Merge pull request #117 from FAIRDataTeam/release/1.8.0

Release 1.8.0

.dockerignore

@@ -1,5 +1,9 @@
+.github
 .idea
-src
+LICENSE
+README.ms
+docs
 target/**
 !target/fdp-spring-boot.jar
 !target/classes/application-production.yml
+nb-configuration.xml

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: "maven"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    target-branch: "develop"

.github/workflows/main.yml

@@ -14,9 +14,9 @@ jobs:
       PRIVATE_IMAGE: ${{ secrets.PRIVATE_REGISTRY_URL }}/fairdatapoint
       TAG_DEVELOP: develop
       TAG_LATEST: latest
-      JDK_VERSION: 11
-      JDK_FILE: openjdk-14.0.1_linux-x64_bin.tar.gz
-      JDK_URL: https://download.java.net/java/GA/jdk14.0.1/664493ef4a6946b186ff29eb326336a2/7/GPL/openjdk-14.0.1_linux-x64_bin.tar.gz
+      JDK_VERSION: 15
+      JDK_FILE: openjdk-15.0.2_linux-x64_bin.tar.gz
+      JDK_URL: https://download.java.net/java/GA/jdk15.0.2/0d1cfde4252546c6931946de8db48ee2/7/GPL/openjdk-15.0.2_linux-x64_bin.tar.gz
 
     services:
       mongo:
@@ -48,17 +48,17 @@ jobs:
         key: ${{ env.JDK_FILE }}
 
 # (2) -> Prepare Java
-    - name: Download Oracle JDK
+    - name: Download JDK
       run: |
         if [ ! -f ~/jdk/$JDK_FILE ]; then
           wget --quiet $JDK_URL -O ~/jdk/$JDK_FILE
         fi
         cp ~/jdk/$JDK_FILE .
 
     - name: Setup Java
-      uses: actions/setup-java@master
+      uses: actions/setup-java@v1
       with:
-        version: ${{ env.JDK_VERSION }}
+        java-version: ${{ env.JDK_VERSION }}
         jdkFile: ${{ env.JDK_FILE }}
 
     - name: Verify Maven and Java

CHANGELOG.md

@@ -2,11 +2,29 @@
 
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres
+to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+## [1.8.0]
+
+### Added
+
+- Denylist for FDP Index pings
+- Endpoints for managing Index settings from [Client]
+
+### Changed
+
+- Upgrade Java JDK from 14 to 15
+- Rate limits use forwarded IP by proxy based on config
+- Index settings are moved to the database
+- Admin trigger now accepts the same DTO as ping
+
+### Fixed
+
+- Fix metadata not found error
+
 ## [1.7.0]
 
 ### Added
@@ -155,4 +173,7 @@ The first release of reference FAIR Data Point implementation.
 [1.4.0]: /../../tree/v1.4.0
 [1.5.0]: /../../tree/v1.5.0
 [1.6.0]: /../../tree/v1.6.0
+
 [1.7.0]: /../../tree/v1.7.0
+
+[1.8.0]: /../../tree/v1.8.0

Dockerfile

@@ -21,7 +21,7 @@
 # THE SOFTWARE.
 #
 
-FROM openjdk:14-jdk-slim
+FROM openjdk:15-jdk-slim
 
 WORKDIR /fdp
 

Dockerfile.build

@@ -0,0 +1,42 @@
+#
+# The MIT License
+# Copyright © 2017 DTL
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+################################################################################
+# BUILD STAGE
+FROM maven:3-openjdk-15 as builder
+
+WORKDIR /builder
+
+ADD . /builder
+
+RUN mvn --quiet -B -U --fail-fast -DskipTests package
+
+################################################################################
+# RUN STAGE
+FROM openjdk:15-jdk-slim
+
+WORKDIR /fdp
+
+COPY --from=builder /builder/target/fdp-spring-boot.jar /fdp/app.jar
+COPY --from=builder /builder/target/classes/application-production.yml /fdp/application.yml
+
+ENTRYPOINT java -jar app.jar --spring.profiles.active=production --spring.config.location=classpath:/application.yml,classpath:/application-production.yml,file:/fdp/application.yml

README.md

@@ -20,13 +20,13 @@ More information about FDP and how to deploy can be found at [FDP Deployment Doc
 
 **Stack:**
 
- - **Java** (minimally JDK 14, or higher)
- - **Maven** (recommended 3.2.5 or higher)
- - **Docker** (recommended 17.09.0-ce or higher) - *for build of production image*
+ - **Java** (minimal: JDK 15)
+ - **Maven** (recommended: 3.2.5 or higher)
+ - **Docker** (recommended: 17.09.0-ce or higher) - *for build of production image*
 
 ### Build & Run
 
-To run the application, a mongodb instance is required to be running. To configure the mongodb address, instruct spring-boot to use the `development` profile. Run these commands from the root of the project.
+To run the application, a MongoDB instance is required to be running. To configure the mongodb address, instruct spring-boot to use the `development` profile. Run these commands from the root of the project.
 
 ```bash
 $ mvn spring-boot:run -Dspring-boot.run.profiles=development
@@ -40,26 +40,34 @@ $ mvn spring-boot:run
 
 ### Run tests
 
-Run these commands from the root of the project
+Run these commands from the root of the project:
 
 ```bash
 $ mvn test
 ```
 
 ### Package the application
 
-Run these commands from the root of the project
+Run these commands from the root of the project:
 
 ```bash
 $ mvn package
 ```
 
 ### Create a Docker image
 
-Run these commands from the root of the project
+Run these commands from the root of the project (requires building jar file using `mvn package`):
 
 ```bash
-$ docker build -t fairdata/fairdatapoint .
+$ docker build -t fairdatapoint:local .
+```
+
+### Build using Docker
+
+If you do not have Java and Maven locally, you can build the Docker image using Docker (instead of using locally built jar file):
+
+```bash
+$ docker build -f Dockefile.build -t fairdatapoint:local .
 ```
 
 ## Security

pom.xml

@@ -10,7 +10,7 @@
     </parent>
     <groupId>nl.dtls</groupId>
     <artifactId>fairdatapoint</artifactId>
-    <version>1.7.0</version>
+    <version>1.8.0</version>
     <packaging>jar</packaging>
 
     <name>FairDataPoint</name>
@@ -41,8 +41,8 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
         <!-- Maven -->
-        <maven.compiler.source>14</maven.compiler.source>
-        <maven.compiler.target>14</maven.compiler.target>
+        <maven.compiler.source>15</maven.compiler.source>
+        <maven.compiler.target>15</maven.compiler.target>
 
         <!-- Project related -->
         <spring.rdf.migration.version>1.1.0.RELEASE</spring.rdf.migration.version>
@@ -54,15 +54,15 @@
         <logback.version>1.2.3</logback.version>
         <rdf4j.version>3.0.0</rdf4j.version>
         <unirest.version>1.4.9</unirest.version>
-        <jwt.version>0.10.5</jwt.version>
-        <lombok.version>1.18.10</lombok.version>
+        <jwt.version>0.11.2</jwt.version>
+        <lombok.version>1.18.18</lombok.version>
 
         <!-- Plugins -->
         <plugin.license.version>3.0</plugin.license.version>
         <plugin.jacoco.version>0.7.6.201602180812</plugin.jacoco.version>
         <plugin.coveralls.version>4.3.0</plugin.coveralls.version>
         <plugin.javax_xml_bind.version>2.3.1</plugin.javax_xml_bind.version>
-        <plugin.git_commit_id.version>2.2.4</plugin.git_commit_id.version>
+        <plugin.git_commit_id.version>4.0.3</plugin.git_commit_id.version>
         <plugin.rdf4j_generator.version>0.2.0</plugin.rdf4j_generator.version>
     </properties>
 
@@ -315,6 +315,21 @@
                     <verbose>false</verbose>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <configuration>
+                    <includes>
+                        <include>**/*.java</include>
+                    </includes>
+                    <excludes>
+                        <exclude>**/*Fixtures.java</exclude>
+                        <exclude>**/*Config.java</exclude>
+                        <exclude>**/Common.java</exclude>
+                        <exclude>**/common/*.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>com.github.kburger</groupId>
                 <artifactId>rdf4j-generator-maven-plugin</artifactId>

src/main/java/nl/dtls/fairdatapoint/api/controller/index/AdminController.java

@@ -24,7 +24,9 @@
 
 import io.swagger.annotations.ApiOperation;
 import lombok.extern.log4j.Log4j2;
+import nl.dtls.fairdatapoint.api.dto.index.ping.PingDTO;
 import nl.dtls.fairdatapoint.entity.index.event.Event;
+import nl.dtls.fairdatapoint.service.UtilityService;
 import nl.dtls.fairdatapoint.service.index.event.EventService;
 import nl.dtls.fairdatapoint.service.index.webhook.WebhookService;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -33,13 +35,17 @@
 import org.springframework.web.bind.annotation.*;
 
 import javax.servlet.http.HttpServletRequest;
+import javax.validation.Valid;
 import java.util.UUID;
 
 @Log4j2
 @RestController
 @RequestMapping("/index/admin")
 public class AdminController {
 
+    @Autowired
+    private UtilityService utilityService;
+
     @Autowired
     private EventService eventService;
 
@@ -50,9 +56,20 @@ public class AdminController {
     @PostMapping("/trigger")
     @PreAuthorize("hasRole('ADMIN')")
     @ResponseStatus(HttpStatus.NO_CONTENT)
-    public void triggerMetadataRetrieve(@RequestParam(required = false) String clientUrl, HttpServletRequest request) {
-        log.info("Received ping from {}", request.getRemoteAddr());
-        final Event event = eventService.acceptAdminTrigger(request, clientUrl);
+    public void triggerMetadataRetrieve(@RequestBody @Valid PingDTO reqDto, HttpServletRequest request) {
+        log.info("Received ping from {}", utilityService.getRemoteAddr(request));
+        final Event event = eventService.acceptAdminTrigger(request, reqDto);
+        webhookService.triggerWebhooks(event);
+        eventService.triggerMetadataRetrieval(event);
+    }
+
+    @ApiOperation(value = "trigger-all", hidden = true)
+    @PostMapping("/trigger-all")
+    @PreAuthorize("hasRole('ADMIN')")
+    @ResponseStatus(HttpStatus.NO_CONTENT)
+    public void triggerMetadataRetrieveAll(HttpServletRequest request) {
+        log.info("Received ping from {}", utilityService.getRemoteAddr(request));
+        final Event event = eventService.acceptAdminTriggerAll(request);
         webhookService.triggerWebhooks(event);
         eventService.triggerMetadataRetrieval(event);
     }
@@ -62,7 +79,7 @@ public void triggerMetadataRetrieve(@RequestParam(required = false) String clien
     @PreAuthorize("hasRole('ADMIN')")
     @ResponseStatus(HttpStatus.NO_CONTENT)
     public void webhookPing(@RequestParam(required = true) UUID webhook, HttpServletRequest request) {
-        log.info("Received webhook {} ping trigger from {}", webhook, request.getRemoteAddr());
+        log.info("Received webhook {} ping trigger from {}", webhook, utilityService.getRemoteAddr(request));
         final Event event = webhookService.handleWebhookPing(request, webhook);
         webhookService.triggerWebhooks(event);
     }

src/main/java/nl/dtls/fairdatapoint/api/controller/index/IndexEntryController.java

@@ -25,18 +25,15 @@
 import nl.dtls.fairdatapoint.api.dto.index.entry.IndexEntryDTO;
 import nl.dtls.fairdatapoint.api.dto.index.entry.IndexEntryDetailDTO;
 import nl.dtls.fairdatapoint.api.dto.index.entry.IndexEntryInfoDTO;
-import nl.dtls.fairdatapoint.service.index.entry.IndexEntryMapper;
 import nl.dtls.fairdatapoint.service.index.entry.IndexEntryService;
-import nl.dtls.fairdatapoint.service.index.event.EventService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.*;
 
 import java.util.List;
 import java.util.Optional;
-import java.util.stream.Collectors;
-import java.util.stream.StreamSupport;
 
 @RestController
 @RequestMapping("/index/entries")
@@ -45,27 +42,26 @@ public class IndexEntryController {
     @Autowired
     private IndexEntryService service;
 
-    @Autowired
-    private EventService eventService;
-
-    @Autowired
-    private IndexEntryMapper mapper;
-
     @GetMapping("")
     public Page<IndexEntryDTO> getEntriesPage(Pageable pageable,
                                               @RequestParam(required = false, defaultValue = "") String state) {
-        return service.getEntriesPage(pageable, state).map(mapper::toDTO);
+        return service.getEntriesPageDTOs(pageable, state);
     }
 
     @RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
     public Optional<IndexEntryDetailDTO> getEntry(@PathVariable final String uuid) {
-        return service.getEntry(uuid).map(entry -> mapper.toDetailDTO(entry,
-                eventService.getEvents(entry.getUuid())));
+        return service.getEntryDetailDTO(uuid);
+    }
+
+    @RequestMapping(value = "/{uuid}", method = RequestMethod.DELETE)
+    @ResponseStatus(HttpStatus.NO_CONTENT)
+    public void deleteEntry(@PathVariable final String uuid) {
+        service.deleteEntry(uuid);
     }
 
     @GetMapping("/all")
     public List<IndexEntryDTO> getEntriesAll() {
-        return StreamSupport.stream(service.getAllEntries().spliterator(), true).map(mapper::toDTO).collect(Collectors.toList());
+        return service.getAllEntriesAsDTOs();
     }
 
     @GetMapping("/info")