDistanceToCity() {
+ return this.additionalInfo.get("Distance to city");
+ }
+
+ public Object getDirectionFromCity() {
+ return this.additionalInfo.get("Direction from city");
+ }
+
+ public Object getComment() {
+ return this.additionalInfo.get("Comment");
+ }
+
+ public List<Map.Entry<String, Object>> getAdditionalInfoProperties() {
+ return additionalInfoProperties;
+ }
+
+ public List<XRefDocumentVO> getCrossReferences() {
+ return crossReferences;
+ }
+
+ public List<MapLocation> getMapLocations() {
+ return MapLocation.locationsToDisplayableMapLocations(Collections.singletonList(this.site));
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..833c45471061a5ef02d7f5fc57319fc9afc8a12b
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyController.java
@@ -0,0 +1,159 @@
+package fr.inra.urgi.faidare.web.study;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import com.google.common.collect.Lists;
+import fr.inra.urgi.faidare.api.NotFoundException;
+import fr.inra.urgi.faidare.config.FaidareProperties;
+import fr.inra.urgi.faidare.domain.criteria.GermplasmPOSTSearchCriteria;
+import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.data.TrialVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.data.study.StudyDetailVO;
+import fr.inra.urgi.faidare.domain.data.variable.ObservationVariableVO;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+import fr.inra.urgi.faidare.repository.es.GermplasmRepository;
+import fr.inra.urgi.faidare.repository.es.LocationRepository;
+import fr.inra.urgi.faidare.repository.es.StudyRepository;
+import fr.inra.urgi.faidare.repository.es.TrialRepository;
+import fr.inra.urgi.faidare.repository.es.XRefDocumentRepository;
+import fr.inra.urgi.faidare.repository.file.CropOntologyRepository;
+import fr.inra.urgi.faidare.web.site.MapLocation;
+import org.apache.logging.log4j.util.Strings;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.servlet.ModelAndView;
+
+/**
+ * Controller used to display a study card based on its ID.
+ * @author JB Nizet
+ */
+@Controller("webStudyController")
+@RequestMapping("/studies")
+public class StudyController {
+
+ private final StudyRepository studyRepository;
+ private final FaidareProperties faidareProperties;
+ private final XRefDocumentRepository xRefDocumentRepository;
+ private final GermplasmRepository germplasmRepository;
+ private final CropOntologyRepository cropOntologyRepository;
+ private final TrialRepository trialRepository;
+ private final LocationRepository locationRepository;
+
+ public StudyController(StudyRepository studyRepository,
+ FaidareProperties faidareProperties,
+ XRefDocumentRepository xRefDocumentRepository,
+ GermplasmRepository germplasmRepository,
+ CropOntologyRepository cropOntologyRepository,
+ TrialRepository trialRepository,
+ LocationRepository locationRepository) {
+ this.studyRepository = studyRepository;
+ this.faidareProperties = faidareProperties;
+ this.xRefDocumentRepository = xRefDocumentRepository;
+ this.germplasmRepository = germplasmRepository;
+ this.cropOntologyRepository = cropOntologyRepository;
+ this.trialRepository = trialRepository;
+ this.locationRepository = locationRepository;
+ }
+
+ @GetMapping("/{studyId}")
+ public ModelAndView get(@PathVariable("studyId") String studyId) {
+ StudyDetailVO study = studyRepository.getById(studyId);
+
+ // List<XRefDocumentVO> crossReferences = xRefDocumentRepository.find(
+ // XRefDocumentSearchCriteria.forXRefId(site.getLocationDbId()));
+ List<XRefDocumentVO> crossReferences = Arrays.asList(
+ createXref("foobar"),
+ createXref("bazbing")
+ );
+
+ // LocationVO site = createSite();
+
+ 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(
+ study,
+ faidareProperties.getByUri(study.getSourceUri()),
+ germplasms,
+ variables,
+ trials,
+ crossReferences,
+ location
+ )
+ );
+ }
+
+ private LocationVO getLocation(StudyDetailVO study) {
+ if (Strings.isBlank(study.getLocationDbId())) {
+ return null;
+ }
+ return locationRepository.getById(study.getLocationDbId());
+ }
+
+ private List<GermplasmVO> getGermplasms(StudyDetailVO study) {
+ if (study.getGermplasmDbIds() == null || study.getGermplasmDbIds().isEmpty()) {
+ return Collections.emptyList();
+ } else {
+ GermplasmPOSTSearchCriteria germplasmCriteria = new GermplasmPOSTSearchCriteria();
+ germplasmCriteria.setGermplasmDbIds(Lists.newArrayList(study.getGermplasmDbIds()));
+ return germplasmRepository.find(germplasmCriteria)
+ .stream()
+ .sorted(Comparator.comparing(GermplasmVO::getGermplasmName))
+ .collect(Collectors.toList());
+ }
+ }
+
+ private List<ObservationVariableVO> getVariables(StudyDetailVO study) {
+ Set<String> variableIds = studyRepository.getVariableIds(study.getStudyDbId());
+ return cropOntologyRepository.getVariableByIds(variableIds)
+ .stream()
+ .sorted(Comparator.comparing(ObservationVariableVO::getObservationVariableDbId))
+ .collect(Collectors.toList());
+ }
+
+ private List<TrialVO> getTrials(StudyDetailVO study) {
+ if (study.getTrialDbIds() == null || study.getTrialDbIds().isEmpty()) {
+ return Collections.emptyList();
+ }
+
+ return study.getTrialDbIds()
+ .stream()
+ .sorted(Comparator.naturalOrder())
+ .map(trialRepository::getById)
+ .filter(Objects::nonNull)
+ .collect(Collectors.toList());
+ }
+
+
+
+ private XRefDocumentVO createXref(String name) {
+ XRefDocumentVO xref = new XRefDocumentVO();
+ xref.setName(name);
+ xref.setDescription("A very large description for the xref " + name + " which has way more than 120 characters bla bla bla bla bla bla bla bla bla bla bla bla");
+ xref.setDatabaseName("db_" + name);
+ xref.setUrl("https://google.com");
+ xref.setEntryType("type " + name);
+ return xref;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyModel.java b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyModel.java
new file mode 100644
index 0000000000000000000000000000000000000000..bc77dfc3d9b9fdb7da63dd7b47afb15ab1e3bff6
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/study/StudyModel.java
@@ -0,0 +1,90 @@
+package fr.inra.urgi.faidare.web.study;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import fr.inra.urgi.faidare.domain.data.LocationVO;
+import fr.inra.urgi.faidare.domain.data.TrialVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.GermplasmVO;
+import fr.inra.urgi.faidare.domain.data.study.StudyDetailVO;
+import fr.inra.urgi.faidare.domain.data.variable.ObservationVariableVO;
+import fr.inra.urgi.faidare.domain.datadiscovery.data.DataSource;
+import fr.inra.urgi.faidare.domain.xref.XRefDocumentVO;
+import fr.inra.urgi.faidare.web.site.MapLocation;
+
+/**
+ * The model used by the study page
+ * @author JB Nizet
+ */
+public final class StudyModel {
+ private final StudyDetailVO study;
+ private final DataSource source;
+ private final List<GermplasmVO> germplasms;
+ private final List<ObservationVariableVO> variables;
+ private final List<TrialVO> trials;
+ private final List<XRefDocumentVO> crossReferences;
+ private final LocationVO location;
+ private final List<Map.Entry<String, Object>> additionalInfoProperties;
+
+ public StudyModel(StudyDetailVO study,
+ DataSource source,
+ List<GermplasmVO> germplasms,
+ List<ObservationVariableVO> variables,
+ List<TrialVO> trials,
+ List<XRefDocumentVO> crossReferences,
+ LocationVO location) {
+ this.study = study;
+ this.source = source;
+ this.germplasms = germplasms;
+ this.variables = variables;
+ this.trials = trials;
+ this.crossReferences = crossReferences;
+ this.location = location;
+
+ Map<String, Object> additionalInfo =
+ study.getAdditionalInfo() == null ? Collections.emptyMap() : study.getAdditionalInfo().getProperties();
+ this.additionalInfoProperties =
+ additionalInfo.entrySet()
+ .stream()
+ .filter(entry -> entry.getValue() != null && !entry.getValue().toString().isEmpty())
+ .sorted(Map.Entry.comparingByKey())
+ .collect(Collectors.toList());
+ }
+
+ public StudyDetailVO getStudy() {
+ return study;
+ }
+
+ public DataSource getSource() {
+ return source;
+ }
+
+ public List<XRefDocumentVO> getCrossReferences() {
+ return crossReferences;
+ }
+
+ public List<GermplasmVO> getGermplasms() {
+ return germplasms;
+ }
+
+ public List<ObservationVariableVO> getVariables() {
+ return variables;
+ }
+
+ public List<TrialVO> getTrials() {
+ return trials;
+ }
+
+ public List<Map.Entry<String, Object>> getAdditionalInfoProperties() {
+ return additionalInfoProperties;
+ }
+
+ public List<MapLocation> getMapLocations() {
+ if (this.location == null) {
+ return Collections.emptyList();
+ }
+ return MapLocation.locationsToDisplayableMapLocations(Collections.singletonList(this.location));
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/Coordinates.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/Coordinates.java
new file mode 100644
index 0000000000000000000000000000000000000000..554929b11d88e103093f808be0ba969118c47772
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/Coordinates.java
@@ -0,0 +1,71 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import java.text.DecimalFormat;
+import java.util.Locale;
+
+/**
+ * The actual object offering Coordinates helper methods to thymeleaf
+ * @author JB Nizet
+ */
+public class Coordinates {
+ private final Locale locale;
+
+ public Coordinates(Locale locale) {
+ this.locale = locale;
+ }
+
+ public String format(Double value) {
+ if (value == null) {
+ return "";
+ }
+ return DecimalFormat.getInstance(locale).format(value);
+ }
+
+ public String formatLatitude(Double value) {
+ if (value == null) {
+ return "";
+ }
+ return this.format(value) + " — " + this.toLatitudeDegrees(value);
+ }
+
+ public String formatLongitude(Double value) {
+ if (value == null) {
+ return "";
+ }
+ return this.format(value) + " — " + this.toLongitudeDegrees(value);
+ }
+
+ public String toLatitudeDegrees(Double latitude) {
+ if (latitude == null) {
+ return "";
+ }
+
+ return toDegrees(latitude) + " " + ((latitude < 0) ? "S" : "N");
+ }
+
+ public String toLongitudeDegrees(Double longitude) {
+ if (longitude == null) {
+ return "";
+ }
+
+ return toDegrees(longitude) + " " + ((longitude < 0) ? "W" : "E");
+ }
+
+ private String toDegrees(double value) {
+ double absoluteDegrees = Math.abs(value);
+ int fullDegrees = (int) absoluteDegrees;
+ double remainingMinutes = (absoluteDegrees - fullDegrees) * 60;
+ int minutes = (int) remainingMinutes;
+ double remainingSeconds = (remainingMinutes - minutes) * 60;
+ int seconds = (int) remainingSeconds;
+ if (seconds == 60) {
+ minutes += 1;
+ seconds = 0;
+ }
+ if (minutes == 60) {
+ fullDegrees += 1;
+ minutes = 0;
+ }
+ return fullDegrees + "°" + minutes + "'" + seconds;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/CoordinatesDialect.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/CoordinatesDialect.java
new file mode 100644
index 0000000000000000000000000000000000000000..d443e589ca1c8e82c00960faeb9f15733db0e102
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/CoordinatesDialect.java
@@ -0,0 +1,28 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import org.springframework.stereotype.Component;
+import org.thymeleaf.dialect.AbstractDialect;
+import org.thymeleaf.dialect.IDialect;
+import org.thymeleaf.dialect.IExpressionObjectDialect;
+import org.thymeleaf.expression.IExpressionObjectFactory;
+import org.thymeleaf.extras.java8time.dialect.Java8TimeExpressionFactory;
+
+/**
+ * A thymeleaf dialect allowing to transform coordinates (latitude and longitude)
+ * to degrees.
+ * @author JB Nizet
+ */
+@Component
+public class CoordinatesDialect extends AbstractDialect implements IExpressionObjectDialect {
+
+ private final IExpressionObjectFactory COORDINATES_EXPRESSION_OBJECTS_FACTORY = new CoordinatesExpressionFactory();
+
+ protected CoordinatesDialect() {
+ super("coordinates");
+ }
+
+ @Override
+ public IExpressionObjectFactory getExpressionObjectFactory() {
+ return COORDINATES_EXPRESSION_OBJECTS_FACTORY;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/CoordinatesExpressionFactory.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/CoordinatesExpressionFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..e3c25cc8577aae0cac73a894915d6c33edd6d8ca
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/CoordinatesExpressionFactory.java
@@ -0,0 +1,36 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.thymeleaf.context.IExpressionContext;
+import org.thymeleaf.expression.IExpressionObjectFactory;
+import org.thymeleaf.extras.java8time.expression.Temporals;
+
+/**
+ * The object factory for the {@link CoordinatesDialect}
+ * @author JB Nizet
+ */
+public class CoordinatesExpressionFactory implements IExpressionObjectFactory {
+ private static final String COORDINATES_EVALUATION_VARIABLE_NAME = "coordinates";
+
+ private static final Set<String> ALL_EXPRESSION_OBJECT_NAMES =
+ Collections.singleton(COORDINATES_EVALUATION_VARIABLE_NAME);
+
+ @Override
+ public Set<String> getAllExpressionObjectNames() {
+ return ALL_EXPRESSION_OBJECT_NAMES;
+ }
+
+ @Override
+ public Object buildObject(IExpressionContext context, String expressionObjectName) {
+ return new Coordinates(context.getLocale());
+ }
+
+ @Override
+ public boolean isCacheable(String expressionObjectName) {
+ return true;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java
new file mode 100644
index 0000000000000000000000000000000000000000..2a02a842a28ba411f8f6d16d6c5254e41a53524b
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareDialect.java
@@ -0,0 +1,25 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import org.springframework.stereotype.Component;
+import org.thymeleaf.dialect.AbstractDialect;
+import org.thymeleaf.dialect.IExpressionObjectDialect;
+import org.thymeleaf.expression.IExpressionObjectFactory;
+
+/**
+ * A thymeleaf dialect allowing to perform various tasks in the template related to Faidare
+ * @author JB Nizet
+ */
+@Component
+public class FaidareDialect extends AbstractDialect implements IExpressionObjectDialect {
+
+ private final IExpressionObjectFactory FAIDARE_EXPRESSION_OBJECTS_FACTORY = new FaidareExpressionFactory();
+
+ protected FaidareDialect() {
+ super("faidare");
+ }
+
+ @Override
+ public IExpressionObjectFactory getExpressionObjectFactory() {
+ return FAIDARE_EXPRESSION_OBJECTS_FACTORY;
+ }
+}
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressionFactory.java b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressionFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..e873375c1a7681d2837c0bf6591174d1aa557e3d
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressionFactory.java
@@ -0,0 +1,33 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import java.util.Collections;
+import java.util.Set;
+
+import org.thymeleaf.context.IExpressionContext;
+import org.thymeleaf.expression.IExpressionObjectFactory;
+
+/**
+ * The object factory for the {@link FaidareDialect}
+ * @author JB Nizet
+ */
+public class FaidareExpressionFactory implements IExpressionObjectFactory {
+ private static final String FAIDARE_EVALUATION_VARIABLE_NAME = "faidare";
+
+ private static final Set<String> ALL_EXPRESSION_OBJECT_NAMES =
+ Collections.singleton(FAIDARE_EVALUATION_VARIABLE_NAME);
+
+ @Override
+ public Set<String> getAllExpressionObjectNames() {
+ return ALL_EXPRESSION_OBJECT_NAMES;
+ }
+
+ @Override
+ public Object buildObject(IExpressionContext context, String expressionObjectName) {
+ return new FaidareExpressions(context.getLocale());
+ }
+
+ @Override
+ public boolean isCacheable(String expressionObjectName) {
+ return true;
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..9ba16d342d94e9097e720c5b3ad2e370d564fe6d
--- /dev/null
+++ b/backend/src/main/java/fr/inra/urgi/faidare/web/thymeleaf/FaidareExpressions.java
@@ -0,0 +1,78 @@
+package fr.inra.urgi.faidare.web.thymeleaf;
+
+import java.nio.charset.StandardCharsets;
+import java.text.DecimalFormat;
+import java.util.Base64;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Locale;
+import java.util.Map;
+import java.util.function.Function;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import fr.inra.urgi.faidare.domain.data.germplasm.CollPopVO;
+import fr.inra.urgi.faidare.domain.data.germplasm.TaxonSourceVO;
+import fr.inra.urgi.faidare.utils.Sites;
+import org.apache.logging.log4j.util.Strings;
+
+/**
+ * The actual object offering Faidare helper methods to thymeleaf
+ * @author JB Nizet
+ */
+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 Map<String, Function<String, String>> createTaxonIdUrlFactories() {
+ Map<String, Function<String, String>> result = new HashMap<>();
+ result.put("NCBI", s -> "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + s);
+ result.put("ThePlantList", s -> "http://www.theplantlist.org/tpl1.1/record/" + s);
+ result.put("TAXREF", s -> "https://inpn.mnhn.fr/espece/cd_nom/" + s);
+ result.put("CatalogueOfLife", s -> "http://www.catalogueoflife.org/col/details/species/id/" + s);
+ return Collections.unmodifiableMap(result);
+ }
+
+ private final Locale locale;
+
+ public FaidareExpressions(Locale locale) {
+ this.locale = locale;
+ }
+
+ public String toSiteParam(String siteId) {
+ return Sites.siteIdToLocationId(siteId);
+ }
+
+ public String collPopTitle(CollPopVO collPopVO) {
+ return collPopTitle(collPopVO, Function.identity());
+ }
+
+ public String collPopTitleWithoutUnderscores(CollPopVO collPopVO) {
+ return collPopTitle(collPopVO, s -> s.replace('_', ' '));
+ }
+
+ public String taxonIdUrl(TaxonSourceVO taxonSource) {
+ Function<String, String> urlFactory =
+ TAXON_ID_URL_FACTORIES_BY_SOURCE_NAME.get(taxonSource.getSourceName());
+ 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);
+ }
+ }
+
+ private String collPopTitle(CollPopVO collPopVO, Function<String, String> nameTransformer) {
+ if (Strings.isBlank(collPopVO.getType())) {
+ return nameTransformer.apply(collPopVO.getName());
+ } else {
+ return nameTransformer.apply(collPopVO.getName()) + " (" + collPopVO.getType() + ")";
+ }
+ }
+}
diff --git a/backend/src/main/main.iml b/backend/src/main/main.iml
deleted file mode 100644
index 50f3d6bc79c58fa92df31bb59ab229d1e7c0c12e..0000000000000000000000000000000000000000
--- a/backend/src/main/main.iml
+++ /dev/null
@@ -1,39 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="true">
- <exclude-output />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/java" isTestSource="false" />
- </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/main/resources/application.yml b/backend/src/main/resources/application.yml
index 26c55fc3839132b3f6aca48b40f00c061a6b180f..2b684f600c3e548456c9e68ef473116839440929 100644
--- a/backend/src/main/resources/application.yml
+++ b/backend/src/main/resources/application.yml
@@ -90,3 +90,11 @@ server:
servlet:
context-path: /faidare-dev
+---
+spring:
+ profiles:
+ dev
+ resources:
+ static-locations:
+ - classpath:/static/
+ - file:./web/build/dist/
diff --git a/backend/src/main/resources/static/assets/images/favicon.ico b/backend/src/main/resources/static/assets/images/favicon.ico
new file mode 100644
index 0000000000000000000000000000000000000000..7fc066f132eb58eeaf30b6259da59f5ed92aca8e
Binary files /dev/null and b/backend/src/main/resources/static/assets/images/favicon.ico differ
diff --git a/backend/src/main/resources/static/assets/images/logo.png b/backend/src/main/resources/static/assets/images/logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..86b3ab108693a19cca5a05c95faebd8573e23389
Binary files /dev/null and b/backend/src/main/resources/static/assets/images/logo.png differ
diff --git a/backend/src/main/resources/static/assets/images/marker-icon-blue.png b/backend/src/main/resources/static/assets/images/marker-icon-blue.png
new file mode 100644
index 0000000000000000000000000000000000000000..e2e9f757f515ded172e6f72c3ce55bbe15579649
Binary files /dev/null and b/backend/src/main/resources/static/assets/images/marker-icon-blue.png differ
diff --git a/backend/src/main/resources/static/assets/images/marker-icon-green.png b/backend/src/main/resources/static/assets/images/marker-icon-green.png
new file mode 100644
index 0000000000000000000000000000000000000000..6b4fb278f611f802d0c4e9cf88edad80e1e1c975
Binary files /dev/null and b/backend/src/main/resources/static/assets/images/marker-icon-green.png differ
diff --git a/backend/src/main/resources/static/assets/images/marker-icon-purple.png b/backend/src/main/resources/static/assets/images/marker-icon-purple.png
new file mode 100644
index 0000000000000000000000000000000000000000..63e423d250842ad5c9666507a4dd843a8f6a2b93
Binary files /dev/null and b/backend/src/main/resources/static/assets/images/marker-icon-purple.png differ
diff --git a/backend/src/main/resources/static/assets/images/marker-icon-red.png b/backend/src/main/resources/static/assets/images/marker-icon-red.png
new file mode 100644
index 0000000000000000000000000000000000000000..e3c0026ef246271f89aad81b6cf47b2ff63596d9
Binary files /dev/null and b/backend/src/main/resources/static/assets/images/marker-icon-red.png differ
diff --git a/backend/src/main/resources/templates/fragments/institute.html b/backend/src/main/resources/templates/fragments/institute.html
new file mode 100644
index 0000000000000000000000000000000000000000..b2e8da3ad2ef0e0d12bccaabfed479d893a2631c
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/institute.html
@@ -0,0 +1,34 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+
+<!--
+Reusable fragment displaying the content of an institute popover.
+Its unique argument (institute) is an InstituteVO
+-->
+
+<th:block th:fragment="institute(institute)">
+ <div class="text-center py-2" th:if="${institute.logo}">
+ <img class="img-fluid" th:src="${institute.logo}" />
+ </div>
+ <div th:replace="fragments/row::text-row(label='Code', text=${institute.instituteCode})"></div>
+ <div th:replace="fragments/row::text-row(label='Acronym', text=${institute.acronym})"></div>
+ <div th:replace="fragments/row::text-row(label='Organization', text=${institute.organisation})"></div>
+ <div th:replace="fragments/row::text-row(label='Type', text=${institute.instituteType})"></div>
+ <div th:replace="fragments/row::text-row(label='Address', text=${institute.address})"></div>
+
+ <th:block th:if="${institute.webSite}">
+ <div th:replace="fragments/row::row(label='Website', content=~{::.institute-website})">
+ <a class="institute-website"
+ target="_blank"
+ th:href="${institute.webSite}"
+ th:text="${#strings.abbreviate(institute.webSite, 25)}"></a>
+ </div>
+ </th:block>
+</th:block>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/fragments/link.html b/backend/src/main/resources/templates/fragments/link.html
new file mode 100644
index 0000000000000000000000000000000000000000..d7c43bbdb422c31c5bce647d302c803270672669
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/link.html
@@ -0,0 +1,20 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+<!--
+Reusable fragment displaying a link with a label if the provided url is not
+empty, or a span with the label if the provided url is empty.
+Both arguments are strings.
+-->
+<th:block th:fragment="link(label, url)">
+ <a th:unless="${#strings.isEmpty(url)}"
+ th:href="${url}"
+ th:text="${label}"></a>
+ <span th:if="${#strings.isEmpty(url)}" th:text="${label}"></span>
+</th:block>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/fragments/map.html b/backend/src/main/resources/templates/fragments/map.html
new file mode 100644
index 0000000000000000000000000000000000000000..35ebed333c5c5eaf55160f400e5ebde01313cf24
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/map.html
@@ -0,0 +1,23 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+<!--
+Reusable fragment displaying a map and its legend.
+The map is initially hidden. The JavaScript displays it if there are locations
+to display
+-->
+<div th:fragment="map" id="map-container" class="d-none">
+ <div id="map" class="border rounded"></div>
+ <div class="map-legend mt-1 small">
+ <img th:src="@{/assets/images/marker-icon-red.png}" id="red"/>
+ <label for="red" class="me-2">Origin site</label>
+ <img th:src="@{/assets/images/marker-icon-blue.png}" id="blue"/>
+ <label for="blue" class="me-2">Collecting site</label>
+ <img th:src="@{/assets/images/marker-icon-green.png}" id="green"/>
+ <label for="green" class="me-2">Evaluation site</label>
+ <img th:src="@{/assets/images/marker-icon-purple.png}" id="purple"/>
+ <label for="purple">Multi-purpose site</label>
+ </div>
+</div>
diff --git a/backend/src/main/resources/templates/fragments/row.html b/backend/src/main/resources/templates/fragments/row.html
new file mode 100644
index 0000000000000000000000000000000000000000..8676b5906b77ae97d6e8c2ca826839450ce28842
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/row.html
@@ -0,0 +1,50 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+
+<!--
+Reusable fragment displaying a responsive row containing a label and a content.
+The label argument is a string.
+The content argument is a fragment which is displayed at the right of the label.
+
+Note that `th:if` is not evaluated when th:replace is used. So if this row must
+be displayed only if some condition is true, the fragment should be enclosed
+into a block with the condition:
+ <th:block th:if="${someCondition}">
+ <div th:replace="fragments/row::row(label='Some label', content=~{::#some-content-id})">
+ <span id="some-content-id">the content here</span>
+ </div>
+ </th:block>
+-->
+
+<div th:fragment="row(label, content)" class="row f-row">
+ <div class="col-md-4 label pb-1 pb-md-0" th:text="${label}"></div>
+ <div class="col">
+ <th:block th:replace="${content}" />
+ </div>
+</div>
+
+<!--
+Reusable fragment displaying a responsive row containing a label and a textual content.
+The label argument is a string.
+The text argument is a string which is displayed at the right of the label.
+The whole row is omitted if the textual content is empty, so the caller does not
+need to test that condition.
+
+Note that `th:if` is not evaluated when th:replace is used. So if this row must
+be displayed only if some other condition is true, the fragment should be enclosed
+into a block with the condition:
+ <th:block th:if="${someCondition}">
+ <div th:replace="fragments/row::text-row(label='Some label', text=${someTextExpression})"></div>
+ </th:block>
+-->
+<div th:fragment="text-row(label, text)" th:unless="${#strings.isEmpty(text)}" class="row f-row">
+ <div class="col-md-4 label pb-1 pb-md-0" th:text="${label}"></div>
+ <div class="col" th:text="${text}"></div>
+</div>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/fragments/source.html b/backend/src/main/resources/templates/fragments/source.html
new file mode 100644
index 0000000000000000000000000000000000000000..b09638810885559be62d0c5448adecd617dbe2fb
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/source.html
@@ -0,0 +1,35 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+
+<!--
+Reusable fragment displaying the source and the data links of an entity (site, study or germplasm).
+The source argument is a DataSource.
+The url argument is a string, which is the URL of the entity.
+The entityType argument is a string, which is used in the message
+"Link to this <entityType>".
+-->
+
+<th:block th:fragment="source(source, url, entityType)">
+ <th:block th:if="${source != null}">
+ <div th:replace="fragments/row::row(label='Source', content=~{::.source})">
+ <a class="source" target="_blank" th:href="${source.url}">
+ <img class="img-fluid" style="max-height: 60px;" th:src="${source.image}" th:alt="${source.name} + ' logo'" />
+ </a>
+ </div>
+ </th:block>
+
+ <th:block th:if="${url != null && source != null}">
+ <div th:replace="fragments/row::row(label='Data link', content=~{::.source-url})">
+ <a class="source-url" target="_blank" th:href="${url}">
+ Link to this <span th:text="${entityType}"></span> on <th:block th:text="${source.name}" />
+ </a>
+ </div>
+ </th:block>
+</th:block>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/fragments/xrefs.html b/backend/src/main/resources/templates/fragments/xrefs.html
new file mode 100644
index 0000000000000000000000000000000000000000..c60310b69c5d852b7a636d9ab7392d0a52d2b553
--- /dev/null
+++ b/backend/src/main/resources/templates/fragments/xrefs.html
@@ -0,0 +1,40 @@
+<!DOCTYPE html>
+
+<html xmlns:th="http://www.thymeleaf.org">
+
+<body>
+
+<!--
+Reusable fragment displaying a cross references section, with its title.
+The unique argument (crossReferences) is a List<XRefDocumentVO>
+-->
+
+<div class="f-card" th:fragment="xrefs(crossReferences)" th:if="${!#lists.isEmpty(crossReferences)}">
+ <h2>Cross references</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container scroll-table-container-big">
+ <table class="table table-sm table-striped table-sticky table-responsive-sm">
+ <thead>
+ <tr>
+ <th scope="col">Name</th>
+ <th scope="col">Source</th>
+ <th scope="col">Type</th>
+ <th scope="col">Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="crossRef : ${crossReferences}">
+ <td><a th:href="${crossRef.url}" target="_blank" th:text="${crossRef.name}"></a></td>
+ <td th:text="${crossRef.databaseName}"></td>
+ <td th:text="${crossRef.entryType}"></td>
+ <td style="min-width: 30rem;" th:text="${#strings.abbreviate(crossRef.description, 120)}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+</div>
+
+</body>
+
+</html>
diff --git a/backend/src/main/resources/templates/germplasm.html b/backend/src/main/resources/templates/germplasm.html
new file mode 100644
index 0000000000000000000000000000000000000000..f5c6a4ce2fdfa2f12bd1e2826f01dfea0c0fa48c
--- /dev/null
+++ b/backend/src/main/resources/templates/germplasm.html
@@ -0,0 +1,452 @@
+<!DOCTYPE html>
+
+<html
+ xmlns:th="http://www.thymeleaf.org"
+ th:replace="~{layout/main :: layout(title=~{::title}, content=~{::main}, script=~{::script})}"
+>
+<head>
+ <title>Germplasm: <th:block th:text="${model.germplasm.germplasmName}" /></title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+</head>
+
+<body>
+<main>
+ <div class="d-flex">
+ <h1 class="flex-grow-1">Germplasm: <th:block th:text="${model.germplasm.germplasmName}" /></h1>
+ <div th:if="${model.germplasm.holdingGenbank != null && model.germplasm.holdingGenbank.logo != null}">
+ <img th:src="${model.germplasm.holdingGenbank.logo}" th:alt="${model.germplasm.holdingGenbank.instituteName}" />
+ </div>
+ </div>
+
+ <div th:replace="fragments/map::map"></div>
+
+ <div class="row align-items-center justify-content-center mt-4">
+ <div class="col-auto field" th:if="${model.germplasm.photo != null && model.germplasm.photo.thumbnailFile != null}">
+ <template id="photo-popover">
+ <div class="card">
+ <img th:src="${model.germplasm.photo.file}" class="card-img-top" alt="">
+ <div class="card-body">
+ <div th:replace="fragments/row::text-row(label='Accession name', text=${model.germplasm.germplasmName})"></div>
+ <div th:replace="fragments/row::text-row(label='Photo name', text=${model.germplasm.photo.photoName})"></div>
+ <div th:replace="fragments/row::text-row(label='Description', text=${model.germplasm.photo.description})"></div>
+ <div th:replace="fragments/row::text-row(label='Copyright', text=${model.germplasm.photo.copyright})"></div>
+ </div>
+ </div>
+ </template>
+
+ <a role="button"
+ class="d-flex flex-column align-items-center"
+ data-bs-toggle="popover"
+ tabindex="0"
+ th:data-bs-title="${model.germplasm.photo.photoName}"
+ data-bs-element="#photo-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus">
+ <img th:src="${model.germplasm.photo.thumbnailFile}" class="img-fluid" />
+
+ <figcaption class="figure-caption">
+ © <span th:text="${model.germplasm.photo.copyright}"></span>
+ </figcaption>
+ </a>
+ </div>
+
+ <div class="col-12 col-lg">
+ <div class="f-card">
+ <h2>Identification</h2>
+
+ <div class="f-card-body">
+ <div th:replace="fragments/row::text-row(label='Germplasm name', text=${model.germplasm.germplasmName})"></div>
+ <div th:replace="fragments/row::text-row(label='Accession number', text=${model.germplasm.accessionNumber})"></div>
+
+ <div th:replace="fragments/source::source(source=${model.source}, url=${model.germplasm.url}, entityType='germplasm')"></div>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.synonyms)}">
+ <div th:replace="fragments/row::row(label='Accession synonyms', content=~{::#accession-synonyms})">
+ <div id="accession-synonyms" class="content-overflow" th:text="${#strings.listJoin(model.germplasm.synonyms, ', ')}"></div>
+ </div>
+ </th:block>
+
+ <th:block th:unless="${#strings.isEmpty(model.taxon)}">
+ <div th:replace="fragments/row::row(label='Taxon', content=~{::#taxon})">
+ <div id="taxon">
+ <template id="taxon-popover">
+ <th:block th:unless="${#strings.isEmpty(model.germplasm.genus)}">
+ <div th:replace="fragments/row::row(label='Genus', content=~{::#taxon-genus})">
+ <em id="taxon-genus" th:text="${model.germplasm.genus}"></em>
+ </div>
+ </th:block>
+ <th:block th:unless="${#strings.isEmpty(model.germplasm.species)}">
+ <div th:replace="fragments/row::row(label='Species', content=~{::#taxon-species})">
+ <span id="taxon-species">
+ <em th:text="${model.germplasm.species}"></em>
+ <span th:unless="${#strings.isEmpty(model.germplasm.speciesAuthority)}"
+ th:text="${'(' + model.germplasm.speciesAuthority + ')'}"></span>
+ </span>
+ </div>
+ </th:block>
+ <th:block th:unless="${#strings.isEmpty(model.germplasm.subtaxa)}">
+ <div th:replace="fragments/row::row(label='Subtaxa', content=~{::#taxon-subtaxa})">
+ <span id="taxon-subtaxa">
+ <em th:text="${model.germplasm.subtaxa}"></em>
+ <span th:unless="${#strings.isEmpty(model.germplasm.subtaxaAuthority)}"
+ th:text="${'(' + model.germplasm.subtaxaAuthority + ')'}"></span>
+ </span>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Authority', text=${model.taxonAuthor})"></div>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.taxonIds)}">
+ <div th:replace="fragments/row::row(label='Taxon IDs', content=~{::#taxon-ids})">
+ <div id="taxon-ids">
+ <div th:each="taxonId : ${model.germplasm.taxonIds}" class="row">
+ <div class="col-6 text-nowrap" th:text="${taxonId.sourceName}"></div>
+ <div class="col-6">
+ <span class="taxon-id"
+ th:replace="fragments/link::link(label=${taxonId.taxonId}, url=${#faidare.taxonIdUrl(taxonId)})"></span>
+ </div>
+ </div>
+ </div>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Comment', text=${model.germplasm.taxonComment})"></div>
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.taxonCommonNames)}">
+ <div th:replace="fragments/row::row(label='Taxon common names', content=~{::#taxon-common-names})">
+ <div id="taxon-common-names" class="content-overflow" th:text="${#strings.listJoin(model.germplasm.taxonCommonNames, ', ')}"></div>
+ </div>
+ </th:block>
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.taxonSynonyms)}">
+ <div th:replace="fragments/row::row(label='Taxon common names', content=~{::#taxon-synonyms})">
+ <div id="taxon-synonyms" class="content-overflow" th:text="${#strings.listJoin(model.germplasm.taxonSynonyms, ', ')}"></div>
+ </div>
+ </th:block>
+ </template>
+ <a role="button"
+ tabindex="0"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.taxon}"
+ data-bs-element="#taxon-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus">
+ <em th:text="${model.taxon}"></em>
+ <th:block th:unless="${#strings.isEmpty(model.taxonAuthor)}">(<span th:text="${model.taxonAuthor}"></span>)</th:block>
+ </a>
+ </div>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Biological status', text=${model.germplasm.biologicalStatusOfAccessionCode})"></div>
+ <div th:replace="fragments/row::text-row(label='Genetic nature', text=${model.germplasm.geneticNature})"></div>
+ <div th:replace="fragments/row::text-row(label='Seed source', text=${model.germplasm.seedSource})"></div>
+ <div th:replace="fragments/row::text-row(label='Pedigree', text=${model.germplasm.pedigree})"></div>
+ <div th:replace="fragments/row::text-row(label='Comments', text=${model.germplasm.comment})"></div>
+
+ <th:block th:if="${model.germplasm.originSite != null && !#strings.isEmpty(model.germplasm.originSite.siteName)}">
+ <div th:replace="fragments/row::row(label='Origin site', content=~{::#origin-site})">
+ <a id="origin-site" th:href="@{/sites/{siteId}(siteId=${#faidare.toSiteParam(model.germplasm.originSite.siteId)})}" th:text="${model.germplasm.originSite.siteName}"></a>
+ </div>
+ </th:block>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div class="f-card" th:if="${model.germplasm.holdingInstitute}">
+ <h2>Depositary</h2>
+ <div class="f-card-body">
+ <template id="holding-institute-popover">
+ <div th:replace="fragments/institute::institute(institute=${model.germplasm.holdingInstitute})"></div>
+ </template>
+ <div th:replace="fragments/row::row(label='Institution', content=~{::#institution})">
+ <a id="institution"
+ role="button"
+ tabindex="0"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.germplasm.holdingInstitute.instituteName}"
+ data-bs-element="#holding-institute-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ th:text="${model.germplasm.holdingInstitute.instituteName}"></a>
+ </div>
+
+ <th:block th:if="${model.germplasm.holdingGenbank != null && !#strings.isEmpty(model.germplasm.holdingGenbank.instituteName) && !#strings.isEmpty(model.germplasm.holdingGenbank.webSite)}">
+ <div th:replace="fragments/row::row(label='Stock center name', content=~{::#stock-center-name})">
+ <a id="stock-center-name"
+ target="_blank"
+ th:href="${model.germplasm.holdingGenbank.webSite}"
+ th:text="${model.germplasm.holdingGenbank.instituteName}"></a>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Presence status', text=${model.germplasm.presenceStatus})"></div>
+ </div>
+ </div>
+
+ <div class="f-card" th:if="${model.collecting}">
+ <h2>Collector</h2>
+ <div class="f-card-body">
+ <th:block th:if="${model.germplasm.collectingSite != null && !#strings.isEmpty(model.germplasm.collectingSite.siteName)}">
+ <div th:replace="fragments/row::row(label='Collecting site', content=~{::#collecting-site})">
+ <a id="collecting-site"
+ th:href="@{/sites/{siteId}(siteId=${#faidare.toSiteParam(model.germplasm.collectingSite.siteId)})}"
+ th:text="${model.germplasm.collectingSite.siteName}"
+ ></a>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Material type', text=${model.germplasm.collector.materialType})"></div>
+ <div th:replace="fragments/row::text-row(label='Collectors', text=${model.germplasm.collector.collectors})"></div>
+
+ <th:block th:if="${!#strings.isEmpty(model.germplasm.acquisitionDate) && model.germplasm.collector.accessionCreationDate == null}">
+ <div th:replace="fragments/row::text-row(label='Acquisition / Creation date', text=${model.germplasm.acquisitionDate})"></div>
+ </th:block>
+
+ <th:block th:if="${model.germplasm.collector.institute != null && !#strings.isEmpty(model.germplasm.collector.institute.instituteName)}">
+ <template id="collector-institute-popover">
+ <div th:replace="fragments/institute::institute(institute=${model.germplasm.collector.institute})"></div>
+ </template>
+ <div th:replace="fragments/row::row(label='Institution', content=~{::#collecting-institution})">
+ <a id="collecting-institution"
+ role="button"
+ tabindex="0"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.germplasm.collector.institute.instituteName}"
+ data-bs-element="#collector-institute-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ th:text="${model.germplasm.collector.institute.instituteName}"></a>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Accession number', text=${model.germplasm.collector.accessionNumber})"></div>
+ </div>
+ </div>
+
+ <div class="f-card" th:if="${model.breeding}">
+ <h2>Breeder</h2>
+ <div class="f-card-body">
+ <th:block th:if="${model.germplasm.breeder.institute != null && !#strings.isEmpty(model.germplasm.breeder.institute.instituteName)}">
+ <template id="breeder-institute-popover">
+ <div th:replace="fragments/institute::institute(institute=${model.germplasm.breeder.institute})"></div>
+ </template>
+ <div th:replace="fragments/row::row(label='Institute', content=~{::#breeding-institution})">
+ <a id="breeding-institution"
+ role="button"
+ tabindex="0"
+ data-bs-toggle="popover"
+ th:data-bs-title="${model.germplasm.breeder.institute.instituteName}"
+ data-bs-element="#breeder-institute-popover"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ th:text="${model.germplasm.breeder.institute.instituteName}"></a>
+ </div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Accession creation year', text=${model.germplasm.breeder.accessionCreationDate})"></div>
+ <div th:replace="fragments/row::text-row(label='Accession number', text=${model.germplasm.breeder.accessionNumber})"></div>
+ <div th:replace="fragments/row::text-row(label='Catalog registration year', text=${model.germplasm.breeder.registrationYear})"></div>
+ <div th:replace="fragments/row::text-row(label='Catalog deregistration year', text=${model.germplasm.breeder.deregistrationYear})"></div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.germplasm.donors)}">
+ <h2>Donors</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container">
+ <table class="table table-sm table-striped table-sticky table-responsive-sm">
+ <thead>
+ <tr>
+ <th scope="col">Institute name</th>
+ <th scope="col">Institute code</th>
+ <th scope="col">Donation date</th>
+ <th scope="col">Accession number</th>
+ <th scope="col">Accession PUI</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row, donorIterStat : ${model.germplasm.donors}">
+ <td>
+ <template th:id="${'donor-institute-popover-' + donorIterStat.index}">
+ <div th:replace="fragments/institute::institute(institute=${row.donorInstitute})"></div>
+ </template>
+ <a role="button"
+ tabindex="0"
+ data-bs-toggle="popover"
+ th:data-bs-title="${row.donorInstitute.instituteName}"
+ th:data-bs-element="${'#donor-institute-popover-' + donorIterStat.index}"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ th:text="${row.donorInstitute.instituteName}"></a>
+ </td>
+ <td th:text="${row.donorInstituteCode}"></td>
+ <td th:text="${row.donationDate}"></td>
+ <td th:text="${row.donorAccessionNumber}"></td>
+ <td th:text="${row.donorGermplasmPUI}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.germplasm.distributors)}">
+ <h2>Distributors</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container">
+ <table class="table table-sm table-striped table-sticky table-responsive-sm">
+ <thead>
+ <tr>
+ <th scope="col">Institute</th>
+ <th scope="col">Accession number</th>
+ <th scope="col">Distribution status</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row, distributorIterStat : ${model.germplasm.distributors}">
+ <td>
+ <template th:id="${'distributor-institute-popover-' + distributorIterStat.index}">
+ <div th:replace="fragments/institute::institute(institute=${row.institute})"></div>
+ </template>
+ <a role="button"
+ tabindex="0"
+ th:data-bs-title="${row.institute.instituteName}"
+ th:data-bs-element="${'#distributor-institute-popover-' + distributorIterStat.index}"
+ data-bs-container="body"
+ data-bs-trigger="focus"
+ th:text="${row.institute.instituteName}"></a>
+ </td>
+ <td th:text="${row.accessionNumber}"></td>
+ <td th:text="${row.distributionStatus}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.attributes)}">
+ <h2>Evaluation Data</h2>
+ <div class="f-card-body">
+ <th:block th:each="descriptor : ${model.attributes}">
+ <div th:replace="fragments/row::text-row(label=${descriptor.attributeName}, text=${descriptor.value})"></div>
+ </th:block>
+ </div>
+ </div>
+
+ <div class="f-card" th:if="${model.genealogyPresent}">
+ <h2>Genealogy</h2>
+ <div class="f-card-body">
+ <th:block th:if="${model.pedigree != null}">
+ <div th:replace="fragments/row::text-row(label='Crossing plan', text=${model.pedigree.crossingPlan})"></div>
+ <div th:replace="fragments/row::text-row(label='Crossing year', text=${model.pedigree.crossingYear})"></div>
+ <div th:replace="fragments/row::text-row(label='Family code', text=${model.pedigree.familyCode})"></div>
+ <th:block th:unless="${#strings.isEmpty(model.pedigree.parent1Name)}">
+ <div th:replace="fragments/row::row(label='Parent accessions', content=~{::#parent-accessions})">
+ <div id="parent-accessions">
+ <th:block th:if="${model.pedigree.parent1DbId}">
+ <div th:replace="fragments/row::row(label=${model.pedigree.parent1Type}, content=~{::#parent1-link})">
+ <a id="parent1-link" th:href="@{/germplasms/{germplasmId}(germplasmId=${model.pedigree.parent1DbId})}" th:text="${model.pedigree.parent1Name}"></a>
+ </div>
+ </th:block>
+
+ <th:block th:if="${model.pedigree.parent2DbId}">
+ <div th:replace="fragments/row::row(label=${model.pedigree.parent2Type}, content=~{::#parent2-link})">
+ <a id="parent2-link" th:href="@{/germplasms/{germplasmId}(germplasmId=${model.pedigree.parent2DbId})}" th:text="${model.pedigree.parent2Name}"></a>
+ </div>
+ </th:block>
+ </div>
+ </div>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.pedigree.siblings)}">
+ <div th:replace="fragments/row::row(label='Sibling accessions', content=~{::#sibling-accessions})">
+ <div id="sibling-accessions" class="content-overflow">
+ <a th:each="sibling : ${model.pedigree.siblings}"
+ th:href="@{/germplasms/{germplasmId}(germplasmId=${sibling.germplasmDbId})}"
+ th:text="${sibling.defaultDisplayName}"></a>
+ </div>
+ </div>
+ </th:block>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.germplasm.children)}">
+ <div th:replace="fragments/row::row(label='Descendants', content=~{::#descendants})">
+ <div id="descendants" class="content-overflow content-overflow-big">
+ <th:block th:each="child : ${model.germplasm.children}">
+ <div th:replace="fragments/row::row(label=${#strings.isEmpty(child.secondParentName) ? ('children of ' + child.firstParentName) : ('children of ' + child.firstParentName + ' x ' + child.secondParentName) }, content=~{::.descendant-child})">
+ <div class="descendant-child">
+ <th:block th:each="sibling, siblingIterStat : ${child.sibblings}">
+ <a th:href="@{/germplasms(pui=${sibling.pui})}"
+ th:text="${sibling.name}"></a><th:block th:unless="${siblingIterStat.last}">, </th:block>
+ </th:block>
+ </div>
+ </div>
+ </th:block>
+ </div>
+ </div>
+ </th:block>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.germplasm.population)}">
+ <h2>Population</h2>
+ <div class="f-card-body">
+ <th:block th:each="population : ${model.germplasm.population}">
+
+ <th:block th:if="${population.germplasmRef != null}">
+ <th:block th:unless="${#strings.isEmpty(population.germplasmRef.pui)}">
+ <div th:replace="fragments/row::row(label=${#faidare.collPopTitle(population)}, content=~{::.population-1})">
+ <div class="population-1">
+ <a th:if="${population.germplasmRef.pui != model.germplasm.germplasmPUI}"
+ th:href="@{/germplasms(pui=${population.germplasmRef.pui})}"
+ th:text="${population.germplasmRef.name}"></a>
+ <span th:if="${population.germplasmRef.pui == model.germplasm.germplasmPUI}"
+ th:text="${population.germplasmRef.name}"></span>
+ is composed by <span th:text="${population.germplasmCount}"></span> accession(s)
+ <!-- TODO there was a link pointing at a search here -->
+ </div>
+ </div>
+ </th:block>
+ </th:block>
+
+ <th:block th:if="${population.germplasmRef == null}">
+ <div th:replace="fragments/row::text-row(label=${#faidare.collPopTitle(population)}, text=${population.germplasmCount + ' accession(s)'})"></div>
+ <!-- TODO there was a link pointing at a search here -->
+ </th:block>
+ </th:block>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.germplasm.collection)}">
+ <h2>Collection</h2>
+ <div class="f-card-body">
+ <th:block th:each="collection : ${model.germplasm.collection}">
+ <div th:replace="fragments/row::text-row(label=${#faidare.collPopTitle(collection)}, text=${collection.germplasmCount + ' accession(s)'})"></div>
+ <!-- TODO there was a link pointing at a search here -->
+ </th:block>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.germplasm.panel)}">
+ <h2>Panel</h2>
+ <div class="f-card-body">
+ <th:block th:each="panel : ${model.germplasm.panel}">
+ <div th:replace="fragments/row::text-row(label=${#faidare.collPopTitleWithoutUnderscores(panel)}, text=${panel.germplasmCount + ' accession(s)'})"></div>
+ <!-- TODO there was a link pointing at a search here -->
+ </th:block>
+ </div>
+ </div>
+
+ <div th:replace="fragments/xrefs::xrefs(crossReferences=${model.crossReferences})"></div>
+</main>
+
+<script th:inline="javascript">
+ faidare.initializePopovers();
+ faidare.initializeMap({
+ contextPath: [[${#request.getContextPath()}]],
+ locations: /*[[${model.mapLocations}]]*/ []
+ });
+</script>
+</body>
+</html>
diff --git a/backend/src/main/resources/templates/index.html b/backend/src/main/resources/templates/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..49f401b0284647d171f51ec5643987e27d836a05
--- /dev/null
+++ b/backend/src/main/resources/templates/index.html
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+
+<html
+ xmlns:th="http://www.thymeleaf.org"
+ th:replace="~{layout/main :: layout(title=~{::title}, content=~{::main})}"
+>
+<head>
+ <title>Faidare</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+</head>
+
+<body>
+<main>
+ <h1>Welcome to Faidare</h1>
+</main>
+</body>
+</html>
diff --git a/backend/src/main/resources/templates/layout/main.html b/backend/src/main/resources/templates/layout/main.html
new file mode 100644
index 0000000000000000000000000000000000000000..22c36a5efb6dfe860a20b41f520ba826d160e96b
--- /dev/null
+++ b/backend/src/main/resources/templates/layout/main.html
@@ -0,0 +1,30 @@
+<!DOCTYPE html>
+<html lang="fr" th:fragment="layout (title, content, script)" xmlns:th="http://www.thymeleaf.org">
+ <head>
+ <title th:replace="${title}">Layout Title</title>
+
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+ <meta content="width=device-width, initial-scale=1" name="viewport" />
+
+ <link th:href="@{/assets/style.css}" rel="stylesheet">
+
+ <link rel="shortcut icon" th:href="@{/static/assets/images/favicon.ico}" type="image/x-icon" />
+ </head>
+
+ <body>
+ <nav class="navbar navbar-expand-lg navbar-light bg-light">
+ <div class="container">
+ <span class="navbar-brand py-0">
+ <img th:src="@{/assets/images/logo.png}" style="height: 40px"/>
+ </span>
+ </div>
+ </nav>
+ <div class="container mt-3">
+ <div th:replace="${content}">
+ <p>Layout content</p>
+ </div>
+ </div>
+ <script type="text/javascript" th:src="@{/assets/script.js}"></script>
+ <script type="text/javascript" th:replace="${script}"></script>
+ </body>
+</html>
diff --git a/backend/src/main/resources/templates/site.html b/backend/src/main/resources/templates/site.html
new file mode 100644
index 0000000000000000000000000000000000000000..69deac41e56ee63e84e22618db267da846f230f1
--- /dev/null
+++ b/backend/src/main/resources/templates/site.html
@@ -0,0 +1,78 @@
+<!DOCTYPE html>
+
+<html
+ xmlns:th="http://www.thymeleaf.org"
+ th:replace="~{layout/main :: layout(title=~{::title}, content=~{::main}, script=~{::script})}"
+>
+<head>
+ <title>Site <th:block th:text="${model.site.locationName}" /></title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+</head>
+
+<body>
+<main>
+ <h1>Site <th:block th:text="${model.site.locationName}" /></h1>
+
+ <div th:replace="fragments/map::map"></div>
+
+ <div class="f-card mt-4">
+ <h2>Details</h2>
+ <div class="f-card-body">
+ <th:block th:if="${model.site.uri != null && !model.site.uri.startsWith('urn:')}">
+ <div th:replace="fragments/row::text-row(label='Permanent unique identifier', text=${model.site.uri})"></div>
+ </th:block>
+
+ <div th:replace="fragments/source::source(source=${model.source}, url=${model.site.url}, entityType='site')"></div>
+
+ <div th:replace="fragments/row::text-row(label='Abbreviation', text=${model.site.abbreviation})"></div>
+ <div th:replace="fragments/row::text-row(label='Type', text=${model.site.locationType})"></div>
+ <div th:replace="fragments/row::text-row(label='Status', text=${model.siteStatus})"></div>
+ <div th:replace="fragments/row::text-row(label='Institution/Landowner', text=${model.site.instituteName})"></div>
+ <div th:replace="fragments/row::text-row(label='Institution address', text=${model.site.instituteAddress})"></div>
+ <div th:replace="fragments/row::text-row(label='Coordinates precision', text=${model.coordinatesPrecision})"></div>
+ <th:block th:if="${model.site.latitude}">
+ <div th:replace="fragments/row::text-row(label='Latitude', text=${#coordinates.formatLatitude(model.site.latitude)})"></div>
+ </th:block>
+ <th:block th:if="${model.site.longitude}">
+ <div th:replace="fragments/row::text-row(label='Longitude', text=${#coordinates.formatLongitude(model.site.longitude)})"></div>
+ </th:block>
+ <div th:replace="fragments/row::text-row(label='Geographical location', text=${model.geographicalLocation})"></div>
+ <th:block th:if="${model.site.countryName != null && model.geographicalLocation == null}">
+ <div th:replace="fragments/row::text-row(label='Country name', text=${model.site.countryName})"></div>
+ </th:block>
+
+ <th:block th:if="${model.site.countryCode != null && model.geographicalLocation == null}">
+ <div th:replace="fragments/row::text-row(label='Country code', text=${model.site.countryName})"></div>
+ </th:block>
+
+ <div th:replace="fragments/row::text-row(label='Altitude', text=${model.site.altitude})"></div>
+ <div th:replace="fragments/row::text-row(label='Slope', text=${model.slope})"></div>
+ <div th:replace="fragments/row::text-row(label='Exposure', text=${model.exposure})"></div>
+ <div th:replace="fragments/row::text-row(label='Topography', text=${model.topography})"></div>
+ <div th:replace="fragments/row::text-row(label='Environment type', text=${model.environmentType})"></div>
+ <div th:replace="fragments/row::text-row(label='Distance to city', text=${model.distanceToCity})"></div>
+ <div th:replace="fragments/row::text-row(label='Direction from city', text=${model.directionFromCity})"></div>
+ <div th:replace="fragments/row::text-row(label='Comment', text=${model.comment})"></div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.additionalInfoProperties)}">
+ <h2>Additional info</h2>
+ <div class="f-card-body">
+ <th:block th:each="prop : ${model.additionalInfoProperties}">
+ <div th:replace="fragments/row::text-row(label=${prop.key}, text=${prop.value})"></div>
+ </th:block>
+ </div>
+ </div>
+
+ <div th:replace="fragments/xrefs::xrefs(crossReferences=${model.crossReferences})"></div>
+</main>
+
+<script th:inline="javascript">
+ faidare.initializeMap({
+ contextPath: [[${#request.getContextPath()}]],
+ locations: /*[[${model.mapLocations}]]*/ []
+ });
+</script>
+</body>
+</html>
diff --git a/backend/src/main/resources/templates/study.html b/backend/src/main/resources/templates/study.html
new file mode 100644
index 0000000000000000000000000000000000000000..5d26f8340dd27dd0bb2d1d850043ad556cd29aec
--- /dev/null
+++ b/backend/src/main/resources/templates/study.html
@@ -0,0 +1,203 @@
+<!DOCTYPE html>
+
+<html
+ xmlns:th="http://www.thymeleaf.org"
+ th:replace="~{layout/main :: layout(title=~{::title}, content=~{::main}, script=~{::script})}"
+>
+<head>
+ <title>Study <th:block th:text="${model.study.studyType}" />: <th:block th:text="${model.study.studyName}" /></title>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+</head>
+
+<body>
+<main>
+ <h1>Study <th:block th:text="${model.study.studyType}" />: <th:block th:text="${model.study.studyName}" /></h1>
+
+ <div th:replace="fragments/map::map"></div>
+
+ <div class="f-card mt-4">
+ <h2>Identification</h2>
+ <div class="f-card-body">
+ <div th:replace="fragments/row::text-row(label='Name', text=${model.study.studyName})"></div>
+ <div th:replace="fragments/row::text-row(label='Identifier', text=${model.study.studyDbId})"></div>
+
+ <div th:replace="fragments/source::source(source=${model.source}, url=${model.study.url}, entityType='study')"></div>
+
+ <div th:replace="fragments/row::text-row(label='Project name', text=${model.study.programName})"></div>
+ <div th:replace="fragments/row::text-row(label='Description', text=${model.study.studyDescription})"></div>
+ <th:block th:if="${model.study.active != null}">
+ <div th:replace="fragments/row::text-row(label='Active', text=${model.study.active ? 'Yes' : 'No'})"></div>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.study.seasons)}">
+ <div th:replace="fragments/row::text-row(label='Seasons', text=${#strings.listJoin(model.study.seasons, ',')})"></div>
+ </th:block>
+ <th:block th:if="${model.study.startDate != null && model.study.endDate != null}">
+ <div th:replace="fragments/row::text-row(label='Date', text=${'From ' + #dates.format(model.study.startDate, 'yyyy-MM-dd') + ' to ' + #dates.format(model.study.endDate, 'yyyy-MM-dd') })"></div>
+ </th:block>
+ <th:block th:if="${model.study.startDate != null && model.study.endDate == null}">
+ <div th:replace="fragments/row::text-row(label='Date', text=${'Started on ' + #dates.format(model.study.startDate, 'yyyy-MM-dd')})"></div>
+ </th:block>
+
+ <th:block th:if="${model.study.locationDbId}">
+ <div th:replace="fragments/row::row(label='Location name', content=~{::#location})">
+ <a id="location" th:href="@{/sites/{siteId}(siteId=${model.study.locationDbId})}" th:text="${model.study.locationName}"></a>
+ </div>
+ </th:block>
+
+ <th:block th:unless="${#lists.isEmpty(model.study.dataLinks)}">
+ <div th:replace="fragments/row::row(label='Data files', content=~{::#data-files})">
+ <ul id="data-files" class="list-unstyled">
+ <li th:each="dataLink : ${model.study.dataLinks}">
+ <a target="_blank" th:href="${dataLink.url}" th:text="${dataLink.name}"></a>
+ </li>
+ </ul>
+ </div>
+ </th:block>
+ </div>
+ </div>
+
+ <div class="f-card" th:unles="${#lists.isEmpty(model.germplasms)}">
+ <h2>Genotype</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container scroll-table-container-big">
+ <table class="table table-sm table-striped table-sticky table-responsive-sm">
+ <thead>
+ <tr>
+ <th scope="col">Accession number</th>
+ <th scope="col">Name</th>
+ <th scope="col">Taxon</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row : ${model.germplasms}">
+ <td>
+ <a th:href="@{/germplasms/{germplasmId}(germplasmId=${row.germplasmDbId})}" th:text="${row.accessionNumber}"></a>
+ </td>
+ <td th:text="${row.germplasmName}"></td>
+ <td th:text="${(row.genus == null ? '' : row.genus) + ' ' + (row.species == null ? '' : row.species)+ ' ' + (row.subtaxa == null ? '' : row.subtaxa) }"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.variables)}">
+ <h2>Variables</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container">
+ <table class="table table-sm table-striped table-sticky table-responsive-sm">
+ <thead>
+ <tr>
+ <th scope="col">Variable ID</th>
+ <th scope="col">Variable short name</th>
+ <th scope="col">Variable long name</th>
+ <th scope="col">Ontology name</th>
+ <th scope="col">Trait description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row : ${model.variables}">
+ <td>
+ <a th:unless="${#strings.isEmpty(row.documentationURL)}" th:href="${row.documentationURL}" th:text="${row.observationVariableDbId}" target="_blank" ></a>
+ <span th:if="${#strings.isEmpty(row.documentationURL)}" th:text="${row.observationVariableDbId}"></span>
+ </td>
+ <td th:text="${row.name}"></td>
+ <td th:text="${#lists.isEmpty(row.synonyms) ? '' : row.synonyms[0]}"></td>
+ <td th:text="${row.ontologyName}"></td>
+ <td th:text="${row.trait.description}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.trials)}">
+ <h2>Data Set</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container scroll-table-container-big">
+ <table class="table table-sm table-striped table-sticky table-responsive-sm">
+ <thead>
+ <tr>
+ <th scope="col">Name</th>
+ <th scope="col">Type</th>
+ <th scope="col">Linked studies identifier</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row : ${model.trials}">
+ <td>
+ <a th:unless="${#strings.isEmpty(row.documentationURL)}" th:href="${row.documentationURL}" th:text="${row.trialName}" target="_blank" ></a>
+ <span th:if="${#strings.isEmpty(row.documentationURL)}" th:text="${row.trialName}"></span>
+ </td>
+ <td th:text="${row.trialType}"></td>
+ <td style="width: 60%">
+ <th:block th:each="trialStudy, iterStat : ${row.studies}"
+ th:if="${trialStudy.studyDbId != model.study.studyDbId}">
+ <a th:href="@{/studies/{studyId}(studyId=${trialStudy.studyDbId})}"
+ th:text="${trialStudy.studyName.trim()}">
+ </a><th:block th:if="${iterStat.last}">; </th:block>
+ </th:block>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.study.contacts)}">
+ <h2>Contact</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container">
+ <table class="table table-sm table-striped table-sticky table-responsive-sm">
+ <thead>
+ <tr>
+ <th scope="col">Role</th>
+ <th scope="col">Name</th>
+ <th scope="col">Email</th>
+ <th scope="col">Institution</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr th:each="row : ${model.study.contacts}">
+ <td th:text="${row.type}"></td>
+ <td th:text="${row.name}"></td>
+ <td th:text="${row.email}"></td>
+ <td th:text="${row.institutionName}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="f-card" th:unless="${#lists.isEmpty(model.additionalInfoProperties)}">
+ <h2>Additional information</h2>
+ <div class="f-card-body">
+ <div class="scroll-table-container">
+ <table class="table table-sm">
+ <tbody>
+ <tr th:each="row : ${model.additionalInfoProperties}">
+ <th class="label" style="width: 33.33%" th:text="${row.key}" scope="row"></th>
+ <td th:text="${row.value}"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div th:replace="fragments/xrefs::xrefs(crossReferences=${model.crossReferences})"></div>
+</main>
+
+<script th:inline="javascript">
+ faidare.initializeMap({
+ contextPath: [[${#request.getContextPath()}]],
+ locations: /*[[${model.mapLocations}]]*/ []
+ });
+</script>
+</body>
+</html>
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/filter/AngularRouteFilterTest.java b/backend/src/test/java/fr/inra/urgi/faidare/filter/AngularRouteFilterTest.java
deleted file mode 100644
index b71e9e39509201d931b6e469ff747524f7a4ddd4..0000000000000000000000000000000000000000
--- a/backend/src/test/java/fr/inra/urgi/faidare/filter/AngularRouteFilterTest.java
+++ /dev/null
@@ -1,105 +0,0 @@
-package fr.inra.urgi.faidare.filter;
-
-import fr.inra.urgi.faidare.Application;
-import fr.inra.urgi.faidare.config.SecurityConfig;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.ValueSource;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.mock.mockito.MockBean;
-import org.springframework.context.annotation.Import;
-import org.springframework.core.io.Resource;
-import org.springframework.core.io.ResourceLoader;
-import org.springframework.test.context.junit.jupiter.SpringExtension;
-import org.springframework.test.util.ReflectionTestUtils;
-import org.springframework.test.web.servlet.MockMvc;
-import org.springframework.test.web.servlet.setup.MockMvcBuilders;
-import org.springframework.web.context.WebApplicationContext;
-
-import java.io.ByteArrayInputStream;
-
-import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.forwardedUrl;
-
-/**
- * Unit tests for {@link AngularRouteFilter}
- *
- * @author gcornut
- */
-@ExtendWith(SpringExtension.class)
-@Import(SecurityConfig.class)
-@SpringBootTest(classes = Application.class)
-class AngularRouteFilterTest {
-
- @Autowired
- private WebApplicationContext context;
-
- @MockBean
- private ResourceLoader resourceLoader;
-
- private MockMvc mockMvc;
-
- private AngularRouteFilter filter;
-
- @BeforeEach
- void setUp() {
- filter = new AngularRouteFilter(resourceLoader);
- mockMvc = MockMvcBuilders.webAppContextSetup(context)
- .addFilter(filter, "/*")
- .build();
- }
-
- @ParameterizedTest
- @ValueSource(strings = {
- // Static files
- "/index.html",
- "/script.js",
- "/style.css",
- "/image.gif",
- "/icon.ico",
- "/image.png",
- "/image.jpg",
- "/font.woff",
- "/font.ttf",
- // APIs
- "/brapi/v1/studies",
- "/faidare/v1/datadiscovery/suggest",
- "/actuator/info",
- })
- void shouldNotForward(String url) throws Exception {
- mockMvc.perform(get(url)).andExpect(forwardedUrl(null));
- }
-
- @ParameterizedTest
- @ValueSource(strings = {
- "/home",
- "/studies/foo",
- "/germplasm/bar",
- })
- void shouldForward(String url) throws Exception {
- String indexBefore = "<html>\n" +
- " <base href=\"./\">\n" +
- "</html>";
- String indexAfter = "<html>\n" +
- " <base href=\"/gnpis-test/faidare/\">\n" +
- "</html>";
-
- ReflectionTestUtils.setField(filter, "serverContextPath", "/gnpis-test/faidare");
-
- Resource mockResource = mock(Resource.class);
- when(mockResource.getInputStream())
- .thenReturn(new ByteArrayInputStream(indexBefore.getBytes()));
- when(resourceLoader.getResource(anyString()))
- .thenReturn(mockResource);
-
- mockMvc.perform(get(url))
- .andExpect(content().string(indexAfter));
- }
-
-}
diff --git a/backend/src/test/test.iml b/backend/src/test/test.iml
deleted file mode 100644
index 6e30bb1c6134aa08b8bcfb9660df0484e83585c6..0000000000000000000000000000000000000000
--- a/backend/src/test/test.iml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="true">
- <exclude-output />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/java" isTestSource="true" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="main" />
- </component>
-</module>
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index 457aad0d98108420a977756b7145c93c8910b076..7454180f2ae8848c63b8b4dea2cb829da983f2fa 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 75b8c7c8c67a003599a36935d1c6a41519fc2207..ffed3a254e91df704a9acc0f2745c0e340d9b582 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.0-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
index af6708ff229fda75da4f7cc4da4747217bac4d53..1b6c787337ffb79f0e3cf8b1e9f00f680a959de1 100755
--- a/gradlew
+++ b/gradlew
@@ -1,78 +1,129 @@
-#!/usr/bin/env sh
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
##############################################################################
-##
-## Gradle start up script for UN*X
-##
+#
+# Gradle start up script for POSIX generated by Gradle.
+#
+# Important for running:
+#
+# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+# noncompliant, but you have some other compliant shell such as ksh or
+# bash, then to run this script, type that shell name before the whole
+# command line, like:
+#
+# ksh Gradle
+#
+# Busybox and similar reduced shells will NOT work, because this script
+# requires all of these POSIX shell features:
+# * functions;
+# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+# * compound commands having a testable exit status, especially «case»;
+# * various built-in commands including «command», «set», and «ulimit».
+#
+# Important for patching:
+#
+# (2) This script targets any POSIX shell, so it avoids extensions provided
+# by Bash, Ksh, etc; in particular arrays are avoided.
+#
+# The "traditional" practice of packing multiple parameters into a
+# space-separated string is a well documented source of bugs and security
+# problems, so this is (mostly) avoided, by progressively accumulating
+# options in "$@", and eventually passing that to Java.
+#
+# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+# see the in-line comments for details.
+#
+# There are tweaks for specific operating systems such as AIX, CygWin,
+# Darwin, MinGW, and NonStop.
+#
+# (3) This script is generated from the Groovy template
+# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+# within the Gradle project.
+#
+# You can find Gradle at https://github.com/gradle/gradle/.
+#
##############################################################################
# Attempt to set APP_HOME
+
# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+ APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
+ [ -h "$app_path" ]
+do
+ ls=$( ls -ld "$app_path" )
+ link=${ls#*' -> '}
+ case $link in #(
+ /*) app_path=$link ;; #(
+ *) app_path=$APP_HOME$link ;;
+ esac
done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
+APP_BASE_NAME=${0##*/}
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m"'
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
warn () {
echo "$*"
-}
+} >&2
die () {
echo
echo "$*"
echo
exit 1
-}
+} >&2
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
+case "$( uname )" in #(
+ CYGWIN* ) cygwin=true ;; #(
+ Darwin* ) darwin=true ;; #(
+ MSYS* | MINGW* ) msys=true ;; #(
+ NONSTOP* ) nonstop=true ;;
esac
CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
# Determine the Java command to use to start the JVM.
if [ -n "$JAVA_HOME" ] ; then
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
# IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
+ JAVACMD=$JAVA_HOME/jre/sh/java
else
- JAVACMD="$JAVA_HOME/bin/java"
+ JAVACMD=$JAVA_HOME/bin/java
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -81,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
- JAVACMD="java"
+ JAVACMD=java
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
@@ -89,84 +140,95 @@ location of your Java installation."
fi
# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+ case $MAX_FD in #(
+ max*)
+ MAX_FD=$( ulimit -H -n ) ||
+ warn "Could not query maximum file descriptor limit"
+ esac
+ case $MAX_FD in #(
+ '' | soft) :;; #(
+ *)
+ ulimit -n "$MAX_FD" ||
+ warn "Could not set maximum file descriptor limit to $MAX_FD"
+ esac
fi
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
+# Collect all arguments for the java command, stacking in reverse order:
+# * args from the command line
+# * the main class name
+# * -classpath
+# * -D...appname settings
+# * --module-path (only if needed)
+# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+ APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+ CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+ JAVACMD=$( cygpath --unix "$JAVACMD" )
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
# Now convert the arguments - kludge to limit ourselves to /bin/sh
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
+ for arg do
+ if
+ case $arg in #(
+ -*) false ;; # don't mess with options #(
+ /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
+ [ -e "$t" ] ;; #(
+ *) false ;;
+ esac
+ then
+ arg=$( cygpath --path --ignore --mixed "$arg" )
fi
- i=$((i+1))
+ # Roll the args list around exactly as many times as the number of
+ # args, so each arg winds up back in the position where it started, but
+ # possibly modified.
+ #
+ # NB: a `for` loop captures its iteration list before it begins, so
+ # changing the positional parameters here affects neither the number of
+ # iterations, nor the values presented in `arg`.
+ shift # remove old arg
+ set -- "$@" "$arg" # push replacement arg
done
- case $i in
- (0) set -- ;;
- (1) set -- "$args0" ;;
- (2) set -- "$args0" "$args1" ;;
- (3) set -- "$args0" "$args1" "$args2" ;;
- (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
fi
-# Escape application args
-save () {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=$(save "$@")
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
-
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
- cd "$(dirname "$0")"
-fi
+# Collect all arguments for the java command;
+# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+# shell script including quotes and variable substitutions, so put them in
+# double quotes to make sure that they get re-expanded; and
+# * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+ "-Dorg.gradle.appname=$APP_BASE_NAME" \
+ -classpath "$CLASSPATH" \
+ org.gradle.wrapper.GradleWrapperMain \
+ "$@"
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+# set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+ printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+ xargs -n1 |
+ sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+ tr '\n' ' '
+ )" '"$@"'
exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
index 6d57edc706c93465988754383a2d7ff353d4e79f..107acd32c4e687021ef32db511e8a206129b88ec 100644
--- a/gradlew.bat
+++ b/gradlew.bat
@@ -1,3 +1,19 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
@if "%DEBUG%" == "" @echo off
@rem ##########################################################################
@rem
@@ -13,15 +29,18 @@ if "%DIRNAME%" == "" set DIRNAME=.
set APP_BASE_NAME=%~n0
set APP_HOME=%DIRNAME%
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m"
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
@rem Find java.exe
if defined JAVA_HOME goto findJavaFromJavaHome
set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if "%ERRORLEVEL%" == "0" goto execute
echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -35,7 +54,7 @@ goto fail
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
echo.
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -45,28 +64,14 @@ echo location of your Java installation.
goto fail
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
:execute
@rem Setup the command line
set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
:end
@rem End local scope for the variables with windows NT shell
diff --git a/settings.gradle.kts b/settings.gradle.kts
index 4bd5a482217fc2c6b3921cafc0bdb602ebd96641..b8faef34872a40284f74d8be029e0dd7861df5d7 100644
--- a/settings.gradle.kts
+++ b/settings.gradle.kts
@@ -1,2 +1,2 @@
rootProject.name = "faidare"
-include("backend", "frontend")
+include("backend", "web")
diff --git a/web/build.gradle.kts b/web/build.gradle.kts
new file mode 100644
index 0000000000000000000000000000000000000000..44076adb023409ae78bfcc8bd986a412a52afc11
--- /dev/null
+++ b/web/build.gradle.kts
@@ -0,0 +1,41 @@
+import com.github.gradle.node.yarn.task.YarnInstallTask
+import com.github.gradle.node.yarn.task.YarnTask
+
+plugins {
+ base
+ id("com.github.node-gradle.node") version "3.0.1"
+}
+
+node {
+ version.set("14.17.0")
+ npmVersion.set("6.14.10")
+ yarnVersion.set("1.22.10")
+ download.set(true)
+}
+
+tasks {
+ npmInstall {
+ enabled = false
+ }
+
+ val prepare by registering {
+ dependsOn(YarnInstallTask.NAME)
+ }
+
+ // This is not a yarn_build task because the task to run is `yarn build:prod`
+ // and tasks with colons are not supported
+ val yarnBuildProd by registering(YarnTask::class) {
+ args.set(listOf("run", "build:prod"))
+ dependsOn(prepare)
+ inputs.file("webpack.config.js")
+ inputs.file("tsconfig.json")
+ inputs.file("package.json")
+ inputs.file("yarn.lock")
+ inputs.dir("src")
+ outputs.dir("$buildDir/dist")
+ }
+
+ assemble {
+ dependsOn(yarnBuildProd)
+ }
+}
diff --git a/web/package.json b/web/package.json
new file mode 100644
index 0000000000000000000000000000000000000000..4ce0986c188f17659ca176c2deb119cd63c73421
--- /dev/null
+++ b/web/package.json
@@ -0,0 +1,35 @@
+{
+ "name": "faidaire-web",
+ "version": "1.0.0",
+ "description": "",
+ "private": true,
+ "scripts": {
+ "build": "webpack --mode development",
+ "build:prod": "webpack --mode production",
+ "watch": "webpack --mode development --watch",
+ "watch:prod": "webpack --mode production --watch",
+ "test": "echo \"Error: no test specified\" && exit 1"
+ },
+ "author": "",
+ "license": "MIT",
+ "dependencies": {
+ "@types/leaflet": "1.7.4",
+ "bootstrap": "5.1.0",
+ "leaflet": "1.7.1"
+ },
+ "devDependencies": {
+ "@types/bootstrap": "5.1.2",
+ "@types/leaflet.markercluster": "1.4.5",
+ "clean-webpack-plugin": "4.0.0-alpha.0",
+ "css-loader": "6.2.0",
+ "css-minimizer-webpack-plugin": "3.0.2",
+ "leaflet.markercluster": "1.5.0",
+ "mini-css-extract-plugin": "2.2.0",
+ "sass": "1.38.1",
+ "sass-loader": "12.1.0",
+ "ts-loader": "9.2.5",
+ "typescript": "4.3.5",
+ "webpack": "5.51.1",
+ "webpack-cli": "4.8.0"
+ }
+}
diff --git a/web/src/bootstrap/popovers.ts b/web/src/bootstrap/popovers.ts
new file mode 100644
index 0000000000000000000000000000000000000000..83b703de77469e545f992f1ad2396706db3621bd
--- /dev/null
+++ b/web/src/bootstrap/popovers.ts
@@ -0,0 +1,19 @@
+import { Popover } from 'bootstrap';
+
+export function initializePopovers() {
+ const popoverTriggerList: Array<HTMLElement> = [].slice.call(document.querySelectorAll('[data-bs-toggle="popover"]'))
+ popoverTriggerList.forEach(popoverTriggerEl => {
+ const options: Partial<Popover.Options> = {};
+ const contentSelector = popoverTriggerEl.dataset.bsElement;
+ if (contentSelector) {
+ const content = document.querySelector(contentSelector);
+ if (content) {
+ options.content = content.innerHTML;
+ options.html = true;
+ } else {
+ throw new Error('element with selector ' + contentSelector + ' not found');
+ }
+ }
+ return new Popover(popoverTriggerEl, options);
+ });
+}
diff --git a/web/src/index.ts b/web/src/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c906b28eb7d5cb4d78785bd6ea5bd01ff4b92fd2
--- /dev/null
+++ b/web/src/index.ts
@@ -0,0 +1,7 @@
+import { initializePopovers } from './bootstrap/popovers';
+import { initializeMap } from './map/map';
+
+(window as any).faidare = {
+ initializePopovers,
+ initializeMap
+}
diff --git a/web/src/map/map.ts b/web/src/map/map.ts
new file mode 100644
index 0000000000000000000000000000000000000000..9fc2a96004bca2ea53eaf342371595c7ea3f5b29
--- /dev/null
+++ b/web/src/map/map.ts
@@ -0,0 +1,93 @@
+import * as L from 'leaflet';
+import 'leaflet.markercluster';
+
+interface MapLocation {
+ locationDbId: string;
+ locationType: 'Origin site' | 'Collecting site' | 'Evaluation site' | null;
+ locationName: string;
+ latitude: number;
+ longitude: number;
+}
+
+interface MapOptions {
+ contextPath: string;
+ locations: Array<MapLocation>;
+}
+
+function markerColor(location: MapLocation) {
+ switch (location.locationType) {
+ case 'Origin site':
+ return 'red';
+ case 'Collecting site':
+ return 'blue';
+ case 'Evaluation site':
+ return 'green';
+ }
+ return 'purple';
+}
+
+function markerIconUrl(contextPath: string, location: MapLocation) {
+ return `${contextPath}/assets/images/marker-icon-${markerColor(location)}.png`;
+}
+
+export function initializeMap(options: MapOptions) {
+ if (!options.locations.length) {
+ return;
+ }
+
+ const mapContainerElement = document.querySelector('#map-container');
+ mapContainerElement!.classList.remove("d-none");
+ const mapElement = document.querySelector('#map') as HTMLElement;
+ const map = L.map(mapElement);
+ L.tileLayer('https://server.arcgisonline.com/ArcGIS/rest/services/World_Street_Map/MapServer/tile/{z}/{y}/{x}', {
+ attribution: 'Tiles © Esri — Source: Esri, DeLorme, NAVTEQ, USGS, Intermap, iPC, NRCAN, Esri Japan, METI, ' +
+ 'Esri China (Hong Kong), Esri (Thailand), TomTom, 2012'
+ }).addTo(map);
+
+ const firstLocation = options.locations[0];
+ map.setView([firstLocation.latitude, firstLocation.longitude], 5);
+
+ const markers = L.markerClusterGroup();
+ const mapMarkers: Array<L.Marker> = [];
+ for (const location of options.locations) {
+ const icon = L.icon({
+ iconUrl: markerIconUrl(options.contextPath, location),
+ iconAnchor: [12, 41], // point of the icon which will correspond to marker's location
+ });
+
+ const popupElement = document.createElement('div');
+
+ const titleElement = document.createElement('strong');
+ titleElement.innerText = location.locationName;
+ popupElement.appendChild(titleElement);
+ popupElement.appendChild(document.createElement('br'));
+
+ if (location.locationType) {
+ const typeElement = document.createElement('span');
+ typeElement.innerText = location.locationType;
+ popupElement.appendChild(typeElement);
+ popupElement.appendChild(document.createElement('br'));
+ }
+
+ const linkElement = document.createElement('a');
+ linkElement.innerText = 'Details';
+ linkElement.href = `${options.contextPath}/sites/${location.locationDbId}`;
+ popupElement.appendChild(linkElement);
+
+ const marker = L.marker(
+ [location.latitude, location.longitude],
+ { icon: icon }
+ );
+ markers.addLayer(marker.bindPopup(popupElement));
+ mapMarkers.push(marker);
+ }
+ const initialZoom = map.getZoom();
+
+ map.fitBounds(L.featureGroup(mapMarkers).getBounds());
+ const markerZoom = map.getZoom();
+
+ setTimeout(() => {
+ map.setZoom(Math.min(initialZoom, markerZoom));
+ map.addLayer(markers);
+ }, 100);
+}
diff --git a/web/src/style/_custom-bootstrap.scss b/web/src/style/_custom-bootstrap.scss
new file mode 100644
index 0000000000000000000000000000000000000000..9de7c3dce4b8fbea20fd88c39b1bc001c72b69a0
--- /dev/null
+++ b/web/src/style/_custom-bootstrap.scss
@@ -0,0 +1,53 @@
+/*!
+ * Bootstrap v5.1.0 (https://getbootstrap.com/)
+ * Copyright 2011-2021 The Bootstrap Authors
+ * Copyright 2011-2021 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
+ */
+
+// scss-docs-start import-stack
+// Configuration
+@import '~bootstrap/scss/functions';
+@import '~bootstrap/scss/variables';
+@import '~bootstrap/scss/mixins';
+@import '~bootstrap/scss/utilities';
+
+// Layout & components
+@import '~bootstrap/scss/root';
+@import '~bootstrap/scss/reboot';
+@import '~bootstrap/scss/type';
+@import '~bootstrap/scss/images';
+@import '~bootstrap/scss/containers';
+@import '~bootstrap/scss/grid';
+@import '~bootstrap/scss/tables';
+// @import '~bootstrap/scss/forms';
+@import '~bootstrap/scss/buttons';
+@import '~bootstrap/scss/transitions';
+@import '~bootstrap/scss/dropdown';
+// @import '~bootstrap/scss/button-group';
+@import '~bootstrap/scss/nav';
+@import '~bootstrap/scss/navbar';
+@import '~bootstrap/scss/card';
+// @import '~bootstrap/scss/accordion';
+// @import '~bootstrap/scss/breadcrumb';
+// @import '~bootstrap/scss/pagination';
+// @import '~bootstrap/scss/badge';
+// @import '~bootstrap/scss/alert';
+// @import '~bootstrap/scss/progress';
+// @import '~bootstrap/scss/list-group';
+// @import '~bootstrap/scss/close';
+// @import '~bootstrap/scss/toasts';
+// @import '~bootstrap/scss/modal';
+// @import '~bootstrap/scss/tooltip';
+@import '~bootstrap/scss/popover';
+// @import '~bootstrap/scss/carousel';
+// @import '~bootstrap/scss/spinners';
+// @import '~bootstrap/scss/offcanvas';
+// @import '~bootstrap/scss/placeholders';
+
+// Helpers
+// @import '~bootstrap/scss/helpers';
+
+// Utilities
+@import '~bootstrap/scss/utilities/api';
+// scss-docs-end import-stack
diff --git a/web/src/style/style.scss b/web/src/style/style.scss
new file mode 100644
index 0000000000000000000000000000000000000000..42aa2bb3a883a5991772d6b9cbe4eddb0eb7d267
--- /dev/null
+++ b/web/src/style/style.scss
@@ -0,0 +1,91 @@
+$headings-color: #0f6191;
+$border-color: #0f6e9f;
+$link-color: #0f6fa1;
+$link-decoration: none;
+$link-hover-decoration: underline;
+$enable-shadows: true;
+$table-border-color: #dee2e6;
+$table-group-separator-color: $table-border-color;
+
+@import 'custom-bootstrap';
+@import '~leaflet/dist/leaflet.css';
+@import '~leaflet.markercluster/dist/MarkerCluster.css';
+@import '~leaflet.markercluster/dist/MarkerCluster.Default.css';
+
+a[role=button] {
+ color: $link-color !important;
+}
+
+.f-row {
+ border-top: 1px solid $gray-300;
+ padding: 0.5rem 0;
+ .label {
+ font-weight: 700;
+ }
+}
+
+.f-card {
+ border: 1px solid $border-color;
+ border-radius: 0.25rem;
+ margin: 0.5rem 0;
+ h2 {
+ font-size: $h4-font-size;
+ padding: 0.5rem 1rem;
+ background-image: repeating-linear-gradient(#0f96cd, #0f6191, #0f76a5);
+ color: $white;
+ }
+ .f-card-body {
+ padding: 0.25rem 1rem;
+ .f-row:first-of-type {
+ border-top: 0;
+ }
+ }
+}
+
+.popover {
+ max-width: min(80vw, 500px);
+}
+
+.popover-header {
+ font-weight: 700;
+}
+
+#map {
+ height: min(400px, 60vh);
+}
+
+.map-legend img {
+ height: 1.5rem;
+}
+
+.content-overflow {
+ max-height: 200px;
+ overflow-y: auto;
+ overflow-x: hidden;
+ &.content-overflow-big {
+ max-height: 275px;
+ }
+}
+
+.scroll-table-container {
+ max-height: 200px;
+ overflow-y: auto;
+ padding-top: 0;
+ &.scroll-table-container-big {
+ max-height: 500px;
+ }
+}
+
+.table-sticky {
+ width: 100%;
+ thead th {
+ position: sticky;
+ position: -webkit-sticky;
+ top: 0;
+ background-color: white;
+ border-top-width: 0;
+ th {
+ padding-top: 0;
+ }
+ }
+}
diff --git a/web/tsconfig.json b/web/tsconfig.json
new file mode 100644
index 0000000000000000000000000000000000000000..714af2e552e4d168d08d85597be03eecb652ac23
--- /dev/null
+++ b/web/tsconfig.json
@@ -0,0 +1,72 @@
+{
+ "compilerOptions": {
+ /* Visit https://aka.ms/tsconfig.json to read more about this file */
+
+ /* Basic Options */
+ // "incremental": true, /* Enable incremental compilation */
+ "target": "es6", /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', 'ES2021', or 'ESNEXT'. */
+ "module": "es2015", /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
+ // "lib": [], /* Specify library files to be included in the compilation. */
+ // "allowJs": true, /* Allow javascript files to be compiled. */
+ // "checkJs": true, /* Report errors in .js files. */
+ // "jsx": "preserve", /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
+ // "declaration": true, /* Generates corresponding '.d.ts' file. */
+ // "declarationMap": true, /* Generates a sourcemap for each corresponding '.d.ts' file. */
+ // "sourceMap": true, /* Generates corresponding '.map' file. */
+ // "outFile": "./", /* Concatenate and emit output to single file. */
+ // "outDir": "./", /* Redirect output structure to the directory. */
+ // "rootDir": "./", /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */
+ // "composite": true, /* Enable project compilation */
+ // "tsBuildInfoFile": "./", /* Specify file to store incremental compilation information */
+ // "removeComments": true, /* Do not emit comments to output. */
+ // "noEmit": true, /* Do not emit outputs. */
+ // "importHelpers": true, /* Import emit helpers from 'tslib'. */
+ // "downlevelIteration": true, /* Provide full support for iterables in 'for-of', spread, and destructuring when targeting 'ES5' or 'ES3'. */
+ // "isolatedModules": true, /* Transpile each file as a separate module (similar to 'ts.transpileModule'). */
+
+ /* Strict Type-Checking Options */
+ "strict": true, /* Enable all strict type-checking options. */
+ // "noImplicitAny": true, /* Raise error on expressions and declarations with an implied 'any' type. */
+ // "strictNullChecks": true, /* Enable strict null checks. */
+ // "strictFunctionTypes": true, /* Enable strict checking of function types. */
+ // "strictBindCallApply": true, /* Enable strict 'bind', 'call', and 'apply' methods on functions. */
+ // "strictPropertyInitialization": true, /* Enable strict checking of property initialization in classes. */
+ // "noImplicitThis": true, /* Raise error on 'this' expressions with an implied 'any' type. */
+ // "alwaysStrict": true, /* Parse in strict mode and emit "use strict" for each source file. */
+
+ /* Additional Checks */
+ // "noUnusedLocals": true, /* Report errors on unused locals. */
+ // "noUnusedParameters": true, /* Report errors on unused parameters. */
+ // "noImplicitReturns": true, /* Report error when not all code paths in function return a value. */
+ // "noFallthroughCasesInSwitch": true, /* Report errors for fallthrough cases in switch statement. */
+ // "noUncheckedIndexedAccess": true, /* Include 'undefined' in index signature results */
+ // "noImplicitOverride": true, /* Ensure overriding members in derived classes are marked with an 'override' modifier. */
+ // "noPropertyAccessFromIndexSignature": true, /* Require undeclared properties from index signatures to use element accesses. */
+
+ /* Module Resolution Options */
+ // "moduleResolution": "node", /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */
+ // "baseUrl": "./", /* Base directory to resolve non-absolute module names. */
+ // "paths": {}, /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */
+ // "rootDirs": [], /* List of root folders whose combined content represents the structure of the project at runtime. */
+ // "typeRoots": [], /* List of folders to include type definitions from. */
+ // "types": [], /* Type declaration files to be included in compilation. */
+ // "allowSyntheticDefaultImports": true, /* Allow default imports from modules with no default export. This does not affect code emit, just typechecking. */
+ "esModuleInterop": true, /* Enables emit interoperability between CommonJS and ES Modules via creation of namespace objects for all imports. Implies 'allowSyntheticDefaultImports'. */
+ // "preserveSymlinks": true, /* Do not resolve the real path of symlinks. */
+ // "allowUmdGlobalAccess": true, /* Allow accessing UMD globals from modules. */
+
+ /* Source Map Options */
+ // "sourceRoot": "", /* Specify the location where debugger should locate TypeScript files instead of source locations. */
+ // "mapRoot": "", /* Specify the location where debugger should locate map files instead of generated locations. */
+ // "inlineSourceMap": true, /* Emit a single file with source maps instead of having a separate file. */
+ // "inlineSources": true, /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */
+
+ /* Experimental Options */
+ // "experimentalDecorators": true, /* Enables experimental support for ES7 decorators. */
+ // "emitDecoratorMetadata": true, /* Enables experimental support for emitting type metadata for decorators. */
+
+ /* Advanced Options */
+ "skipLibCheck": true, /* Skip type checking of declaration files. */
+ "forceConsistentCasingInFileNames": true /* Disallow inconsistently-cased references to the same file. */
+ }
+}
diff --git a/web/webpack.config.js b/web/webpack.config.js
new file mode 100644
index 0000000000000000000000000000000000000000..1c7b808029f88e4107f429df70a5fb93e383a29b
--- /dev/null
+++ b/web/webpack.config.js
@@ -0,0 +1,67 @@
+const path = require('path');
+const { CleanWebpackPlugin } = require('clean-webpack-plugin');
+const MiniCssExtractPlugin = require("mini-css-extract-plugin");
+const CssMinimizerPlugin = require("css-minimizer-webpack-plugin");
+
+module.exports = (env, argv) => ({
+ context: path.resolve(__dirname, '.'),
+ // inline source maps only in development mode
+ devtool: argv.mode === 'production' ? undefined : 'inline-source-map',
+ plugins: [
+ // allows extracting the CSS into a CSS file instead of bundling it in a JS file
+ new MiniCssExtractPlugin({
+ filename: argv.mode === 'production' ? '[name].[contenthash].css' : '[name].css'
+ }),
+ // cleans the output directory before each build
+ new CleanWebpackPlugin({
+ // and the empty, useless style.js after each build
+ protectWebpackAssets: false,
+ cleanAfterEveryBuildPatterns: ['style*.js']
+ })
+ ],
+ entry: {
+ // a JS bundle is generated for the index.ts entry point. Since the application is really small
+ // and does not have much JavaScript logic, a single bundle is sufficient
+ script: './src/index.ts',
+ // A CSS bundle is generated for the style.scss entry point.
+ style: './src/style/style.scss'
+ },
+ module: {
+ rules: [
+ {
+ test: /\.tsx?$/,
+ use: 'ts-loader',
+ exclude: /node_modules/,
+ },
+ {
+ // .scss files are loaded by the sass-loader, which transforms them into css loaded by the css-loader
+ // which are then bundled into a css file by the MiniCssExtractPlugin loader
+ test: /\.scss$/i,
+ use: [
+ MiniCssExtractPlugin.loader,
+ 'css-loader',
+ 'sass-loader'
+ ],
+ },
+ ],
+ },
+ resolve: {
+ // our files are .ts files, but libraries are bundled in .js files
+ extensions: ['.ts', '.js'],
+ },
+ output: {
+ // the output is stored in build/dist/assets
+ path: path.resolve(__dirname, 'build/dist/assets'),
+ filename: argv.mode === 'production' ? '[name].[contenthash].js' : '[name].js'
+ },
+ optimization: {
+ minimizer: [
+ '...',
+ new CssMinimizerPlugin()
+ ]
+ },
+ performance: {
+ maxAssetSize: 300000,
+ maxEntrypointSize: 300000
+ }
+});
diff --git a/web/yarn.lock b/web/yarn.lock
new file mode 100644
index 0000000000000000000000000000000000000000..ba30e63f6aa70b15fb6a0bde06e91ea9c5230bf2
--- /dev/null
+++ b/web/yarn.lock
@@ -0,0 +1,1826 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
+"@discoveryjs/json-ext@^0.5.0":
+ version "0.5.3"
+ resolved "https://registry.yarnpkg.com/@discoveryjs/json-ext/-/json-ext-0.5.3.tgz#90420f9f9c6d3987f176a19a7d8e764271a2f55d"
+ integrity sha512-Fxt+AfXgjMoin2maPIYzFZnQjAXjAL0PHscM5pRTtatFqB+vZxAM9tLp2Optnuw3QOQC40jTNeGYFOMvyf7v9g==
+
+"@popperjs/core@^2.9.2":
+ version "2.9.3"
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+
+"@trysound/sax@0.1.1":
+ version "0.1.1"
+ resolved "https://registry.yarnpkg.com/@trysound/sax/-/sax-0.1.1.tgz#3348564048e7a2d7398c935d466c0414ebb6a669"
+ integrity sha512-Z6DoceYb/1xSg5+e+ZlPZ9v0N16ZvZ+wYMraFue4HYrE4ttONKtsvruIRf6t9TBR0YvSOfi1hUU0fJfBLCDYow==
+
+"@types/bootstrap@5.1.2":
+ version "5.1.2"
+ resolved "https://registry.yarnpkg.com/@types/bootstrap/-/bootstrap-5.1.2.tgz#24f08f1957ff5859633f4bf620e921d296e6c3a2"
+ integrity sha512-dSQvMi2dMyNwJU6LZjP0pimuBowsMUvGScYdfqqeiDUoj9TxXZCpfu0cTl94U0Zvw/tdH9j/9ToOhi4LKNLZhg==
+ dependencies:
+ "@popperjs/core" "^2.9.2"
+ "@types/jquery" "*"
+
+"@types/eslint-scope@^3.7.0":
+ version "3.7.1"
+ resolved "https://registry.yarnpkg.com/@types/eslint-scope/-/eslint-scope-3.7.1.tgz#8dc390a7b4f9dd9f1284629efce982e41612116e"
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+ dependencies:
+ "@types/eslint" "*"
+ "@types/estree" "*"
+
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+ version "7.28.0"
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+ dependencies:
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+ "@types/json-schema" "*"
+
+"@types/estree@*", "@types/estree@^0.0.50":
+ version "0.0.50"
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+
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+ version "7946.0.8"
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+
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+ version "7.1.4"
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+ dependencies:
+ "@types/minimatch" "*"
+ "@types/node" "*"
+
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+ version "3.5.6"
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+ dependencies:
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+
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+ version "1.4.5"
+ resolved "https://registry.yarnpkg.com/@types/leaflet.markercluster/-/leaflet.markercluster-1.4.5.tgz#dc4457e2dff9baaacc17c9c04c65ab69b5f361f7"
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+ dependencies:
+ "@types/leaflet" "*"
+
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+ version "1.7.4"
+ resolved "https://registry.yarnpkg.com/@types/leaflet/-/leaflet-1.7.4.tgz#bb9430f69d588ca5829c1ba82657e179454f93a1"
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+ dependencies:
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+ integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==
+
+yaml@^1.10.2:
+ version "1.10.2"
+ resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.2.tgz#2301c5ffbf12b467de8da2333a459e29e7920e4b"
+ integrity sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==
+
+yocto-queue@^0.1.0:
+ version "0.1.0"
+ resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b"
+ integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==