diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index 0c174c7a926a665afd13d79f6400c4d924f4bd62..0000000000000000000000000000000000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "src/test/db"]
- path = src/test/db
- url = ssh://git@lab01560.intranet.chuv:2222/mip-portal/portal-db.git
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 1d24297ed36ea5281519e7b6e6a33b628c37d4df..0000000000000000000000000000000000000000
--- a/Dockerfile
+++ /dev/null
@@ -1,14 +0,0 @@
-# This Dockerfile encapsulate the MIP portal backend application for development purposes.
-# We use it to bootstrap the generation of the Hibernate mapping file and the application jar.
-
-FROM maven:3-jdk-8
-
-COPY ./src/docker/init/build-in-docker.sh /build-in-docker.sh
-
-CMD mkdir /opt/portal/
-
-VOLUME /opt/portal/
-
-WORKDIR /opt/portal/
-
-CMD ["/build-in-docker.sh"]
diff --git a/README.md b/README.md
index ce9c373c3c20a5b07e8620e7c0d2079dad7ca5f3..7656211a77aeb1eca4651d816ddf99192ed70d26 100644
--- a/README.md
+++ b/README.md
@@ -1,32 +1,17 @@
## Introduction
-This is the MIP implementation.
+This is the MIP backend.
## Usage
-Build the project with `./build` and run it with `./run`.
+* Build and run the project (including clean target): `./go.sh`
+* Build the project (including clean target): `./build.sh`
+* Run the project: `./run.sh`
+* Show live logs: `./log.sh` (CTRL+C to quit)
+* Stop and remove the running container: `./halt.sh`
+* Clean Maven cache, etc: `./clean.sh`
-## API Documentation using Swagger (Springfox)
+## Generate PDF API documentation on build
-The API documentation is available at `<BASE URL>/swagger-ui.html`. A JSON version is available at `<BASE URL>/v2/api-docs`
-
-## TODO
-
-* Implement SoapUI tests;
-* Clean code (both back-end front-end);
-* Sync with original Swagger description;
-* Externalize configuration (DB parameters, security enabled/disabled, ...);
-* Make user tests with multiple users;
-* Fix bugs.
-
-## BUGS
-
-* Export PDF does not work;
-
-### Maintenance
-
-* To keep an updated API documentation, the developers should keep synchronized both the auto-generated swagger file (from Java annotations) with the hand written one. You can follow this method to get a YAML description from the Java-annotated code:
- * Add annotations to the Java code;
- * Get JSON from `<BASE URL>/v2/api-docs`;
- * Convert JSON to YAML on [http://jsontoyaml.com](http://jsontoyaml.com).
-
\ No newline at end of file
+Uncomment the following line in src/docker/build/build-in-docker.sh :
+`mvn swagger2markup:convertSwagger2markup asciidoctor:process-asciidoc`
diff --git a/after-git-clone.sh b/after-git-clone.sh
deleted file mode 100755
index 423f04205dc182d5ab78d9e1e32bc8a3c0f88635..0000000000000000000000000000000000000000
--- a/after-git-clone.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-git submodule update --init
diff --git a/after-update.sh b/after-update.sh
deleted file mode 100755
index c70bd5d6716f6d10e03a1d446958b58ea2ee7a6b..0000000000000000000000000000000000000000
--- a/after-update.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-
-git submodule sync
-git submodule update --init
-git submodule foreach git pull origin master
diff --git a/build.sh b/build.sh
index 748d7fb5c3af2af5940511f0c5df9206f5f57c4f..e29e8d77076c421f9f0a98bc49d4d61b9454c2bd 100755
--- a/build.sh
+++ b/build.sh
@@ -1,13 +1,5 @@
-#!/bin/bash -e
+#!/usr/bin/env bash
-if groups $USER | grep &>/dev/null '\bdocker\b'; then
- DOCKER_COMPOSE="docker-compose"
-else
- DOCKER_COMPOSE="sudo docker-compose"
-fi
-
-# TODO: Cannot clean otherwise the build fails because of Hibernate schema generation
-mvn package
-cp target/mip.jar src/docker/build/
-
-$DOCKER_COMPOSE build
+./halt.sh
+docker-compose -f ./docker-compose_build.yml build
+docker-compose -f ./docker-compose_build.yml run --rm backend_build
diff --git a/clean.sh b/clean.sh
new file mode 100755
index 0000000000000000000000000000000000000000..55a2f1aee44299fce253f3d085abf053854d0298
--- /dev/null
+++ b/clean.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+./halt.sh
+sudo rm -r ./.m2/
+sudo rm -r ./target/
+sudo rm -r ./pgdata/
\ No newline at end of file
diff --git a/config/application.yml b/config/application.yml
index 6f752d822bf63ecaf3bfb238dd920f177f05e2f3..05b35323155e50d61963cbe6b4480f53a40c73e2 100644
--- a/config/application.yml
+++ b/config/application.yml
@@ -1,9 +1,17 @@
-# Configuration for the portal running inside a Docker container for development
+# Configuration for the portal running inside a Docker container
-connection:
- url: "jdbc:postgresql://portaldb:5432/postgres"
- username: "postgres"
- password: "test"
+spring:
+ datasource:
+ url: jdbc:postgresql://db:5432/postgres
+ username: postgres
+ password: pass
+ driver-class-name: org.postgresql.Driver
+ jpa:
+ hibernate:
+ dialect: org.hibernate.dialect.PostgreSQL9Dialect
+ resources:
+ chain:
+ enabled: true
security:
enabled: false
@@ -17,9 +25,6 @@ hbp:
tokenName: oauth_token
authenticationScheme: query
clientAuthenticationScheme: form
- # use-current-uri: false # For both production and HBPS1 deployments
- # pre-established-redirect-uri: https://mip.humanbrainproject.eu/services/login/hbp # For production deployment
- # pre-established-redirect-uri: http://hbps1.chuv.ch/services/login/hbp # For HBPS1 deployment
resource:
userInfoUri: https://services.humanbrainproject.eu/oidc/userinfo
@@ -27,11 +32,6 @@ logging:
level:
org.springframework.security: DEBUG
-spring:
- resources:
- chain:
- enabled: true
-
server:
contextPath: /services
port: 8080
@@ -45,3 +45,6 @@ workflow:
miningMipUrl: http://dockerhost:8087/mining
miningExaremeUrl: http://hbps2.chuv.ch:9090/mining/query
+frontend:
+ redirect:
+ url: http://frontend/home
diff --git a/docker-compose.init.yml b/docker-compose.init.yml
deleted file mode 100644
index e5828d70bd0765e4ea7b22decc6685d3a6551456..0000000000000000000000000000000000000000
--- a/docker-compose.init.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-# Build the application and regenerate the Hibernate mapping
-
-portaldb:
- image: postgres:9.5.3
- container_name: portaldb
- ports:
- - "55432:5432"
- volumes:
- - ./src/test/db/sql:/docker-entrypoint-initdb.d/
- environment:
- POSTGRES_PASSWORD: test
-
-portal-backend:
- build: .
- volumes:
- - ./:/portal/
- - ./.m2/:/root/.m2/
- links:
- - portaldb
- ports:
- - "8080:8080"
diff --git a/docker-compose.yml b/docker-compose.yml
index ad6a91c77c771a297d969a83a5cd6f464c14735e..ca9461e4de83255ad5d6b13d3ecb1698e79bcd78 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,20 +1,26 @@
+version: '2'
-portaldb:
- image: postgres:9.5.3
- container_name: portaldb
- ports:
- - "55432:5432"
- volumes:
- - ./src/test/db/sql:/docker-entrypoint-initdb.d/
- environment:
- POSTGRES_PASSWORD: test
-
-portal-backend:
- build: ./src/docker/build
- volumes:
- - ./src/test/docker/:/opt/portal/config/
- - ./target/:/opt/portal/lib/
- links:
- - portaldb
- ports:
- - "8080:8080"
+services:
+ backend:
+ container_name: backend
+ build:
+ context: .
+ dockerfile: ./src/docker/run/Dockerfile
+ depends_on:
+ - "db"
+ ports:
+ - "8080:8080"
+ links:
+ - "db"
+ volumes:
+ - ./config:/config
+ db:
+ container_name: db
+ image: postgres:9.5.3
+ ports:
+ - "5432:5432"
+ volumes:
+ - ./pgdata:/var/lib/postgresql/data/pgdata
+ environment:
+ POSTGRES_USER: postgres
+ PGDATA: /var/lib/postgresql/data/pgdata
diff --git a/docker-compose_build.yml b/docker-compose_build.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b29bf59ecd0f6a068269bcc0fed3f0498bb9505d
--- /dev/null
+++ b/docker-compose_build.yml
@@ -0,0 +1,11 @@
+version: '2'
+
+services:
+ backend_build:
+ container_name: backend_build
+ build: ./src/docker/build/
+ volumes:
+ - ./:/opt/portal/
+ - .m2:/root/.m2/
+ ports:
+ - "8080:8080"
diff --git a/go.sh b/go.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2d044fe98b7c6eab6d5f6b38794762d9659f5e56
--- /dev/null
+++ b/go.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+./build.sh
+./run.sh
diff --git a/halt.sh b/halt.sh
new file mode 100755
index 0000000000000000000000000000000000000000..7b9c9e76afdaad93310047eeef58c64326caffb9
--- /dev/null
+++ b/halt.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+docker-compose kill
+docker-compose rm -f
diff --git a/log.sh b/log.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f1cd4924d74ad499aef9188c070880d2be956cf2
--- /dev/null
+++ b/log.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+docker-compose logs -f backend
diff --git a/pom.xml b/pom.xml
index a9cb39f28e7cf809c411420afed6756ec9965b9e..2726b792b10f1c0eb89bde75ea2b578390aa8f4b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
<groupId>org.hbp.mip</groupId>
<artifactId>backend-services</artifactId>
- <version>0.1.0</version>
+ <version>DOCKER_BUILD</version>
<packaging>jar</packaging>
<name>backend-services</name>
@@ -15,63 +15,46 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.3.2.RELEASE</version>
- <relativePath /> <!-- lookup parent from repository -->
+ <relativePath />
</parent>
- <profiles>
- <profile>
- <id>prod</id>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <java.version>1.8</java.version>
- <connection.driver_class>org.postgresql.Driver</connection.driver_class>
- <connection.url>jdbc:postgresql://hbpmdw1.chuv.ch:31432/portal</connection.url>
- <connection.username>portal</connection.username>
- <connection.password>iaezXODVLb1e70I</connection.password>
- <hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
- <schema.deploy>false</schema.deploy>
- <frontend.redirect>https://mip.humanbrainproject.eu/home</frontend.redirect>
- <flyway.url>${connection.url}</flyway.url>
- <flyway.user>${connection.username}</flyway.user>
- <flyway.password>${connection.password}</flyway.password>
- </properties>
- </profile>
- <profile>
- <id>dev</id>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <java.version>1.8</java.version>
- <connection.driver_class>org.postgresql.Driver</connection.driver_class>
- <connection.url>jdbc:postgresql://portaldb:5432/postgres</connection.url>
- <connection.username>postgres</connection.username>
- <connection.password>test</connection.password>
- <hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
- <schema.deploy>false</schema.deploy>
- <frontend.redirect>http://frontend/home</frontend.redirect>
- <flyway.url>${connection.url}</flyway.url>
- <flyway.user>${connection.username}</flyway.user>
- <flyway.password>${connection.password}</flyway.password>
- </properties>
- </profile>
- <profile>
- <id>hbps1</id>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <java.version>1.8</java.version>
- <connection.driver_class>org.postgresql.Driver</connection.driver_class>
- <connection.url>jdbc:postgresql://portaldb:5432/postgres</connection.url>
- <connection.username>postgres</connection.username>
- <connection.password>test</connection.password>
- <hibernate.dialect>org.hibernate.dialect.PostgreSQL82Dialect</hibernate.dialect>
- <schema.deploy>false</schema.deploy>
- <frontend.redirect>http://hbps1.chuv.ch/home</frontend.redirect>
- <flyway.url>${connection.url}</flyway.url>
- <flyway.user>${connection.username}</flyway.user>
- <flyway.password>${connection.password}</flyway.password>
- </properties>
- </profile>
- </profiles>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <sonar.host.url>http://dockerhost:9000</sonar.host.url>
+ <sonar.projectName>MIP Backend</sonar.projectName>
+ <sonar.sources>src/main/java/</sonar.sources>
+ <java.version>1.8</java.version>
+ <asciidoctor.maven.plugin.version>1.5.3</asciidoctor.maven.plugin.version>
+ <asciidoctorj.pdf.version>1.5.0-alpha.11</asciidoctorj.pdf.version>
+ <asciidoctorj.version>1.5.4</asciidoctorj.version>
+ <spring-data-commons.version>1.12.2.RELEASE</spring-data-commons.version>
+ <angularjs.version>1.4.3</angularjs.version>
+ <jquery.version>2.1.1</jquery.version>
+ <bootstrap.version>3.2.0</bootstrap.version>
+ <hibernate-jpa-2.1-api.version>1.0.0.Final</hibernate-jpa-2.1-api.version>
+ <hibernate-core.version>4.3.8.Final</hibernate-core.version>
+ <hibernate-entitymanager.version>4.3.8.Final</hibernate-entitymanager.version>
+ <h2.version>1.4.187</h2.version>
+ <postgresql.version>9.4-1205-jdbc42</postgresql.version>
+ <springfox-swagger2.version>2.3.1</springfox-swagger2.version>
+ <springfox-swagger-ui.version>2.3.1</springfox-swagger-ui.version>
+ <gson.version>2.5</gson.version>
+ <slugify.version>2.1.4</slugify.version>
+ <spring-data-jpa.version>1.10.2.RELEASE</spring-data-jpa.version>
+ <maven-resources-plugin.version>2.3</maven-resources-plugin.version>
+ <sonar-maven-plugin.version>3.0.1</sonar-maven-plugin.version>
+ <swagger2markup-maven-plugin.version>1.0.0</swagger2markup-maven-plugin.version>
+ <maven-compiler-plugin.version>3.1</maven-compiler-plugin.version>
+ <hibernate4-maven-plugin.version>1.1.0</hibernate4-maven-plugin.version>
+ <flyway-core.version>4.0.3</flyway-core.version>
+ </properties>
<dependencies>
+ <dependency>
+ <groupId>org.springframework.data</groupId>
+ <artifactId>spring-data-commons</artifactId>
+ <version>${spring-data-commons.version}</version>
+ </dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
@@ -95,17 +78,17 @@
<dependency>
<groupId>org.webjars</groupId>
<artifactId>angularjs</artifactId>
- <version>1.4.3</version>
+ <version>${angularjs.version}</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>jquery</artifactId>
- <version>2.1.1</version>
+ <version>${jquery.version}</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
- <version>3.2.0</version>
+ <version>${bootstrap.version}</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
@@ -119,47 +102,64 @@
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId>
- <version>1.0.0.Final</version>
+ <version>${hibernate-jpa-2.1-api.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
- <version>4.3.8.Final</version>
+ <version>${hibernate-core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.hibernate</groupId>
+ <artifactId>hibernate-entitymanager</artifactId>
+ <version>${hibernate-entitymanager.version}</version>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
- <version>1.4.187</version>
+ <version>${h2.version}</version>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
- <version>9.4-1205-jdbc42</version>
+ <version>${postgresql.version}</version>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger2</artifactId>
- <version>2.3.1</version>
+ <version>${springfox-swagger2.version}</version>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger-ui</artifactId>
- <version>2.3.1</version>
+ <version>${springfox-swagger-ui.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
- <version>2.5</version>
+ <version>${gson.version}</version>
</dependency>
<dependency>
<groupId>com.github.slugify</groupId>
<artifactId>slugify</artifactId>
- <version>2.1.4</version>
+ <version>${slugify.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework.data</groupId>
+ <artifactId>spring-data-jpa</artifactId>
+ <version>${spring-data-jpa.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-dbcp</groupId>
+ <artifactId>commons-dbcp</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.flywaydb</groupId>
+ <artifactId>flyway-core</artifactId>
+ <version>${flyway-core.version}</version>
</dependency>
</dependencies>
-
-
<pluginRepositories>
<pluginRepository>
<id>jcenter-snapshots</id>
@@ -176,15 +176,6 @@
</pluginRepository>
</pluginRepositories>
- <properties>
- <asciidoctor.maven.plugin.version>1.5.3</asciidoctor.maven.plugin.version>
- <asciidoctorj.pdf.version>1.5.0-alpha.11</asciidoctorj.pdf.version>
- <asciidoctorj.version>1.5.4</asciidoctorj.version>
- <sonar.host.url>http://dockerhost:9000</sonar.host.url>
- <sonar.projectName>MIP Backend</sonar.projectName>
- <sonar.sources>src/main/java/</sonar.sources>
- </properties>
-
<build>
<resources>
<resource>
@@ -193,6 +184,7 @@
<include>**/*.xml</include>
<include>**/*.json</include>
<include>**/*.csv</include>
+ <include>**/*.sql</include>
</includes>
<filtering>true</filtering>
</resource>
@@ -202,7 +194,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
- <version>2.3</version>
+ <version>${maven-resources-plugin.version}</version>
<configuration>
<!-- specify UTF-8, ISO-8859-1 or any other file encoding -->
<encoding>UTF-8</encoding>
@@ -215,7 +207,7 @@
<plugin>
<groupId>de.juplo</groupId>
<artifactId>hibernate4-maven-plugin</artifactId>
- <version>1.1.0</version>
+ <version>${hibernate4-maven-plugin.version}</version>
<executions>
<execution>
<phase>compile</phase>
@@ -224,21 +216,16 @@
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
- <version>3.1</version>
+ <version>${maven-compiler-plugin.version}</version>
<configuration>
- <source>1.8</source>
- <target>1.8</target>
+ <source>${java.version}</source>
+ <target>${java.version}</target>
</configuration>
</plugin>
- <plugin>
- <groupId>org.flywaydb</groupId>
- <artifactId>flyway-maven-plugin</artifactId>
- <version>4.0.1</version>
- </plugin>
<plugin>
<groupId>io.github.swagger2markup</groupId>
<artifactId>swagger2markup-maven-plugin</artifactId>
- <version>1.0.0</version>
+ <version>${swagger2markup-maven-plugin.version}</version>
<configuration>
<swaggerInput>http://localhost:8080/services/v2/api-docs</swaggerInput>
<outputFile>${project.build.directory}/asciidoc/api</outputFile>
@@ -270,7 +257,7 @@
<plugin>
<groupId>org.sonarsource.scanner.maven</groupId>
<artifactId>sonar-maven-plugin</artifactId>
- <version>3.0.1</version>
+ <version>${sonar-maven-plugin.version}</version>
</plugin>
</plugins>
</build>
diff --git a/run.sh b/run.sh
index 3483bbcfcb1c7446b56537d6792375c48896efe9..5d9339d5dd5ee1458a5d47d420904917ac0cef13 100755
--- a/run.sh
+++ b/run.sh
@@ -1,20 +1,12 @@
-#!/bin/bash -e
+#!/usr/bin/env bash
-# Run the backend in a Docker container and start the database.
-# The current project is compiler inside the Docker container
+docker-compose build
+docker-compose up -d db
-if groups $USER | grep &>/dev/null '\bdocker\b'; then
- DOCKER_COMPOSE="docker-compose"
-else
- DOCKER_COMPOSE="sudo docker-compose"
-fi
+echo 'Waiting for database to be ready...'
+until [ $(docker-compose exec db psql -U postgres -c "\q" | wc -l) -eq 0 ]; do
+ printf '.'
+ sleep 1
+done
-# Create a symlink to the local Maven repository
-[ -L .m2 ] || ln -s -t . ~/.m2
-
-$DOCKER_COMPOSE --file=docker-compose.init.yml --project-name=portal-backend-init up
-
-echo "Need to set the current user as owner of the files generated in target directory..."
-sudo chown -R $USER:$USER ./target
-
-echo "Done"
+docker-compose up -d backend
diff --git a/src/docker/build/.gitignore b/src/docker/build/.gitignore
deleted file mode 100644
index d392f0e82c4ac6dd2e7bb17eb9253e1b30d07105..0000000000000000000000000000000000000000
--- a/src/docker/build/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-*.jar
diff --git a/src/docker/build/Dockerfile b/src/docker/build/Dockerfile
index 1369edf76009678d08db82e5e5ce87ef7b829f85..b4318d788f65cf01d672e59aab38c69b6e4aa17f 100644
--- a/src/docker/build/Dockerfile
+++ b/src/docker/build/Dockerfile
@@ -1,19 +1,8 @@
-# This Dockerfile encapsulate the MIP portal backend application for development purposes.
-
FROM maven:3-jdk-8
-RUN apt-get update && apt-get install -y wget
-RUN wget https://github.com/jwilder/dockerize/releases/download/v0.2.0/dockerize-linux-amd64-v0.2.0.tar.gz
-RUN tar -C /usr/local/bin -xzvf dockerize-linux-amd64-v0.2.0.tar.gz
-
-COPY mip.sh /opt/portal/
-COPY mip.jar /opt/portal/lib/
-RUN chmod +x /opt/portal/mip.sh
-EXPOSE 8080
-
-VOLUME /opt/portal/config/
-VOLUME /opt/portal/lib/
+COPY ./build-in-docker.sh /build-in-docker.sh
+VOLUME /opt/portal/
WORKDIR /opt/portal/
-CMD ["/usr/local/bin/dockerize", "-timeout", "240s", "-wait", "tcp://portaldb:5432", "/opt/portal/mip.sh"]
+CMD ["bash", "/build-in-docker.sh"]
diff --git a/src/docker/build/build-in-docker.sh b/src/docker/build/build-in-docker.sh
new file mode 100644
index 0000000000000000000000000000000000000000..7b77f1e6688bd0b49f0ea3462cdf75ca86c79be0
--- /dev/null
+++ b/src/docker/build/build-in-docker.sh
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+echo 'Removing old target folder...'
+rm -r target/
+
+echo 'Packaging...'
+mvn package
diff --git a/src/docker/build/mip.sh b/src/docker/build/mip.sh
deleted file mode 100644
index cfae68474c42a1e66b80edb0ea849911ddd8eef4..0000000000000000000000000000000000000000
--- a/src/docker/build/mip.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env bash
-
-/usr/bin/java -DconfigFile=/opt/portal/config/application.yml -jar /opt/portal/lib/mip.jar
diff --git a/src/docker/init/build-in-docker.sh b/src/docker/init/build-in-docker.sh
deleted file mode 100644
index aff4c2e6c8eaabb623c62b16339b0dde606ead82..0000000000000000000000000000000000000000
--- a/src/docker/init/build-in-docker.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh -e
-
-echo ">>> Building inside Docker"
-cd /portal
-
-mvn package
-
-echo ">>> Press Ctrl+C to stop, build is complete"
diff --git a/src/docker/run/Dockerfile b/src/docker/run/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..b3a112a35d01fdb2bd1644ea5e21e79154c2c365
--- /dev/null
+++ b/src/docker/run/Dockerfile
@@ -0,0 +1,6 @@
+FROM frolvlad/alpine-oraclejdk8:slim
+
+VOLUME /config
+
+COPY ./target/backend-services-DOCKER_BUILD.jar backend.jar
+CMD ["java", "-jar", "backend.jar"]
diff --git a/src/main/java/org/hbp/mip/MIPApplication.java b/src/main/java/org/hbp/mip/MIPApplication.java
index f6d5aeb3d156eeac8afd31340c8bf1b190065e61..4814eb9e11f657e89133218e9d21622ad215eaf8 100644
--- a/src/main/java/org/hbp/mip/MIPApplication.java
+++ b/src/main/java/org/hbp/mip/MIPApplication.java
@@ -5,275 +5,14 @@
package org.hbp.mip;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiParam;
-import org.apache.log4j.Logger;
-import org.hbp.mip.model.User;
-import org.hbp.mip.utils.CORSFilter;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.boot.autoconfigure.security.oauth2.resource.ResourceServerProperties;
-import org.springframework.boot.context.embedded.FilterRegistrationBean;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.ImportResource;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.security.config.annotation.web.builders.HttpSecurity;
-import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.AuthenticationException;
-import org.springframework.security.core.context.SecurityContextHolder;
-import org.springframework.security.oauth2.client.OAuth2ClientContext;
-import org.springframework.security.oauth2.client.filter.OAuth2ClientAuthenticationProcessingFilter;
-import org.springframework.security.oauth2.client.filter.OAuth2ClientContextFilter;
-import org.springframework.security.oauth2.client.resource.OAuth2ProtectedResourceDetails;
-import org.springframework.security.oauth2.client.token.grant.code.AuthorizationCodeResourceDetails;
-import org.springframework.security.oauth2.config.annotation.web.configuration.EnableOAuth2Client;
-import org.springframework.security.oauth2.provider.OAuth2Authentication;
-import org.springframework.security.web.access.channel.ChannelProcessingFilter;
-import org.springframework.security.web.authentication.LoginUrlAuthenticationEntryPoint;
-import org.springframework.security.web.authentication.www.BasicAuthenticationFilter;
-import org.springframework.security.web.csrf.CsrfFilter;
-import org.springframework.security.web.csrf.CsrfToken;
-import org.springframework.security.web.csrf.CsrfTokenRepository;
-import org.springframework.security.web.csrf.HttpSessionCsrfTokenRepository;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-import org.springframework.web.filter.OncePerRequestFilter;
-import org.springframework.web.util.WebUtils;
-import springfox.documentation.builders.ApiInfoBuilder;
-import springfox.documentation.builders.RequestHandlerSelectors;
-import springfox.documentation.service.ApiInfo;
-import springfox.documentation.spi.DocumentationType;
-import springfox.documentation.spring.web.plugins.Docket;
-import springfox.documentation.swagger.web.UiConfiguration;
-import springfox.documentation.swagger2.annotations.EnableSwagger2;
-
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.ServletException;
-import javax.servlet.http.Cookie;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.security.Principal;
@SpringBootApplication
-@Configuration
-@ImportResource("classpath:spring/application-context.xml")
-@RestController
-@EnableOAuth2Client
-@EnableSwagger2
-@Api(value = "/", description = "MIP API")
-public class MIPApplication extends WebSecurityConfigurerAdapter {
-
- private static final Logger LOGGER = Logger.getLogger(MIPApplication.class);
-
- @Autowired
- OAuth2ClientContext oauth2ClientContext;
-
- @Autowired
- HttpSessionCsrfTokenRepository httpSessionCsrfTokenRepository;
-
- @Autowired
- OAuth2ClientAuthenticationProcessingFilter hbpFilter;
-
+public class MIPApplication {
public static void main(String[] args) {
SpringApplication.run(MIPApplication.class, args);
}
- public String getUserInfos() {
- OAuth2Authentication oAuth2Authentication = (OAuth2Authentication) SecurityContextHolder.getContext().getAuthentication();
- Authentication userAuthentication = oAuth2Authentication.getUserAuthentication();
- return userAuthentication.getDetails().toString();
- }
-
- /**
- * returns the user for the current session.
- *
- * the "synchronized" keyword is there to avoid a bug that the transaction is supposed to protect me from.
- * To test if your solution to removing it works, do the following:
- * - clean DB from scratch
- * - restart DB and backend (no session or anything like that)
- * - log in using the front end
- * - check you have no 500 error in the network logs.
- * @return
- */
- public synchronized User getUser() {
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- User user = new User(getUserInfos());
- try {
- session.beginTransaction();
- Boolean agreeNDA = (Boolean) session
- .createQuery("SELECT agreeNDA FROM User WHERE username= :username")
- .setString("username", user.getUsername())
- .uniqueResult();
- user.setAgreeNDA(agreeNDA);
- session.merge(user);
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return user;
- }
-
- @Bean
- public Docket documentation() {
- return new Docket(DocumentationType.SWAGGER_2)
- .select()
- .apis(RequestHandlerSelectors.basePackage("org.hbp.mip.controllers"))
- .build()
- .pathMapping("/")
- .apiInfo(metadata());
- }
-
- @Bean
- public UiConfiguration uiConfig() {
- return UiConfiguration.DEFAULT;
- }
-
- private ApiInfo metadata() {
- return new ApiInfoBuilder()
- .title("Medical Informatics Platform API")
- .description("Serve the MIP Frontend")
- .version("1.0")
- .contact("mirco.nasuti@chuv.ch")
- .build();
- }
-
- @RequestMapping(path = "/user", method = RequestMethod.GET)
- public Principal user(Principal principal, HttpServletResponse response) {
- ObjectMapper mapper = new ObjectMapper();
-
- try {
- String userJSON = mapper.writeValueAsString(getUser());
- Cookie cookie = new Cookie("user", URLEncoder.encode(userJSON, "UTF-8"));
- cookie.setSecure(true);
- cookie.setPath("/");
- response.addCookie(cookie);
- } catch (JsonProcessingException | UnsupportedEncodingException e) {
- LOGGER.trace(e);
- }
- return principal;
- }
-
- @RequestMapping(path = "/user", method = RequestMethod.POST)
- public ResponseEntity<Void> postUser(@ApiParam(value = "Has the user agreed on the NDA") @RequestParam(value = "agreeNDA", required = true) Boolean agreeNDA) {
- String username = getUser().getUsername();
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try {
- session.beginTransaction();
- User user = (User) session
- .createQuery("from User where username= :username")
- .setString("username", username)
- .uniqueResult();
- if (user != null) {
- user.setAgreeNDA(agreeNDA);
- session.update(user);
- }
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
- }
-
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
-
- @Override
- protected void configure(HttpSecurity http) throws Exception {
- // @formatter:off
- http.addFilterBefore(new CORSFilter(), ChannelProcessingFilter.class);
- http.antMatcher("/**")
- .authorizeRequests()
- .antMatchers("/", "/frontend/**", "/webjars/**", "/v2/api-docs").permitAll()
- .anyRequest().authenticated()
- .and().exceptionHandling().authenticationEntryPoint(new CustomLoginUrlAuthenticationEntryPoint("/login/hbp"))
- .and().logout().logoutSuccessUrl("/login/hbp").permitAll()
- .and().logout().logoutUrl("/logout").permitAll()
- .and().csrf().ignoringAntMatchers("/logout").csrfTokenRepository(csrfTokenRepository())
- .and().addFilterAfter(csrfHeaderFilter(), CsrfFilter.class)
- .addFilterBefore(hbpFilter, BasicAuthenticationFilter.class);
- }
-
- @Bean
- public FilterRegistrationBean oauth2ClientFilterRegistration(
- OAuth2ClientContextFilter filter) {
- FilterRegistrationBean registration = new FilterRegistrationBean();
- registration.setFilter(filter);
- registration.setOrder(-100);
- return registration;
- }
-
- @Bean(name="hbp")
- @ConfigurationProperties("hbp.client")
- OAuth2ProtectedResourceDetails hbp() {
- return new AuthorizationCodeResourceDetails();
- }
-
- @Bean(name="hbpResource")
- @ConfigurationProperties("hbp.resource")
- ResourceServerProperties hbpResource() {
- return new ResourceServerProperties();
- }
-
- private Filter csrfHeaderFilter() {
- return new OncePerRequestFilter() {
- @Override
- protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response,
- FilterChain filterChain) throws ServletException, IOException {
- CsrfToken csrf = (CsrfToken) request.getAttribute(CsrfToken.class.getName());
- if (csrf != null) {
- Cookie cookie = WebUtils.getCookie(request, "XSRF-TOKEN");
- String token = csrf.getToken();
- if (cookie == null || token != null && !token.equals(cookie.getValue())) {
- cookie = new Cookie("XSRF-TOKEN", token);
- cookie.setPath("/");
- response.addCookie(cookie);
- }
- }
- filterChain.doFilter(request, response);
- }
- };
- }
-
- private CsrfTokenRepository csrfTokenRepository() {
- return httpSessionCsrfTokenRepository;
- }
-
-}
-
-class CustomLoginUrlAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoint {
-
- public CustomLoginUrlAuthenticationEntryPoint(String url) {
- super(url);
- }
-
- @Override
- public void commence(HttpServletRequest request, HttpServletResponse response, AuthenticationException authException) throws IOException, ServletException {
- response.sendError(HttpServletResponse.SC_UNAUTHORIZED);
- }
-}
+}
\ No newline at end of file
diff --git a/src/main/java/org/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/org/hbp/mip/configuration/PersistenceConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..35ce472e97215226e3bc4bd26e647d22d3498b2b
--- /dev/null
+++ b/src/main/java/org/hbp/mip/configuration/PersistenceConfiguration.java
@@ -0,0 +1,52 @@
+package org.hbp.mip.configuration;
+
+import org.flywaydb.core.Flyway;
+import org.hbp.mip.utils.CSVUtil;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.orm.jpa.EntityScan;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.DependsOn;
+import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.orm.jpa.JpaVendorAdapter;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
+
+import javax.sql.DataSource;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+@Configuration
+@EnableJpaRepositories(value = "org.hbp.mip.repositories")
+@EntityScan(basePackages = "org.hbp.mip.model")
+public class PersistenceConfiguration {
+
+ @Autowired
+ DataSource dataSource;
+
+ @Bean
+ public CSVUtil csvUtil() {
+ return new CSVUtil();
+ }
+
+ @Bean
+ @DependsOn("flyway")
+ public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+ LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
+ em.setDataSource(dataSource);
+ JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
+ em.setJpaVendorAdapter(vendorAdapter);
+ return em;
+ }
+
+ @Bean(initMethod = "migrate")
+ public Flyway flyway() {
+ Flyway flyway = new Flyway();
+ flyway.setBaselineOnMigrate(true);
+ flyway.setDataSource(dataSource);
+ return flyway;
+ }
+
+}
diff --git a/src/main/java/org/hbp/mip/configuration/SecurityConfiguration.java b/src/main/java/org/hbp/mip/configuration/SecurityConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..79b437fed3218f9337b3b0486357244c8c5a861f
--- /dev/null
+++ b/src/main/java/org/hbp/mip/configuration/SecurityConfiguration.java
@@ -0,0 +1,212 @@
+package org.hbp.mip.configuration;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import io.swagger.annotations.ApiParam;
+import org.apache.log4j.Logger;
+import org.hbp.mip.controllers.ArticlesApi;
+import org.hbp.mip.model.User;
+import org.hbp.mip.repositories.UserRepository;
+import org.hbp.mip.utils.CORSFilter;
+import org.hbp.mip.utils.CustomLoginUrlAuthenticationEntryPoint;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.autoconfigure.security.oauth2.resource.ResourceServerProperties;
+import org.springframework.boot.autoconfigure.security.oauth2.resource.UserInfoTokenServices;
+import org.springframework.boot.context.embedded.FilterRegistrationBean;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.config.annotation.web.builders.HttpSecurity;
+import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.security.oauth2.client.OAuth2ClientContext;
+import org.springframework.security.oauth2.client.OAuth2RestTemplate;
+import org.springframework.security.oauth2.client.filter.OAuth2ClientAuthenticationProcessingFilter;
+import org.springframework.security.oauth2.client.filter.OAuth2ClientContextFilter;
+import org.springframework.security.oauth2.client.resource.OAuth2ProtectedResourceDetails;
+import org.springframework.security.oauth2.client.token.grant.code.AuthorizationCodeResourceDetails;
+import org.springframework.security.oauth2.config.annotation.web.configuration.EnableOAuth2Client;
+import org.springframework.security.oauth2.provider.OAuth2Authentication;
+import org.springframework.security.web.access.channel.ChannelProcessingFilter;
+import org.springframework.security.web.authentication.SimpleUrlAuthenticationSuccessHandler;
+import org.springframework.security.web.authentication.www.BasicAuthenticationFilter;
+import org.springframework.security.web.csrf.CsrfFilter;
+import org.springframework.security.web.csrf.CsrfToken;
+import org.springframework.security.web.csrf.CsrfTokenRepository;
+import org.springframework.security.web.csrf.HttpSessionCsrfTokenRepository;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.filter.OncePerRequestFilter;
+import org.springframework.web.util.WebUtils;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.ServletException;
+import javax.servlet.http.Cookie;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.security.Principal;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+@Configuration
+@EnableOAuth2Client
+@RestController
+public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
+
+ private static final Logger LOGGER = Logger.getLogger(ArticlesApi.class);
+
+ @Autowired
+ OAuth2ClientContext oauth2ClientContext;
+
+ @Autowired
+ UserRepository userRepository;
+
+ @Value("#{'${hbp.client.pre-established-redirect-uri:/login/hbp}'}")
+ String loginUrl;
+
+ @Value("#{'${hbp.client.logout-uri:/logout}'}")
+ String logoutUrl;
+
+ @Value("#{'${frontend.redirect.url:http://frontend/home}'}")
+ String frontendRedirect;
+
+ @Override
+ protected void configure(HttpSecurity http) throws Exception {
+ // @formatter:off
+ http.addFilterBefore(new CORSFilter(), ChannelProcessingFilter.class);
+ http.antMatcher("/**")
+ .authorizeRequests()
+ .antMatchers("/", "/frontend/**", "/webjars/**", "/v2/api-docs").permitAll()
+ .anyRequest().authenticated()
+ .and().exceptionHandling().authenticationEntryPoint(new CustomLoginUrlAuthenticationEntryPoint(loginUrl))
+ .and().logout().logoutSuccessUrl(loginUrl).permitAll()
+ .and().logout().logoutUrl(logoutUrl).permitAll()
+ .and().csrf().ignoringAntMatchers(logoutUrl).csrfTokenRepository(csrfTokenRepository())
+ .and().addFilterAfter(csrfHeaderFilter(), CsrfFilter.class)
+ .addFilterBefore(ssoFilter(), BasicAuthenticationFilter.class);
+ }
+
+ private Filter ssoFilter() {
+ OAuth2ClientAuthenticationProcessingFilter hbpFilter = new OAuth2ClientAuthenticationProcessingFilter(loginUrl);
+ OAuth2RestTemplate hbpTemplate = new OAuth2RestTemplate(hbp(), oauth2ClientContext);
+ hbpFilter.setAuthenticationSuccessHandler(new SimpleUrlAuthenticationSuccessHandler(frontendRedirect));
+ hbpFilter.setRestTemplate(hbpTemplate);
+ hbpFilter.setTokenServices(new UserInfoTokenServices(hbpResource().getUserInfoUri(), hbp().getClientId()));
+ return hbpFilter;
+ }
+
+ @Bean
+ public FilterRegistrationBean oauth2ClientFilterRegistration(
+ OAuth2ClientContextFilter filter) {
+ FilterRegistrationBean registration = new FilterRegistrationBean();
+ registration.setFilter(filter);
+ registration.setOrder(-100);
+ return registration;
+ }
+
+ @Bean(name="hbp")
+ @ConfigurationProperties("hbp.client")
+ OAuth2ProtectedResourceDetails hbp() {
+ return new AuthorizationCodeResourceDetails();
+ }
+
+ @Bean(name="hbpResource")
+ @ConfigurationProperties("hbp.resource")
+ ResourceServerProperties hbpResource() {
+ return new ResourceServerProperties();
+ }
+
+ private Filter csrfHeaderFilter() {
+ return new OncePerRequestFilter() {
+ @Override
+ protected void doFilterInternal(HttpServletRequest request, HttpServletResponse response,
+ FilterChain filterChain) throws ServletException, IOException {
+ CsrfToken csrf = (CsrfToken) request.getAttribute(CsrfToken.class.getName());
+ if (csrf != null) {
+ Cookie cookie = WebUtils.getCookie(request, "XSRF-TOKEN");
+ String token = csrf.getToken();
+ if (cookie == null || token != null && !token.equals(cookie.getValue())) {
+ cookie = new Cookie("XSRF-TOKEN", token);
+ cookie.setPath("/");
+ response.addCookie(cookie);
+ }
+ }
+ filterChain.doFilter(request, response);
+ }
+ };
+ }
+
+ private CsrfTokenRepository csrfTokenRepository() {
+ HttpSessionCsrfTokenRepository repository = new HttpSessionCsrfTokenRepository();
+ repository.setHeaderName("X-XSRF-TOKEN");
+ return repository;
+ }
+
+ public String getUserInfos() {
+ OAuth2Authentication oAuth2Authentication = (OAuth2Authentication) SecurityContextHolder.getContext().getAuthentication();
+ Authentication userAuthentication = oAuth2Authentication.getUserAuthentication();
+ return userAuthentication.getDetails().toString();
+ }
+
+ /**
+ * returns the user for the current session.
+ * <p>
+ * the "synchronized" keyword is there to avoid a bug that the transaction is supposed to protect me from.
+ * To test if your solution to removing it works, do the following:
+ * - clean DB from scratch
+ * - restart DB and backend (no session or anything like that)
+ * - log in using the front end
+ * - check you have no 500 error in the network logs.
+ *
+ * @return
+ */
+ public synchronized User getUser() {
+ User user = new User(getUserInfos());
+ User foundUser = userRepository.findOne(user.getUsername());
+ if(foundUser != null)
+ {
+ user.setAgreeNDA(foundUser.getAgreeNDA());
+ }
+ userRepository.save(user);
+ return user;
+ }
+
+ @RequestMapping(path = "/user", method = RequestMethod.GET)
+ public Principal user(Principal principal, HttpServletResponse response) {
+ ObjectMapper mapper = new ObjectMapper();
+
+ try {
+ String userJSON = mapper.writeValueAsString(getUser());
+ Cookie cookie = new Cookie("user", URLEncoder.encode(userJSON, "UTF-8"));
+ cookie.setSecure(true);
+ cookie.setPath("/");
+ response.addCookie(cookie);
+ } catch (JsonProcessingException | UnsupportedEncodingException e) {
+ LOGGER.trace(e);
+ }
+ return principal;
+ }
+
+ @RequestMapping(path = "/user", method = RequestMethod.POST)
+ public ResponseEntity<Void> postUser(@ApiParam(value = "Has the user agreed on the NDA") @RequestParam(value = "agreeNDA", required = true) Boolean agreeNDA) {
+ User user = getUser();
+ if (user != null) {
+ user.setAgreeNDA(agreeNDA);
+ userRepository.save(user);
+ }
+ return new ResponseEntity<>(HttpStatus.NO_CONTENT);
+ }
+
+}
diff --git a/src/main/java/org/hbp/mip/configuration/WebConfiguration.java b/src/main/java/org/hbp/mip/configuration/WebConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..888fbd1e7e58c5725c60782c2c02aa220e3e33cc
--- /dev/null
+++ b/src/main/java/org/hbp/mip/configuration/WebConfiguration.java
@@ -0,0 +1,46 @@
+package org.hbp.mip.configuration;
+
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.data.web.config.EnableSpringDataWebSupport;
+import springfox.documentation.builders.ApiInfoBuilder;
+import springfox.documentation.builders.RequestHandlerSelectors;
+import springfox.documentation.service.ApiInfo;
+import springfox.documentation.spi.DocumentationType;
+import springfox.documentation.spring.web.plugins.Docket;
+import springfox.documentation.swagger.web.UiConfiguration;
+import springfox.documentation.swagger2.annotations.EnableSwagger2;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+@Configuration
+@EnableSwagger2
+@EnableSpringDataWebSupport
+public class WebConfiguration {
+
+ @Bean
+ public UiConfiguration uiConfig() {
+ return UiConfiguration.DEFAULT;
+ }
+
+ @Bean
+ public Docket documentation() {
+ return new Docket(DocumentationType.SWAGGER_2)
+ .select()
+ .apis(RequestHandlerSelectors.basePackage("org.hbp.mip.controllers"))
+ .build()
+ .pathMapping("/")
+ .apiInfo(metadata());
+ }
+
+ private ApiInfo metadata() {
+ return new ApiInfoBuilder()
+ .title("Medical Informatics Platform API")
+ .description("Serve the MIP Frontend")
+ .version("1.0")
+ .contact("mirco.nasuti@chuv.ch")
+ .build();
+ }
+}
diff --git a/src/main/java/org/hbp/mip/controllers/AppsApi.java b/src/main/java/org/hbp/mip/controllers/AppsApi.java
index b89ef31b4836ba1e52966ae8a002e341bdb13546..351a2efb069e6b23831857e461a2a7db6f16a1a2 100644
--- a/src/main/java/org/hbp/mip/controllers/AppsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/AppsApi.java
@@ -6,14 +6,13 @@ package org.hbp.mip.controllers;
import io.swagger.annotations.*;
import org.apache.log4j.Logger;
-import org.hbp.mip.MIPApplication;
+import org.hbp.mip.configuration.SecurityConfiguration;
import org.hbp.mip.model.App;
import org.hbp.mip.model.User;
import org.hbp.mip.model.Vote;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.NonUniqueObjectException;
-import org.hibernate.Query;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.AppRepository;
+import org.hbp.mip.repositories.UserRepository;
+import org.hbp.mip.repositories.VoteRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -22,9 +21,7 @@ import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
-import javax.validation.ConstraintViolationException;
-import java.util.LinkedList;
-import java.util.List;
+import java.util.Iterator;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -36,31 +33,23 @@ public class AppsApi {
private static final Logger LOGGER = Logger.getLogger(AppsApi.class);
@Autowired
- MIPApplication mipApplication;
+ SecurityConfiguration securityConfiguration;
+
+ @Autowired
+ AppRepository appRepository;
+
+ @Autowired
+ VoteRepository voteRepository;
+
+ @Autowired
+ UserRepository userRepository;
@ApiOperation(value = "Get apps", response = App.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getApps(
+ public ResponseEntity<Iterable> getApps(
) {
- List apps = new LinkedList<>();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try {
- session.beginTransaction();
- Query query = session.createQuery("FROM App");
- apps = query.list();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(apps);
+ return ResponseEntity.ok(appRepository.findAll());
}
@ApiOperation(value = "Post a vote")
@@ -70,69 +59,26 @@ public class AppsApi {
@ApiParam(value = "id", required = true) @PathVariable("id") Integer id,
@ApiParam(value = "value", required = true) @PathVariable("value") Integer value
) {
+ User user = userRepository.findOne(securityConfiguration.getUser().getUsername());
+ App app = appRepository.findOne(id);
+ Vote vote;
- User user = mipApplication.getUser();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try {
- session.beginTransaction();
-
- Vote vote = (Vote) session.createQuery("" +
- "SELECT v FROM Vote v, User u, App a " +
- "WHERE u=v.user " +
- "AND a=v.app " +
- "AND u.username= :username " +
- "AND a.id= :app_id")
- .setString("username", user.getUsername())
- .setLong("app_id", id)
- .uniqueResult();
- App app = (App) session.createQuery("FROM App where id= :id").setLong("id", id).uniqueResult();
-
- if (vote != null) {
- vote.setValue(value);
-
- session.update(vote);
- session.getTransaction().commit();
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
- else
- {
- vote = new Vote();
- vote.setUser(user);
- vote.setValue(value);
- vote.setApp(app);
-
- session.save(vote);
- session.getTransaction().commit();
- return new ResponseEntity<>(HttpStatus.CREATED);
- }
- }
- catch (ConstraintViolationException cve)
- {
- LOGGER.trace(cve);
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- }
- return new ResponseEntity<>(HttpStatus.BAD_REQUEST);
- }
- catch (NonUniqueObjectException nuoe)
+ Iterator<Vote> voteIter = voteRepository.findByUserAndApp(user, app).iterator();
+ if(voteIter.hasNext())
{
- LOGGER.trace(nuoe);
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- }
- return new ResponseEntity<>(HttpStatus.CONFLICT);
+ vote = voteIter.next();
}
- catch (Exception e)
+ else
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
+ vote = new Vote();
+ vote.setUser(user);
+ vote.setApp(app);
}
+
+ vote.setValue(value);
+ voteRepository.save(vote);
+
+ return new ResponseEntity<>(HttpStatus.CREATED);
+
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
index 99fe8334aef8fa27ba2fde647794b472b1cdb196..83eed713395da1593b216eb44431370fdcd8d214 100644
--- a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
@@ -8,12 +8,10 @@ package org.hbp.mip.controllers;
import com.github.slugify.Slugify;
import io.swagger.annotations.*;
import org.apache.log4j.Logger;
-import org.hbp.mip.MIPApplication;
+import org.hbp.mip.configuration.SecurityConfiguration;
import org.hbp.mip.model.Article;
import org.hbp.mip.model.User;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.ArticleRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -22,8 +20,7 @@ import org.springframework.web.bind.annotation.*;
import javax.validation.Valid;
import java.io.IOException;
import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
+import java.util.Iterator;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -35,54 +32,44 @@ public class ArticlesApi {
private static final Logger LOGGER = Logger.getLogger(ArticlesApi.class);
@Autowired
- MIPApplication mipApplication;
+ SecurityConfiguration securityConfiguration;
+
+ @Autowired
+ ArticleRepository articleRepository;
@ApiOperation(value = "Get articles", response = Article.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getArticles(
+ public ResponseEntity<Iterable> getArticles(
@ApiParam(value = "Only ask own articles") @RequestParam(value = "own", required = false) Boolean own,
@ApiParam(value = "Only ask results matching status", allowableValues = "{values=[draft, published, closed]}") @RequestParam(value = "status", required = false) String status,
@ApiParam(value = "Only ask articles from own team") @RequestParam(value = "team", required = false) Boolean team
) {
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
+ Iterable<Article> articles;
- String queryString = "SELECT a FROM Article a, User u WHERE a.createdBy=u.username";
- if(status != null)
- {
- queryString += " AND status= :status";
- }
if(own != null && own)
{
- queryString += " AND u.username= :username";
+ articles = articleRepository.findByCreatedBy(user);
}
else
{
- queryString += " AND (status='published' or u.username= :username)";
+ articles = articleRepository.findByStatusOrCreatedBy("published", user);
}
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- List articles = new LinkedList<>();
- try {
- session.beginTransaction();
- Query query = session.createQuery(queryString);
- if (status != null) {
- query.setString("status", status);
- }
- query.setString("username", user.getUsername());
- articles = query.list();
- session.getTransaction().commit();
- } catch (Exception e)
+ if(status != null)
{
- if(session.getTransaction() != null)
+ for(Iterator<Article> i = articles.iterator(); i.hasNext();)
{
- session.getTransaction().rollback();
- throw e;
+ Article a = i.next();
+ if(!status.equals(a.getStatus()))
+ {
+ i.remove();
+ }
}
}
-
return ResponseEntity.ok(articles);
}
@@ -94,7 +81,7 @@ public class ArticlesApi {
@RequestBody @ApiParam(value = "Article to create", required = true) @Valid Article article
) {
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
article.setCreatedAt(new Date());
if ("published".equals(article.getStatus())) {
@@ -102,62 +89,45 @@ public class ArticlesApi {
}
article.setCreatedBy(user);
- Long count;
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try{
- session.beginTransaction();
-
- int i = 0;
- do{
- i++;
- count = (Long) session
- .createQuery("select count(*) from Article where title= :title")
- .setString("title", article.getTitle())
- .uniqueResult();
+ long count = 1;
+ for(int i = 1; count > 0; i++)
+ {
+ count = articleRepository.countByTitle(article.getTitle());
- if(count > 0)
- {
- String title = article.getTitle();
- if(i > 1)
- {
- title = title.substring(0, title.length()-4);
- }
- article.setTitle(title + " (" + i + ")");
- }
- } while(count > 0);
-
- String slug = new Slugify().slugify(article.getTitle());
-
- i = 0;
- do {
- i++;
- count = (Long) session
- .createQuery("select count(*) from Article where slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
- if(count > 0)
+ if(count > 0)
+ {
+ String title = article.getTitle();
+ if(i > 1)
{
- if(i > 1)
- {
- slug = slug.substring(0, slug.length()-2);
- }
- slug += "-"+i;
+ title = title.substring(0, title.length()-4);
}
- article.setSlug(slug);
- } while(count > 0);
+ article.setTitle(title + " (" + i + ")");
+ }
+ }
- session.save(article);
- session.getTransaction().commit();
+ String slug;
+ try {
+ slug = new Slugify().slugify(article.getTitle());
} catch (IOException e) {
- LOGGER.trace(e);
- } catch (Exception e) {
- if(session.getTransaction() != null)
+ slug = "";
+ LOGGER.trace(e);
+ }
+
+ boolean alreadyExists = true;
+ for(int i = 1; alreadyExists; i++)
+ {
+ alreadyExists = articleRepository.exists(slug);
+ if(alreadyExists)
{
- session.getTransaction().rollback();
- throw e;
+ if(i > 1)
+ {
+ slug = slug.substring(0, slug.length()-2);
+ }
+ slug += "-"+i;
}
- return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
+ article.setSlug(slug);
}
+ articleRepository.save(article);
return new ResponseEntity<>(HttpStatus.CREATED);
}
@@ -170,33 +140,13 @@ public class ArticlesApi {
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
) {
- User user = mipApplication.getUser();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Article article = null;
- try{
- session.beginTransaction();
-
- article = (Article) session
- .createQuery("FROM Article WHERE slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
-
- session.getTransaction().commit();
-
- if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername()))
- {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
- } catch (Exception e)
+ User user = securityConfiguration.getUser();
+ Article article;
+ article = articleRepository.findOne(slug);
+ if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername()))
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
+ return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
-
return ResponseEntity.ok(article);
}
@@ -209,60 +159,36 @@ public class ArticlesApi {
@RequestBody @ApiParam(value = "Article to update", required = true) @Valid Article article
) {
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try{
- session.beginTransaction();
+ String author = articleRepository.findOne(slug).getCreatedBy().getUsername();
- String author = (String) session
- .createQuery("select U.username from User U, Article A where A.createdBy = U.username and A.slug = :slug")
- .setString("slug", slug)
- .uniqueResult();
+ if(!user.getUsername().equals(author))
+ {
+ return new ResponseEntity<>(HttpStatus.FORBIDDEN);
+ }
- if(!user.getUsername().equals(author))
- {
- session.getTransaction().commit();
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
+ String oldTitle = articleRepository.findOne(slug).getTitle();
- String oldTitle = (String) session
- .createQuery("select title from Article where slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
-
- String newTitle = article.getTitle();
-
- if(!newTitle.equals(oldTitle)) {
- Long count;
- int i = 0;
- do {
- i++;
- newTitle = article.getTitle();
- count = (Long) session
- .createQuery("select count(*) from Article where title= :title")
- .setString("title", newTitle)
- .uniqueResult();
- if (count > 0 && !newTitle.equals(oldTitle)) {
- if (i > 1) {
- newTitle = newTitle.substring(0, newTitle.length() - 4);
- }
- article.setTitle(newTitle + " (" + i + ")");
- }
- } while (count > 0 && !newTitle.equals(oldTitle));
- }
+ String newTitle = article.getTitle();
- session.update(article);
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
+ if(!newTitle.equals(oldTitle)) {
+ long count = 1;
+ for(int i = 1; count > 0 && !newTitle.equals(oldTitle); i++)
{
- session.getTransaction().rollback();
- throw e;
+ newTitle = article.getTitle();
+ count = articleRepository.countByTitle(newTitle);
+ if (count > 0 && !newTitle.equals(oldTitle)) {
+ if (i > 1) {
+ newTitle = newTitle.substring(0, newTitle.length() - 4);
+ }
+ article.setTitle(newTitle + " (" + i + ")");
+ }
}
}
+ articleRepository.save(article);
+
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
diff --git a/src/main/java/org/hbp/mip/controllers/DatasetsApi.java b/src/main/java/org/hbp/mip/controllers/DatasetsApi.java
index 4f3b67bfb063cd6504f7df85cf99c8cc4089a1d7..05fc11d6a8b93a573e0c5ffe149de1e2d2a9a1fc 100644
--- a/src/main/java/org/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/DatasetsApi.java
@@ -7,8 +7,8 @@ package org.hbp.mip.controllers;
import io.swagger.annotations.*;
import org.hbp.mip.model.Dataset;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.DatasetRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -22,32 +22,16 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/datasets", description = "the datasets API")
public class DatasetsApi {
+ @Autowired
+ DatasetRepository datasetRepository;
+
@ApiOperation(value = "Get a dataset", response = Dataset.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(value = "/{code}", method = RequestMethod.GET)
public ResponseEntity<Dataset> getADataset(
@ApiParam(value = "code", required = true) @PathVariable("code") String code
) {
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Dataset dataset = null;
- try{
- session.beginTransaction();
- dataset = (Dataset) session
- .createQuery("from Dataset where code= :code")
- .setString("code", code)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(dataset);
+ return ResponseEntity.ok(datasetRepository.findOne(code));
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
index 5adbdaa35ffd233717ea958b54e6a3cdfc7f78a2..99275314da2f0fdd068157e99e927b57aa949ca8 100644
--- a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
@@ -1,18 +1,16 @@
package org.hbp.mip.controllers;
+import com.google.common.collect.Lists;
import com.google.gson.*;
import io.swagger.annotations.*;
import org.apache.log4j.Logger;
-import org.hbp.mip.MIPApplication;
+import org.hbp.mip.configuration.SecurityConfiguration;
import org.hbp.mip.model.Experiment;
-import org.hbp.mip.model.Model;
import org.hbp.mip.model.User;
+import org.hbp.mip.repositories.ExperimentRepository;
+import org.hbp.mip.repositories.ModelRepository;
import org.hbp.mip.utils.HTTPUtil;
-import org.hbp.mip.utils.HibernateUtil;
import org.hbp.mip.utils.JSONUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
-import org.hibernate.Transaction;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
@@ -24,7 +22,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.MalformedURLException;
-import java.util.LinkedList;
+import java.util.Date;
import java.util.List;
import java.util.UUID;
@@ -61,7 +59,13 @@ public class ExperimentApi {
private String miningExaremeQueryUrl;
@Autowired
- MIPApplication mipApplication;
+ SecurityConfiguration securityConfiguration;
+
+ @Autowired
+ ModelRepository modelRepository;
+
+ @Autowired
+ ExperimentRepository experimentRepository;
@ApiOperation(value = "Send a request to the workflow to run an experiment", response = Experiment.class)
@@ -72,35 +76,14 @@ public class ExperimentApi {
Experiment experiment = new Experiment();
experiment.setUuid(UUID.randomUUID());
- User user = mipApplication.getUser();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Transaction transaction = session.beginTransaction();
-
- try {
+ User user = securityConfiguration.getUser();
- experiment.setAlgorithms(incomingQuery.get("algorithms").toString());
- experiment.setValidations(incomingQuery.get("validations").toString());
- experiment.setName(incomingQuery.get("name").getAsString());
- experiment.setCreatedBy(user);
-
- Query hibernateQuery = session.createQuery("from Model as model where model.slug = :slug");
- hibernateQuery.setParameter("slug", incomingQuery.get("model").getAsString());
- experiment.setModel((Model)hibernateQuery.uniqueResult());
-
- session.save(experiment);
- transaction.commit();
-
- } catch (Exception e) {
- if(transaction != null)
- {
- transaction.rollback();
- }
- LOGGER.trace(e);
- LOGGER.warn("Cannot create experiment to run ! This is probably caused by a bad request !");
- // 400 here probably
- return new ResponseEntity<>(e.getMessage(), HttpStatus.BAD_REQUEST);
- }
+ experiment.setAlgorithms(incomingQuery.get("algorithms").toString());
+ experiment.setValidations(incomingQuery.get("validations").toString());
+ experiment.setName(incomingQuery.get("name").getAsString());
+ experiment.setCreatedBy(user);
+ experiment.setModel(modelRepository.findOne(incomingQuery.get("model").getAsString()));
+ experimentRepository.save(experiment);
try {
if(isExaremeAlgo(experiment))
@@ -130,23 +113,7 @@ public class ExperimentApi {
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
-
- try {
- session.beginTransaction();
-
- Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
- hibernateQuery.setParameter("uuid", experimentUuid);
- experiment = (Experiment) hibernateQuery.uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e) {
- // 404 here probably
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- }
- throw e;
- }
+ experiment = experimentRepository.findOne(experimentUuid);
if (experiment == null) {
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
@@ -161,7 +128,7 @@ public class ExperimentApi {
Experiment experiment;
UUID experimentUuid;
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
@@ -170,31 +137,11 @@ public class ExperimentApi {
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Transaction transaction = null;
- try {
- transaction = session.beginTransaction();
-
- Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
- hibernateQuery.setParameter("uuid", experimentUuid);
- experiment = (Experiment) hibernateQuery.uniqueResult();
-
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
-
- experiment.setResultsViewed(true);
- session.update(experiment);
-
- transaction.commit();
- } catch (Exception e) {
- // 404 here probably
- if(transaction != null)
- {
- transaction.rollback();
- }
- throw e;
- }
-
+ experiment = experimentRepository.findOne(experimentUuid);;
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
+ experiment.setResultsViewed(true);
+ experimentRepository.save(experiment);
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
@@ -265,61 +212,38 @@ public class ExperimentApi {
int maxResultCount,
String modelSlug
) {
- List<Experiment> experiments = new LinkedList<>();
- User user = mipApplication.getUser();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
-
- try {
- session.beginTransaction();
-
- Query hibernateQuery;
- String baseQuery = "from Experiment as e WHERE ";
-
- baseQuery += mine ? "e.createdBy = :user" : "(e.createdBy = :user OR e.shared is true)";
-
- if (modelSlug == null || "".equals(modelSlug)) {
- hibernateQuery = session.createQuery(baseQuery);
- } else {
- baseQuery += " AND e.model.slug = :slug";
- hibernateQuery = session.createQuery(baseQuery);
- hibernateQuery.setParameter("slug", modelSlug);
- }
- hibernateQuery.setParameter("user", user);
-
- if (maxResultCount > 0)
- hibernateQuery.setMaxResults(maxResultCount);
-
- for (Object experiment: hibernateQuery.list()) {
- if (experiment instanceof Experiment) { // should definitely be true
- Experiment experiment1 = (Experiment) experiment;
- // remove some fields because it is costly and not useful to send them over the network
- experiment1.setResult(null);
- experiment1.setAlgorithms(null);
- experiment1.setValidations(null);
- experiments.add(experiment1);
-
- }
+ User user = securityConfiguration.getUser();
+ Iterable<Experiment> experiments = null;
+
+ Iterable<Experiment> myExperiments = experimentRepository.findByCreatedBy(user);
+ List<Experiment> expList = Lists.newLinkedList(myExperiments);
+ if(!mine)
+ {
+ Iterable<Experiment> sharedExperiments = experimentRepository.findByShared(true);
+ List<Experiment> sharedExpList = Lists.newLinkedList(sharedExperiments);
+ expList.addAll(sharedExpList);
+ }
- }
- } catch (Exception e) {
- // 404 here probably
- LOGGER.trace(e);
- throw e;
- } finally {
- if(session.getTransaction() != null)
+ if (modelSlug != null && !"".equals(modelSlug)) {
+ for(Experiment e : expList)
{
- session.getTransaction().rollback();
+ e.setResult(null);
+ e.setAlgorithms(null);
+ e.setValidations(null);
+ if(!e.getModel().getSlug().equals(modelSlug))
+ {
+ expList.remove(e);
+ }
}
}
- return new ResponseEntity<>(gson.toJson(experiments), HttpStatus.OK);
+ return new ResponseEntity<>(gson.toJson(expList), HttpStatus.OK);
}
private ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
Experiment experiment;
UUID experimentUuid;
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
@@ -328,30 +252,13 @@ public class ExperimentApi {
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Transaction transaction = null;
- try {
- transaction = session.beginTransaction();
-
- Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
- hibernateQuery.setParameter("uuid", experimentUuid);
- experiment = (Experiment) hibernateQuery.uniqueResult();
+ experiment = experimentRepository.findOne(experimentUuid);
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
- experiment.setShared(shared);
- session.update(experiment);
-
- transaction.commit();
- } catch (Exception e) {
- // 404 here probably
- if(transaction != null)
- {
- transaction.rollback();
- }
- throw e;
- }
+ experiment.setShared(shared);
+ experimentRepository.save(experiment);
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
@@ -361,10 +268,10 @@ public class ExperimentApi {
new Thread() {
@Override
public void run() {
- String url = experimentUrl;
- String query = experiment.computeQuery();
+ String url = experimentUrl;
+ String query = experiment.computeQuery();
- // Results are stored in the experiment object
+ // Results are stored in the experiment object
try {
executeExperiment(url, query, experiment);
} catch (IOException e) {
@@ -372,8 +279,7 @@ public class ExperimentApi {
LOGGER.warn("Experiment failed to run properly !");
setExperimentError(e, experiment);
}
-
- experiment.finish();
+ finishExpermient(experiment);
}
}.start();
}
@@ -399,12 +305,17 @@ public class ExperimentApi {
{
experiment.setResult("Unsupported variables !");
}
-
- experiment.finish();
+ finishExpermient(experiment);
}
}.start();
}
+ private void finishExpermient(Experiment experiment)
+ {
+ experiment.setFinished(new Date());
+ experimentRepository.save(experiment);
+ }
+
private static void executeExperiment(String url, String query, Experiment experiment) throws IOException {
StringBuilder results = new StringBuilder();
int code = HTTPUtil.sendPost(url, query, results);
diff --git a/src/main/java/org/hbp/mip/controllers/GroupsApi.java b/src/main/java/org/hbp/mip/controllers/GroupsApi.java
index 9f23ad3b43b379ceb8c148900aaac129ac3ae0ad..48574e48cec79d8a23005db34c3125521d7f9c7a 100644
--- a/src/main/java/org/hbp/mip/controllers/GroupsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/GroupsApi.java
@@ -9,8 +9,8 @@ import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiResponse;
import io.swagger.annotations.ApiResponses;
import org.hbp.mip.model.Group;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.GroupRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
@@ -23,32 +23,16 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/groups", description = "the groups API")
public class GroupsApi {
+ private static final String ROOT_CODE = "root";
+
+ @Autowired
+ GroupRepository groupRepository;
+
@ApiOperation(value = "Get the root group (containing all subgroups)", response = Group.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<Group> getTheRootGroup() {
-
- String rootCode = "root";
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Group group = null;
- try{
- session.beginTransaction();
- group = (Group) session
- .createQuery("FROM Group WHERE code= :code")
- .setString("code", rootCode)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(group);
+ return ResponseEntity.ok(groupRepository.findOne(ROOT_CODE));
}
diff --git a/src/main/java/org/hbp/mip/controllers/ModelsApi.java b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
index 21b102e1858a508f92bff344a4aded93006c10f2..2570b9a6770cd6b264549d472528ec55fd517e34 100644
--- a/src/main/java/org/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
@@ -7,12 +7,13 @@ package org.hbp.mip.controllers;
import com.github.slugify.Slugify;
import io.swagger.annotations.*;
import org.apache.log4j.Logger;
-import org.hbp.mip.MIPApplication;
+import org.hbp.mip.configuration.SecurityConfiguration;
import org.hbp.mip.model.*;
+import org.hbp.mip.repositories.ConfigRepository;
+import org.hbp.mip.repositories.DatasetRepository;
+import org.hbp.mip.repositories.ModelRepository;
+import org.hbp.mip.repositories.QueryRepository;
import org.hbp.mip.utils.CSVUtil;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -32,88 +33,62 @@ public class ModelsApi {
private static final Logger LOGGER = Logger.getLogger(ModelsApi.class);
@Autowired
- MIPApplication mipApplication;
+ SecurityConfiguration securityConfiguration;
+
+ @Autowired
+ CSVUtil csvUtil;
+
+ @Autowired
+ DatasetRepository datasetRepository;
+
+ @Autowired
+ ModelRepository modelRepository;
+
+ @Autowired
+ QueryRepository queryRepository;
+
+ @Autowired
+ ConfigRepository configRepository;
private static final String DATA_FILE = "data/values.csv";
@ApiOperation(value = "Get models", response = Model.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List<Model>> getModels(
+ public ResponseEntity<Iterable> getModels(
@ApiParam(value = "Max number of results") @RequestParam(value = "limit", required = false) Integer limit,
@ApiParam(value = "Only ask own models") @RequestParam(value = "own", required = false) Boolean own,
@ApiParam(value = "Only ask models from own team") @RequestParam(value = "team", required = false) Boolean team,
@ApiParam(value = "Only ask published models") @RequestParam(value = "valid", required = false) Boolean valid
) {
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
+ Iterable<Model> models = null;
- String queryString = "SELECT m FROM Model m, User u WHERE m.createdBy=u.username";
- if(valid != null && valid)
- {
- queryString += " AND m.valid= :valid";
- }
if(own != null && own)
{
- queryString += " AND u.username= :username";
+ models = modelRepository.findByCreatedByOrderByCreatedAt(user);
}
else
{
- queryString += " AND (m.valid=true or u.username= :username)";
+ models = modelRepository.findByValidOrCreatedByOrderByCreatedAt(true, user);
}
- queryString += " ORDER BY m.createdAt DESC";
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- List<Model> models = new LinkedList<>();
- try{
- session.beginTransaction();
- Query query = session.createQuery(queryString);
- if(valid != null)
- {
- query.setBoolean("valid", valid);
- }
- query.setString("username", user.getUsername());
- if(limit != null)
- {
- query.setMaxResults(limit); // Pagination : Use query.setFirstResult(...) to set begining index
- }
- models = query.list();
- session.getTransaction().commit();
- } catch (Exception e)
+ if(valid != null && models != null)
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- for(Model model:models){
- String dsCode = model.getDataset().getCode();
-
- session = HibernateUtil.getSessionFactory().getCurrentSession();
- Dataset dataset = null;
- try{
- session.beginTransaction();
- dataset = (Dataset) session
- .createQuery("from Dataset where code= :code")
- .setString("code", dsCode)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
+ for (Iterator<Model> i = models.iterator(); i.hasNext(); )
{
- if(session.getTransaction() != null)
+ Model m = i.next();
+ m.setDataset(datasetRepository.findOne(m.getDataset().getCode()));
+ if(valid != m.getValid())
{
- session.getTransaction().rollback();
- throw e;
+ i.remove();
}
}
-
- model.setDataset(dataset);
}
return new ResponseEntity<List<Model>>(HttpStatus.OK).ok(models);
+
}
@@ -124,7 +99,7 @@ public class ModelsApi {
@RequestBody @ApiParam(value = "Model to create", required = true) Model model
) {
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
model.setTitle(model.getConfig().getTitle().get("text"));
model.setCreatedBy(user);
@@ -134,67 +109,54 @@ public class ModelsApi {
model.setValid(false);
}
- Long count;
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try{
- session.beginTransaction();
-
- int i = 0;
- do{
- i++;
- count = (Long) session
- .createQuery("select count(*) from Model where title= :title")
- .setString("title", model.getTitle())
- .uniqueResult();
+ long count = 1;
+ for(int i = 1; count > 0; i++)
+ {
+ count = modelRepository.countByTitle(model.getTitle());
- if(count > 0)
- {
- String title = model.getTitle();
- if(i > 1)
- {
- title = title.substring(0, title.length()-4);
- }
- model.setTitle(title + " (" + i + ")");
- }
- } while(count > 0);
-
- String slug = new Slugify().slugify(model.getTitle());
-
- i = 0;
- do {
- i++;
- count = (Long) session
- .createQuery("select count(*) from Model where slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
- if(count > 0)
+ if(count > 0)
+ {
+ String title = model.getTitle();
+ if(i > 1)
{
- if(i > 1)
- {
- slug = slug.substring(0, slug.length()-2);
- }
- slug += "-"+i;
+ title = title.substring(0, title.length()-4);
}
- model.setSlug(slug);
- } while(count > 0);
-
- Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
- map.put("text", model.getTitle());
- model.getConfig().setTitle(map);
+ model.setTitle(title + " (" + i + ")");
+ }
+ }
- session.save(model);
- session.getTransaction().commit();
+ String slug = null;
+ try {
+ slug = new Slugify().slugify(model.getTitle());
} catch (IOException e) {
+ slug = "";
LOGGER.trace(e);
- } catch (Exception e)
+ }
+
+ boolean alreadyExists = true;
+ for(int i = 1; alreadyExists; i++)
{
- if(session.getTransaction() != null)
+ alreadyExists = modelRepository.exists(slug);
+ if(alreadyExists)
{
- session.getTransaction().rollback();
- throw e;
+ if(i > 1)
+ {
+ slug = slug.substring(0, slug.length()-2);
+ }
+ slug += "-"+i;
}
+ model.setSlug(slug);
}
+ Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
+ map.put("text", model.getTitle());
+ model.getConfig().setTitle(map);
+
+ configRepository.save(model.getConfig());
+ queryRepository.save(model.getQuery());
+ datasetRepository.save(model.getDataset());
+ modelRepository.save(model);
+
return new ResponseEntity<Model>(HttpStatus.CREATED).ok(model);
}
@@ -205,100 +167,49 @@ public class ModelsApi {
@ApiParam(value = "slug", required = true) @PathVariable("slug") String slug
) {
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
Model model = null;
- try {
- session.beginTransaction();
- model = (Model) session
- .createQuery("FROM Model WHERE slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
- session.getTransaction().commit();
-
- if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername()))
- {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- } catch (Exception e)
+ model = modelRepository.findOne(slug);
+ if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername()))
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
+ return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
+ if(model != null)
+ {
+ List<String> yAxisVars = configRepository.findOne(model.getConfig().getId()).getyAxisVariables();
+ Collection<String> yAxisVarsColl = new LinkedHashSet<>(yAxisVars);
+ model.getConfig().setyAxisVariables(new LinkedList<>(yAxisVarsColl));
- if(model != null) {
- session = HibernateUtil.getSessionFactory().getCurrentSession();
- org.hbp.mip.model.Query q = null;
-
- try {
- session.beginTransaction();
- q = (org.hbp.mip.model.Query) session
- .createQuery("FROM Query WHERE id= :id")
- .setLong("id", model.getQuery().getId())
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- if(q != null) {
-
- List<Variable> vars = new LinkedList<>();
- for (Variable var : q.getVariables()) {
- Variable v = new Variable();
- v.setCode(var.getCode());
- vars.add(v);
- }
-
- List<Variable> covs = new LinkedList<>();
- for (Variable cov : q.getCovariables()) {
- Variable v = new Variable();
- v.setCode(cov.getCode());
- covs.add(v);
- }
+ List<Variable> varsQuery = queryRepository.findOne(model.getQuery().getId()).getVariables();
+ Collection<Variable> varsQueryColl = new LinkedHashSet<>(varsQuery);
+ model.getQuery().setVariables(new LinkedList<>(varsQueryColl));
- List<Variable> grps = new LinkedList<>();
- for (Variable grp : q.getGrouping()) {
- Variable v = new Variable();
- v.setCode(grp.getCode());
- grps.add(v);
- }
+ List<Variable> grpgsQuery = queryRepository.findOne(model.getQuery().getId()).getGrouping();
+ Collection<Variable> grpgsQueryColl = new LinkedHashSet<>(grpgsQuery);
+ model.getQuery().setGrouping(new LinkedList<>(grpgsQueryColl));
- List<Filter> fltrs = new LinkedList<>();
- for (Filter fltr : q.getFilters()) {
- Filter f = new Filter();
- f.setId(fltr.getId());
- f.setOperator(fltr.getOperator());
- f.setValues(fltr.getValues());
- f.setVariable(fltr.getVariable());
- fltrs.add(f);
- }
+ List<Variable> covarsQuery = queryRepository.findOne(model.getQuery().getId()).getCovariables();
+ Collection<Variable> covarsQueryColl = new LinkedHashSet<>(covarsQuery);
+ model.getQuery().setCovariables(new LinkedList<>(covarsQueryColl));
- org.hbp.mip.model.Query myQuery = new org.hbp.mip.model.Query();
- myQuery.setId(q.getId());
- myQuery.setVariables(vars);
- myQuery.setCovariables(covs);
- myQuery.setGrouping(grps);
- myQuery.setFilters(fltrs);
+ List<Filter> fltrs = queryRepository.findOne(model.getQuery().getId()).getFilters();
+ Collection<Filter> fltrsColl = new LinkedHashSet<>(fltrs);
+ model.getQuery().setFilters(new LinkedList<>(fltrsColl));
- model.setQuery(myQuery);
- }
+ List<String> varsDS = datasetRepository.findOne(model.getDataset().getCode()).getVariable();
+ Collection<String> varsDSColl = new LinkedHashSet<>(varsDS);
+ model.getDataset().setVariable(new LinkedList<>(varsDSColl));
- Dataset ds = CSVUtil.parseValues(DATA_FILE, model.getQuery());
- model.setDataset(ds);
+ List<String> grpgsDS = datasetRepository.findOne(model.getDataset().getCode()).getGrouping();
+ Collection<String> grpgsDSColl = new LinkedHashSet<>(grpgsDS);
+ model.getDataset().setGrouping(new LinkedList<>(grpgsDSColl));
+ List<String> headersDS = datasetRepository.findOne(model.getDataset().getCode()).getHeader();
+ Collection<String> headersDSColl = new LinkedHashSet<>(headersDS);
+ model.getDataset().setHeader(new LinkedList<>(headersDSColl));
}
return new ResponseEntity<>(HttpStatus.OK).ok(model);
@@ -313,66 +224,46 @@ public class ModelsApi {
@RequestBody @ApiParam(value = "Model to update", required = true) Model model
) {
- User user = mipApplication.getUser();
+ User user = securityConfiguration.getUser();
model.setTitle(model.getConfig().getTitle().get("text"));
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try{
- session.beginTransaction();
-
- String author = (String) session
- .createQuery("select U.username from User U, Model M where M.createdBy = U.username and M.slug = :slug")
- .setString("slug", slug)
- .uniqueResult();
+ Model oldModel = modelRepository.findOne(slug);
- if(!user.getUsername().equals(author))
- {
- session.getTransaction().commit();
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
+ String author = oldModel.getCreatedBy().getUsername();
- String oldTitle = (String) session
- .createQuery("select title from Model where slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
-
- String newTitle = model.getTitle();
-
- if(!newTitle.equals(oldTitle)) {
- Long count;
- int i = 0;
- do {
- i++;
- newTitle = model.getTitle();
- count = (Long) session
- .createQuery("select count(*) from Model where title= :title")
- .setString("title", newTitle)
- .uniqueResult();
- if (count > 0 && !newTitle.equals(oldTitle)) {
- if (i > 1) {
- newTitle = newTitle.substring(0, newTitle.length() - 4);
- }
- model.setTitle(newTitle + " (" + i + ")");
- }
- } while (count > 0 && !newTitle.equals(oldTitle));
- }
+ if(!user.getUsername().equals(author))
+ {
+ return new ResponseEntity<>(HttpStatus.FORBIDDEN);
+ }
- Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
- map.put("text", model.getTitle());
- model.getConfig().setTitle(map);
+ String oldTitle = oldModel.getTitle();
+ String newTitle = model.getTitle();
- session.update(model);
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
+ if(!newTitle.equals(oldTitle)) {
+ long count = 1;
+ for(int i = 1; count > 0 && !newTitle.equals(oldTitle); i++)
{
- session.getTransaction().rollback();
- throw e;
+ newTitle = model.getTitle();
+ count = modelRepository.countByTitle(newTitle);
+ if (count > 0 && !newTitle.equals(oldTitle)) {
+ if (i > 1) {
+ newTitle = newTitle.substring(0, newTitle.length() - 4);
+ }
+ model.setTitle(newTitle + " (" + i + ")");
+ }
}
}
+ Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
+ map.put("text", model.getTitle());
+ model.getConfig().setTitle(map);
+
+ configRepository.save(model.getConfig());
+ queryRepository.save(model.getQuery());
+ datasetRepository.save(model.getDataset());
+ modelRepository.save(model);
+
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
diff --git a/src/main/java/org/hbp/mip/controllers/RequestsApi.java b/src/main/java/org/hbp/mip/controllers/RequestsApi.java
index b60a53b558a33a205bb07ff404a25bba7e5af2d1..76527eba6de906c48a50823ed348c4388cfc2dc0 100644
--- a/src/main/java/org/hbp/mip/controllers/RequestsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/RequestsApi.java
@@ -8,6 +8,7 @@ import io.swagger.annotations.*;
import org.hbp.mip.model.Dataset;
import org.hbp.mip.model.Query;
import org.hbp.mip.utils.CSVUtil;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -23,16 +24,16 @@ public class RequestsApi {
private static final String DATA_FILE = "data/values.csv";
+ @Autowired
+ CSVUtil csvUtil;
+
@ApiOperation(value = "Send a request", response = Dataset.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.POST)
public ResponseEntity<Dataset> postRequests(
@RequestBody @ApiParam(value = "Query to process", required = true) Query query
) {
-
- Dataset dataset = CSVUtil.parseValues(DATA_FILE, query);
-
- return ResponseEntity.ok(dataset);
+ return ResponseEntity.ok(csvUtil.parseValues(DATA_FILE, query));
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/StatsApi.java b/src/main/java/org/hbp/mip/controllers/StatsApi.java
index e40a3becf1ee8715ecca6dea068dcc09cb855823..3f6883f28f9d19e7887519105e9a07bd58d5679d 100644
--- a/src/main/java/org/hbp/mip/controllers/StatsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/StatsApi.java
@@ -9,9 +9,10 @@ import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiResponse;
import io.swagger.annotations.ApiResponses;
import org.hbp.mip.model.GeneralStats;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.ArticleRepository;
+import org.hbp.mip.repositories.UserRepository;
+import org.hbp.mip.repositories.VariableRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
@@ -24,44 +25,25 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/stats", description = "the stats API")
public class StatsApi {
+ @Autowired
+ UserRepository userRepository;
+
+ @Autowired
+ ArticleRepository articleRepository;
+
+ @Autowired
+ VariableRepository variableRepository;
+
@ApiOperation(value = "Get general statistics", response = GeneralStats.class)
@ApiResponses(value = {@ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<GeneralStats> getGeneralStatistics() {
GeneralStats stats = new GeneralStats();
- Long nbUsers = 0L;
- Long nbArticles = 0L;
- Long nbVariables = 0L;
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
-
- try{
-
- session.beginTransaction();
-
- Query countUsersQuery = session.createQuery("SELECT COUNT(*) FROM User");
- Query countArticlesQuery = session.createQuery("SELECT COUNT(*) FROM Article");
- Query countVariablesQuery = session.createQuery("SELECT COUNT(*) FROM Variable");
-
- nbUsers = (Long) countUsersQuery.uniqueResult();
- nbArticles = (Long) countArticlesQuery.uniqueResult();
- nbVariables = (Long) countVariablesQuery.uniqueResult();
-
- session.getTransaction().commit();
-
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
- stats.setUsers(nbUsers);
- stats.setArticles(nbArticles);
- stats.setVariables(nbVariables);
+ stats.setUsers(userRepository.count());
+ stats.setArticles(articleRepository.count());
+ stats.setVariables(variableRepository.count());
return ResponseEntity.ok(stats);
}
diff --git a/src/main/java/org/hbp/mip/controllers/UsersApi.java b/src/main/java/org/hbp/mip/controllers/UsersApi.java
index bdd2e6745173a7fb9362ae31392ca157007d8231..eabeffca1e196a3201a9068b46c1dc395946f2fb 100644
--- a/src/main/java/org/hbp/mip/controllers/UsersApi.java
+++ b/src/main/java/org/hbp/mip/controllers/UsersApi.java
@@ -6,8 +6,8 @@ package org.hbp.mip.controllers;
import io.swagger.annotations.*;
import org.hbp.mip.model.User;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.UserRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -21,6 +21,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/users", description = "the users API")
public class UsersApi {
+ @Autowired
+ UserRepository userRepository;
@ApiOperation(value = "Get a user", response = User.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
@@ -28,25 +30,6 @@ public class UsersApi {
public ResponseEntity<User> getAUser(
@ApiParam(value = "username", required = true) @PathVariable("username") String username
) {
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- User user = null;
- try{
- session.beginTransaction();
- user = (User) session
- .createQuery("from User where username= :username")
- .setString("username", username)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(user);
+ return ResponseEntity.ok(userRepository.findOne(username));
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/VariablesApi.java b/src/main/java/org/hbp/mip/controllers/VariablesApi.java
index f69f98dedd82c9eb8707b858e86e27a0fd55a2fb..b5f2d72f2f5ea151070fb2598007f22a49b475f6 100644
--- a/src/main/java/org/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/VariablesApi.java
@@ -8,12 +8,11 @@ package org.hbp.mip.controllers;
import io.swagger.annotations.*;
import org.hbp.mip.model.Value;
import org.hbp.mip.model.Variable;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.VariableRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
-import java.util.LinkedList;
import java.util.List;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -23,10 +22,13 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/variables", description = "the variables API")
public class VariablesApi {
+ @Autowired
+ VariableRepository variableRepository;
+
@ApiOperation(value = "Get variables", response = Variable.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getVariables(
+ public ResponseEntity<Iterable> getVariables(
@ApiParam(value = "List of groups formatted like : (\"val1\", \"val2\", ...)") @RequestParam(value = "group", required = false) String group,
@ApiParam(value = "List of subgroups formatted like : (\"val1\", \"val2\", ...)") @RequestParam(value = "subgroup", required = false) String subgroup,
@ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isVariable", required = false) String isVariable,
@@ -34,25 +36,7 @@ public class VariablesApi {
@ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isCovariable", required = false) String isCovariable,
@ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isFilter", required = false) String isFilter
) {
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- List variables = new LinkedList<>();
- try{
- session.beginTransaction();
- variables = session
- .createQuery("from Variable")
- .list();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(variables);
+ return ResponseEntity.ok(variableRepository.findAll());
}
@ApiOperation(value = "Get a variable", response = Variable.class)
@@ -61,27 +45,7 @@ public class VariablesApi {
public ResponseEntity<Variable> getAVariable(
@ApiParam(value = "code of the variable ( multiple codes are allowed, separated by \",\" )", required = true) @PathVariable("code") String code
) {
-
- // Query DB
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Variable variable = null;
- try{
- session.beginTransaction();
- variable = (Variable) session
- .createQuery("from Variable where code= :code")
- .setString("code", code)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(variable);
+ return ResponseEntity.ok(variableRepository.findOne(code));
}
@@ -92,27 +56,7 @@ public class VariablesApi {
@ApiParam(value = "code", required = true) @PathVariable("code") String code,
@ApiParam(value = "Pattern to match") @RequestParam(value = "q", required = false) String q
) {
-
- // Query DB
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- List values = new LinkedList<>();
- try{
- session.beginTransaction();
- values = session
- .createQuery("select values from Variable where code= :code")
- .setString("code", code)
- .list();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(values);
+ return ResponseEntity.ok(variableRepository.findOne(code).getValues());
}
diff --git a/src/main/java/org/hbp/mip/model/Experiment.java b/src/main/java/org/hbp/mip/model/Experiment.java
index d87949be04dc8da5d7080d4e20ace726e22ff267..f42ffbd6cbc11aa6e297bde4adfdc383b23ea5dd 100644
--- a/src/main/java/org/hbp/mip/model/Experiment.java
+++ b/src/main/java/org/hbp/mip/model/Experiment.java
@@ -6,15 +6,9 @@ import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.annotations.Expose;
import org.apache.log4j.Logger;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
-import org.hibernate.Transaction;
-import org.hibernate.annotations.*;
-import org.hibernate.exception.DataException;
+import org.hibernate.annotations.Cascade;
import javax.persistence.*;
-import javax.persistence.Entity;
-import javax.persistence.Table;
import java.util.Date;
import java.util.LinkedList;
import java.util.List;
@@ -145,21 +139,6 @@ public class Experiment {
return new Gson().toJson(queryElements);
}
- public void finish() {
- this.setFinished(new Date());
-
- try {
- Session session = HibernateUtil.getSessionFactory().openSession();
- Transaction transaction = session.beginTransaction();
- session.update(this);
- transaction.commit();
- session.close();
- } catch (DataException e) {
- LOGGER.trace(e);
- throw e;
- }
- }
-
public String getValidations() {
return validations;
}
diff --git a/src/main/java/org/hbp/mip/repositories/AppRepository.java b/src/main/java/org/hbp/mip/repositories/AppRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..ba00367afe2b6419d61f1a810b5f21acfb7596f6
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/AppRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.App;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface AppRepository extends CrudRepository<App, Integer> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/ArticleRepository.java b/src/main/java/org/hbp/mip/repositories/ArticleRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..b27ecfaa4d7d44a66d7f80e065f06df545a69dfd
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/ArticleRepository.java
@@ -0,0 +1,15 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Article;
+import org.hbp.mip.model.User;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface ArticleRepository extends CrudRepository<Article, String> {
+ Long countByTitle(String title);
+ Iterable<Article> findByCreatedBy(User user);
+ Iterable<Article> findByStatusOrCreatedBy(String status, User user);
+}
diff --git a/src/main/java/org/hbp/mip/repositories/ConfigRepository.java b/src/main/java/org/hbp/mip/repositories/ConfigRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..f54f379144b1769eda2bca8db2b9be623c98fd06
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/ConfigRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Config;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface ConfigRepository extends CrudRepository<Config, Long> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/DatasetRepository.java b/src/main/java/org/hbp/mip/repositories/DatasetRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..53883eb21f504b1fcd90178b44d1105785129fba
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/DatasetRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Dataset;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface DatasetRepository extends CrudRepository<Dataset, String> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/org/hbp/mip/repositories/ExperimentRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..3815879beab40747df7fba83f2a96d950af3ece9
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/ExperimentRepository.java
@@ -0,0 +1,16 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Experiment;
+import org.hbp.mip.model.User;
+import org.springframework.data.repository.CrudRepository;
+
+import java.util.UUID;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface ExperimentRepository extends CrudRepository<Experiment, UUID> {
+ Iterable<Experiment> findByCreatedBy(User user);
+ Iterable<Experiment> findByShared(Boolean shared);
+}
diff --git a/src/main/java/org/hbp/mip/repositories/FilterRepository.java b/src/main/java/org/hbp/mip/repositories/FilterRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..7f4a1556924d00bbd33fd92135169f176fe749e6
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/FilterRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Filter;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface FilterRepository extends CrudRepository<Filter, Long> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/GroupRepository.java b/src/main/java/org/hbp/mip/repositories/GroupRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..548653269f2c788bef529e1748b4b9fdca04126d
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/GroupRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Group;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface GroupRepository extends CrudRepository<Group, String> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/ModelRepository.java b/src/main/java/org/hbp/mip/repositories/ModelRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..9da1df5bd11936471fde140ce86b60689c5a499c
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/ModelRepository.java
@@ -0,0 +1,15 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Model;
+import org.hbp.mip.model.User;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface ModelRepository extends CrudRepository<Model, String> {
+ Long countByTitle(String Title);
+ Iterable<Model> findByCreatedByOrderByCreatedAt(User user);
+ Iterable<Model> findByValidOrCreatedByOrderByCreatedAt(Boolean valid, User user);
+}
diff --git a/src/main/java/org/hbp/mip/repositories/QueryRepository.java b/src/main/java/org/hbp/mip/repositories/QueryRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..44dc9527b480447e28205322e87e7a962f09f285
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/QueryRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Query;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface QueryRepository extends CrudRepository<Query, Long> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/TagRepository.java b/src/main/java/org/hbp/mip/repositories/TagRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..155d65d17170b6171170a3b41ae12f981cf9fbf0
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/TagRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Tag;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface TagRepository extends CrudRepository<Tag, String> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/UserRepository.java b/src/main/java/org/hbp/mip/repositories/UserRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..04338433fe84ada90f446232715c71d63ba904f4
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/UserRepository.java
@@ -0,0 +1,12 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.User;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface UserRepository extends CrudRepository<User, String> {
+
+}
diff --git a/src/main/java/org/hbp/mip/repositories/ValueRepository.java b/src/main/java/org/hbp/mip/repositories/ValueRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..c3b088462874f72489c507576aa9fb9ce5d221fc
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/ValueRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Value;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface ValueRepository extends CrudRepository<Value, String> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/VariableRepository.java b/src/main/java/org/hbp/mip/repositories/VariableRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..ac241ca7a16f06b75e7c2135724675bcafecefaa
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/VariableRepository.java
@@ -0,0 +1,11 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.Variable;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface VariableRepository extends CrudRepository<Variable, String> {
+}
diff --git a/src/main/java/org/hbp/mip/repositories/VoteRepository.java b/src/main/java/org/hbp/mip/repositories/VoteRepository.java
new file mode 100644
index 0000000000000000000000000000000000000000..78d760b9cb998b65a444d3472bbf3326a3052979
--- /dev/null
+++ b/src/main/java/org/hbp/mip/repositories/VoteRepository.java
@@ -0,0 +1,14 @@
+package org.hbp.mip.repositories;
+
+import org.hbp.mip.model.App;
+import org.hbp.mip.model.User;
+import org.hbp.mip.model.Vote;
+import org.springframework.data.repository.CrudRepository;
+
+/**
+ * Created by mirco on 11.07.16.
+ */
+
+public interface VoteRepository extends CrudRepository<Vote, Long> {
+ Iterable<Vote> findByUserAndApp(User user, App app);
+}
diff --git a/src/main/java/org/hbp/mip/utils/CSVUtil.java b/src/main/java/org/hbp/mip/utils/CSVUtil.java
index b3f6850be795983ec8728624da7dfcf733369dfe..a91d390ce42533abaef1f65f00aab7ca9e57a394 100644
--- a/src/main/java/org/hbp/mip/utils/CSVUtil.java
+++ b/src/main/java/org/hbp/mip/utils/CSVUtil.java
@@ -4,7 +4,8 @@ import org.apache.log4j.Logger;
import org.hbp.mip.model.Dataset;
import org.hbp.mip.model.Query;
import org.hbp.mip.model.Variable;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.VariableRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import java.io.BufferedReader;
import java.io.IOException;
@@ -24,13 +25,10 @@ public class CSVUtil {
private static final String SEPARATOR = ",";
- private CSVUtil()
- {
- /* Hide implicit public constructor */
- throw new IllegalAccessError("CSVUtil class");
- }
+ @Autowired
+ VariableRepository variableRepository;
- public static Dataset parseValues(String filename, Query query)
+ public Dataset parseValues(String filename, Query query)
{
List<String[]> rows = getRows(filename);
@@ -161,7 +159,7 @@ public class CSVUtil {
return result;
}
- private static List<String[]> getRows(String filename) {
+ private List<String[]> getRows(String filename) {
List<String[]> rows = new LinkedList<>();
try {
InputStream is = CSVUtil.class.getClassLoader().getResourceAsStream(filename);
@@ -183,7 +181,7 @@ public class CSVUtil {
return rows;
}
- private static int find(String code, String[] firstRow) {
+ private int find(String code, String[] firstRow) {
for (int i = 0; i < firstRow.length; i++) {
if (firstRow[i].equals(code))
return i;
@@ -191,7 +189,7 @@ public class CSVUtil {
return -1;
}
- private static String generateDSCode(Query query) {
+ private String generateDSCode(Query query) {
String prefix = "DS";
String queryStr = Integer.toString(query.hashCode());
String memId;
@@ -206,24 +204,9 @@ public class CSVUtil {
return prefix + memId;
}
- private static String getTypeFromDB(Variable v)
+ private String getTypeFromDB(Variable v)
{
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- String type = null;
- try{
- session.beginTransaction();
- org.hibernate.Query q = session.createQuery("SELECT type FROM Variable where code= :code").setString("code", v.getCode());
- type = (String) q.uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
+ String type = variableRepository.findOne(v.getCode()).getType();
if(type == null)
{
type = "unknown";
diff --git a/src/main/java/org/hbp/mip/utils/CustomLoginUrlAuthenticationEntryPoint.java b/src/main/java/org/hbp/mip/utils/CustomLoginUrlAuthenticationEntryPoint.java
new file mode 100644
index 0000000000000000000000000000000000000000..437052aa882be5f901a312cd269b58578c2b4d0b
--- /dev/null
+++ b/src/main/java/org/hbp/mip/utils/CustomLoginUrlAuthenticationEntryPoint.java
@@ -0,0 +1,21 @@
+package org.hbp.mip.utils;
+
+import org.springframework.security.core.AuthenticationException;
+import org.springframework.security.web.authentication.LoginUrlAuthenticationEntryPoint;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+
+public class CustomLoginUrlAuthenticationEntryPoint extends LoginUrlAuthenticationEntryPoint {
+
+ public CustomLoginUrlAuthenticationEntryPoint(String url) {
+ super(url);
+ }
+
+ @Override
+ public void commence(HttpServletRequest request, HttpServletResponse response, AuthenticationException authException) throws IOException, ServletException {
+ response.sendError(HttpServletResponse.SC_UNAUTHORIZED);
+ }
+}
diff --git a/src/main/java/org/hbp/mip/utils/HibernateUtil.java b/src/main/java/org/hbp/mip/utils/HibernateUtil.java
deleted file mode 100644
index 87cde9618993e4070518b70d2bf6e4d058d54760..0000000000000000000000000000000000000000
--- a/src/main/java/org/hbp/mip/utils/HibernateUtil.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/**
- * Created by mirco on 07.12.15.
- */
-
-package org.hbp.mip.utils;
-
-import org.apache.log4j.Logger;
-import org.hibernate.SessionFactory;
-import org.hibernate.boot.registry.StandardServiceRegistryBuilder;
-import org.hibernate.cfg.Configuration;
-import org.hibernate.service.ServiceRegistry;
-
-public class HibernateUtil {
-
- private static final Logger LOGGER = Logger.getLogger(CSVUtil.class);
-
- private static ServiceRegistry serviceRegistry;
-
- private static SessionFactory sessionFactory = buildSessionFactory();
-
- private HibernateUtil() {
- /* Hide implicit public constructor */
- throw new IllegalAccessError("HibernateUtil class");
- }
-
- private static SessionFactory buildSessionFactory() {
- try {
- Configuration configuration = new Configuration();
- configuration.configure();
- serviceRegistry = new StandardServiceRegistryBuilder().applySettings(
- configuration.getProperties()).build();
- sessionFactory = configuration.buildSessionFactory(serviceRegistry);
- return sessionFactory;
- } catch (RuntimeException ex) {
- LOGGER.error("Initial SessionFactory creation failed." + ex);
- throw new ExceptionInInitializerError(ex);
- }
- }
-
- public static SessionFactory getSessionFactory() {
- return sessionFactory;
- }
-}
diff --git a/src/main/resources/db/migration/V1_1__Create.sql b/src/main/resources/db/migration/V1_1__Create.sql
index 777f0f39d32b319df4f56f30dcc85b2642c6bbcf..2dfa346e9efffbe82f6dd3fc6107601ae27918b9 100644
--- a/src/main/resources/db/migration/V1_1__Create.sql
+++ b/src/main/resources/db/migration/V1_1__Create.sql
@@ -66,7 +66,7 @@ ALTER TABLE app OWNER TO postgres;
CREATE TABLE article (
slug character varying(255) NOT NULL,
- _abstract text,
+ abstract text,
content text,
createdat timestamp without time zone,
publishedat timestamp without time zone,
diff --git a/src/main/resources/hibernate.cfg.xml b/src/main/resources/hibernate.cfg.xml
deleted file mode 100644
index e769d47db76d641651c9a209b8a98bdd18142625..0000000000000000000000000000000000000000
--- a/src/main/resources/hibernate.cfg.xml
+++ /dev/null
@@ -1,36 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<!DOCTYPE hibernate-configuration PUBLIC
- "-//Hibernate/Hibernate Configuration DTD 3.0//EN"
- "http://www.hibernate.org/dtd/hibernate-configuration-3.0.dtd">
-
-<hibernate-configuration>
- <session-factory>
- <property name="connection.driver_class">${connection.driver_class}</property>
- <property name="connection.url">${connection.url}</property>
- <property name="connection.username">${connection.username}</property>
- <property name="connection.password">${connection.password}</property>
- <property name="hibernate.format_sql">true</property>
- <property name="connection.pool_size">1</property>
- <property name="hibernate.dialect">${hibernate.dialect}</property>
- <property name="current_session_context_class">thread</property>
- <property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>
- <property name="hibernate.show_sql">false</property>
- <property name="hibernate.hbm2ddl.auto">update</property>
-
- <mapping class="org.hbp.mip.model.Article"/>
- <mapping class="org.hbp.mip.model.Dataset"/>
- <mapping class="org.hbp.mip.model.Model"/>
- <mapping class="org.hbp.mip.model.Experiment"/>
- <mapping class="org.hbp.mip.model.Query"/>
- <mapping class="org.hbp.mip.model.Tag"/>
- <mapping class="org.hbp.mip.model.User"/>
- <mapping class="org.hbp.mip.model.Value"/>
- <mapping class="org.hbp.mip.model.Variable"/>
- <mapping class="org.hbp.mip.model.Filter"/>
- <mapping class="org.hbp.mip.model.Group"/>
- <mapping class="org.hbp.mip.model.Config"/>
- <mapping class="org.hbp.mip.model.App"/>
- <mapping class="org.hbp.mip.model.Vote"/>
-
- </session-factory>
-</hibernate-configuration>
diff --git a/src/main/resources/spring/application-context.xml b/src/main/resources/spring/application-context.xml
deleted file mode 100644
index 9d283991f37a1e72277f9b85d8905b9f45725da8..0000000000000000000000000000000000000000
--- a/src/main/resources/spring/application-context.xml
+++ /dev/null
@@ -1,36 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:context="http://www.springframework.org/schema/context"
- xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-4.2.xsd">
-
- <context:component-scan base-package="org.hbp.mip" />
-
- <bean id="httpSessionCsrfTokenRepository" class="org.springframework.security.web.csrf.HttpSessionCsrfTokenRepository">
- <property name="headerName" value="X-XSRF-TOKEN" />
- </bean>
-
- <bean id="hbpFilter" class="org.springframework.security.oauth2.client.filter.OAuth2ClientAuthenticationProcessingFilter">
- <constructor-arg value="/login/hbp"></constructor-arg>
- <property name="authenticationSuccessHandler">
- <bean class="org.springframework.security.web.authentication.SimpleUrlAuthenticationSuccessHandler">
- <property name="defaultTargetUrl" value="${frontend.redirect}" />
- </bean>
- </property>
- <property name="restTemplate">
- <bean class="org.springframework.security.oauth2.client.OAuth2RestTemplate">
- <constructor-arg name="resource" ref="hbp" />
- <constructor-arg name="context" ref="oauth2ClientContext" />
- </bean>
- </property>
- <property name="tokenServices">
- <bean class="org.springframework.boot.autoconfigure.security.oauth2.resource.UserInfoTokenServices">
- <constructor-arg name="clientId" value="996f97c5-a3ca-460e-b18b-00df3e2be89a" />
- <constructor-arg name="userInfoEndpointUrl" value="https://services.humanbrainproject.eu/oidc/userinfo" />
- </bean>
- </property>
- </bean>
-
-
-</beans>
diff --git a/src/test/java/org/hbp/mip/MIPApplicationTests.java b/src/test/java/org/hbp/mip/MIPApplicationTests.java
index bfe9832163384494b33694d93d0223c35cba6c12..3beac4281a34611ace1b20b0fcc9c4822afe96d3 100644
--- a/src/test/java/org/hbp/mip/MIPApplicationTests.java
+++ b/src/test/java/org/hbp/mip/MIPApplicationTests.java
@@ -15,13 +15,20 @@
*/
package org.hbp.mip;
+import org.junit.Assert;
+import org.junit.Test;
import org.junit.runner.RunWith;
-import org.springframework.boot.test.SpringApplicationConfiguration;
+import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.test.context.web.WebAppConfiguration;
+import org.springframework.test.context.support.GenericXmlContextLoader;
@RunWith(SpringJUnit4ClassRunner.class)
-@WebAppConfiguration
-@SpringApplicationConfiguration(classes=MIPApplication.class, locations={"classpath:spring/application-context.xml"})
+@ContextConfiguration(loader = GenericXmlContextLoader.class)
public class MIPApplicationTests {
+
+ @Test
+ public void testHello()
+ {
+ Assert.assertNotNull("test");
+ }
}
diff --git a/start.bat b/start.bat
deleted file mode 100644
index af12a1b5207ddf687faaa0fd0f34405c1f966ed3..0000000000000000000000000000000000000000
--- a/start.bat
+++ /dev/null
@@ -1 +0,0 @@
-start java -jar target\backend-services-0.0.1-SNAPSHOT.jar --spring.config.location=config\application.yml
\ No newline at end of file
diff --git a/stop.sh b/stop.sh
deleted file mode 100755
index 3bc6146acfc2c199f78ff4ceb66ae10aaf91ab51..0000000000000000000000000000000000000000
--- a/stop.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh
-if groups $USER | grep &>/dev/null '\bdocker\b'; then
- DOCKER_COMPOSE="docker-compose"
-else
- DOCKER_COMPOSE="sudo docker-compose"
-fi
-
-$DOCKER_COMPOSE rm -f