From 9ef0a24a6fdb9d3dd2c6e2889aeccd64c125e103 Mon Sep 17 00:00:00 2001
From: Ludovic Claude <ludovic.claude54@gmail.com>
Date: Mon, 1 May 2017 19:19:55 +0200
Subject: [PATCH] Modernise release management
---
.bumpversion.cfg | 14 +++
.pre-commit-config.yaml | 8 ++
Dockerfile | 43 +++++----
LICENSE | 17 +++-
README.md | 18 +++-
after-git-clone.sh | 3 +
after-update.sh | 3 +
build.sh | 8 +-
docker/runner/README.md | 12 +--
docker/runner/config/application.tmpl | 16 ++--
docker/runner/run.sh | 4 +-
docker_push.sh | 32 -------
hbp.yml | 94 +++++++++++++++++++
pom.xml | 2 +-
publish.sh | 89 ++++++++++++++++++
slack.json | 1 +
.../PersistenceConfiguration.java | 18 ++--
src/main/java/eu/hbp/mip/utils/DataUtil.java | 12 +--
.../resources/data/exareme_algorithms.json | 2 +-
tests/integration/algorithmsFactory/test.sh | 2 +-
tests/post-test-run.sh | 8 +-
tests/pre-test-run.sh | 22 ++---
22 files changed, 317 insertions(+), 111 deletions(-)
create mode 100644 .bumpversion.cfg
create mode 100644 .pre-commit-config.yaml
create mode 100755 after-git-clone.sh
create mode 100755 after-update.sh
delete mode 100755 docker_push.sh
create mode 100644 hbp.yml
create mode 100755 publish.sh
create mode 100644 slack.json
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
new file mode 100644
index 000000000..226f068d6
--- /dev/null
+++ b/.bumpversion.cfg
@@ -0,0 +1,14 @@
+[bumpversion]
+current_version = 2.0.0
+commit = True
+tag = True
+tag_name = {new_version}
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)-(?P<package>\d+)
+serialize = {major}.{minor}.{patch}-{package}
+
+[bumpversion:file:pom.xml]
+search = <version>{current_version}</version><!-- BUMP_VERSION -->
+
+[bumpversion:file:Dockerfile]
+
+[bumpversion:file:hbp.yml]
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 000000000..eee6314bc
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,8 @@
+- repo: git://github.com/pre-commit/pre-commit-hooks
+ sha: v0.7.1
+ hooks:
+ - id: trailing-whitespace
+ - id: end-of-file-fixer
+ - id: check-merge-conflict
+ - id: check-added-large-files
+ - id: check-yaml
diff --git a/Dockerfile b/Dockerfile
index aed589bde..4196234ab 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,36 +1,39 @@
-FROM java:openjdk-8u92-jdk-alpine
+FROM openjdk:8u121-jre-alpine
+MAINTAINER Mirco Nasuti <mirco.nasuti@chuv.ch>
-MAINTAINER mirco.nasuti@chuv.ch
+ARG BUILD_DATE
+ARG VCS_REF
+ARG VERSION
-ENV DOCKERIZE_VERSION=v0.2.0
+ENV DOCKERIZE_VERSION=v0.4.0
RUN apk add --update ca-certificates wget \
- && rm -rf /var/cache/apk/* /tmp/* \
&& update-ca-certificates \
&& wget -O /tmp/dockerize.tar.gz https://github.com/jwilder/dockerize/releases/download/$DOCKERIZE_VERSION/dockerize-linux-amd64-${DOCKERIZE_VERSION}.tar.gz \
&& tar -C /usr/local/bin -xzvf /tmp/dockerize.tar.gz \
- && rm -rf /tmp/dockerize.tar.gz
+ && rm -rf /var/cache/apk/* /tmp/*
COPY docker/runner/config/application.tmpl /config/application.tmpl
COPY docker/runner/README.md docker/runner/run.sh /
-ENV PORTAL_BACKEND_VERSION=1.1
+ENV PORTAL_BACKEND_VERSION=2.0.0
COPY target/portal-backend-$PORTAL_BACKEND_VERSION.jar backend.jar
-# org.label-schema.build-date=$BUILD_DATE
-# org.label-schema.vcs-ref=$VCS_REF
-LABEL org.label-schema.schema-version="1.0" \
- org.label-schema.license="AGPLv3" \
- org.label-schema.name="portal-backend" \
- org.label-schema.description="Java backend for the MIP portal" \
- org.label-schema.url="https://mip.humanbrainproject.eu" \
- org.label-schema.vcs-type="git" \
- org.label-schema.vcs-url="https://github.com/LREN-CHUV/portal-backend" \
- org.label-schema.vendor="LREN CHUV" \
- org.label-schema.docker.dockerfile="Dockerfile" \
- org.label-schema.memory-hint="2048"
-
EXPOSE 8080
-CMD ["./run.sh"]
+ENTRYPOINT ["/run.sh"]
+
+LABEL org.label-schema.build-date=$BUILD_DATE \
+ org.label-schema.name="hbpmip/portal-backend" \
+ org.label-schema.description="Java backend for the MIP portal" \
+ org.label-schema.url="https://mip.humanbrainproject.eu" \
+ org.label-schema.vcs-type="git" \
+ org.label-schema.vcs-ref=$VCS_REF \
+ org.label-schema.vcs-url="https://github.com/LREN-CHUV/portal-backend" \
+ org.label-schema.version="$VERSION" \
+ org.label-schema.vendor="LREN CHUV" \
+ org.label-schema.license="AGPLv3" \
+ org.label-schema.docker.dockerfile="Dockerfile" \
+ org.label-schema.memory-hint="2048" \
+ org.label-schema.schema-version="1.0"
diff --git a/LICENSE b/LICENSE
index 2ac9d7ccd..3f6f8acee 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,17 @@
+Original developer’s Attribution Information
+____________________________________________
+
+Attribution Copyright Notice: © 2016-2017 LREN CHUV.
+Attribution Phrase: Powered by the Medical Informatics Platform of the Human Brain Project
+Attribution URL: https://mip.humanbrainproject.eu
+
+All trademarks, service marks and/or trade names contained within the Attribution
+Information distributed with the covered code are the exclusive property of their
+owners and may only be used with the permission of their owners, or under
+circumstances otherwise permitted by law or as expressly set out in this License.
+
+---
+
GNU AFFERO GENERAL PUBLIC LICENSE
Version 3, 19 November 2007
@@ -65,7 +79,7 @@ License.
"Copyright" also means copyright-like laws that apply to other kinds
of works, such as semiconductor masks.
-
+
"The Program" refers to any copyrightable work licensed under this
License. Each licensee is addressed as "you". "Licensees" and
"recipients" may be individuals or organizations.
@@ -660,4 +674,3 @@ specific requirements.
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU AGPL, see
<http://www.gnu.org/licenses/>.
-
diff --git a/README.md b/README.md
index 3bbf48727..c47cd7e00 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,10 @@
-## Backend for the MIP portal
-
-[](https://www.gnu.org/licenses/agpl-3.0.html)
-[](https://www.codacy.com/app/mirco-nasuti/portal-backend?utm_source=github.com&utm_medium=referral&utm_content=LREN-CHUV/portal-backend&utm_campaign=Badge_Grade)
+[](https://www.unil.ch/lren/en/home.html) [](https://www.gnu.org/licenses/agpl-3.0.html)
+[](https://www.codacy.com/app/hbp-mip/portal-backend?utm_source=github.com&utm_medium=referral&utm_content=LREN-CHUV/portal-backend&utm_campaign=Badge_Grade)
[](https://hub.docker.com/r/hbpmip/portal-backend/)
[](https://circleci.com/gh/LREN-CHUV/portal-backend/tree/master)
+# Backend for the MIP portal
+
## Usage
* Build a versioned image: `./build.sh`
@@ -14,9 +14,17 @@
* See here: https://hub.docker.com/r/hbpmip/portal-backend/
+## Build
+
+Run: `./build.sh`
+
+## Publish on Docker Hub
+
+Run: `./publish.sh`
+
## License
-Copyright © 2016 LREN CHUV
+Copyright © 2016-2017 LREN CHUV
Licensed under the GNU Affero General Public License, Version 3.0 (the "License");
you may not use this file except in compliance with the License.
diff --git a/after-git-clone.sh b/after-git-clone.sh
new file mode 100755
index 000000000..2f72056fb
--- /dev/null
+++ b/after-git-clone.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+pre-commit install
diff --git a/after-update.sh b/after-update.sh
new file mode 100755
index 000000000..2f72056fb
--- /dev/null
+++ b/after-update.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+pre-commit install
diff --git a/build.sh b/build.sh
index ef6b40804..4573daa4a 100755
--- a/build.sh
+++ b/build.sh
@@ -13,8 +13,6 @@ get_script_dir () {
pwd
}
-export WORKSPACE=$(get_script_dir)
-
if pgrep -lf sshuttle > /dev/null ; then
echo "sshuttle detected. Please close this program as it messes with networking and prevents builds inside Docker to work"
exit 1
@@ -26,4 +24,8 @@ else
CAPTAIN="sudo captain"
fi
-$CAPTAIN build
+BUILD_DATE=$(date --iso-8601=seconds) \
+ VCS_REF=$(git describe --tags --dirty) \
+ VERSION=$(git describe --tags --dirty) \
+ WORKSPACE=$(get_script_dir) \
+ $CAPTAIN build
diff --git a/docker/runner/README.md b/docker/runner/README.md
index 2831fc1f5..49c72eaec 100644
--- a/docker/runner/README.md
+++ b/docker/runner/README.md
@@ -21,12 +21,12 @@ Environment variables:
* META_DB_USER: User to use when connecting to the metadata database
* META_DB_PASSWORD: Password to use when connecting to the metadata database
-* SCIENCE_DB_URL: JDBC URL to connect to the science database
-* SCIENCE_DB_SCHEMA: Database schema, default value is "public"
-* SCIENCE_DB_SERVER: optional, address of the science database server. Used to wait for the database to be up and running.
-* SCIENCE_DB_USER: User to use when connecting to the science database
-* SCIENCE_DB_PASSWORD: Password to use when connecting to the science database
-* SCIENCE_DB_MAIN_TABLE: Table that contains the scientific data to use, default value is adni_merge
+* FEATURES_DB_URL: JDBC URL to connect to the features database
+* FEATURES_DB_SCHEMA: Database schema, default value is "public"
+* FEATURES_DB_SERVER: optional, address of the features database server. Used to wait for the database to be up and running.
+* FEATURES_DB_USER: User to use when connecting to the features database
+* FEATURES_DB_PASSWORD: Password to use when connecting to the features database
+* FEATURES_DB_MAIN_TABLE: Table that contains the scientific data to use, default value is adni_merge
* CONTEXT_PATH: context path appended to all services running in this container. Default to "/services"
diff --git a/docker/runner/config/application.tmpl b/docker/runner/config/application.tmpl
index 6e5eb6791..ac7ed4cef 100644
--- a/docker/runner/config/application.tmpl
+++ b/docker/runner/config/application.tmpl
@@ -14,12 +14,12 @@ spring:
username: {{ default .Env.META_DB_USER "postgres" }}
password: {{ .Env.META_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
- scienceDatasource:
- url: {{ default .Env.SCIENCE_DB_URL "jdbc:postgresql://172.22.0.1:5433/science" }}
- schema: {{ default .Env.SCIENCE_DB_SCHEMA "public" }}
- main-table: {{ default .Env.SCIENCE_DB_MAIN_TABLE "adni_merge" }}
- username: {{ default .Env.SCIENCE_DB_USER "postgres" }}
- password: {{ .Env.SCIENCE_DB_PASSWORD }}
+ featuresDatasource:
+ url: {{ default .Env.FEATURES_DB_URL "jdbc:postgresql://172.22.0.1:5433/features" }}
+ schema: {{ default .Env.FEATURES_DB_SCHEMA "public" }}
+ main-table: {{ default .Env.FEATURES_DB_MAIN_TABLE "adni_merge" }}
+ username: {{ default .Env.FEATURES_DB_USER "postgres" }}
+ password: {{ .Env.FEATURES_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
jpa:
hibernate:
@@ -86,5 +86,5 @@ services:
akka:
woken:
host: {{ default .Env.WOKEN_HOST "woken" }}
- port: {{ default .Env.WOKEN_PORT "8088" }}
- path: {{ default .Env.WOKEN_PATH "/user/entrypoint" }}
+ port: {{ default .Env.WOKEN_AKKA_PORT "8088" }}
+ path: {{ default .Env.WOKEN_AKKA_PATH "/user/entrypoint" }}
diff --git a/docker/runner/run.sh b/docker/runner/run.sh
index 5da303862..3654d5cbe 100755
--- a/docker/runner/run.sh
+++ b/docker/runner/run.sh
@@ -7,7 +7,7 @@ fi
if [ ! -z "$META_DB_SERVER" ]; then
OPTS="$OPTS -wait tcp://$META_DB_SERVER -timeout 60s"
fi
-if [ ! -z "$SCIENCE_DB_SERVER" ]; then
- OPTS="$OPTS -wait tcp://$SCIENCE_DB_SERVER -timeout 60s"
+if [ ! -z "$FEATURES_DB_SERVER" ]; then
+ OPTS="$OPTS -wait tcp://$FEATURES_DB_SERVER -timeout 60s"
fi
dockerize $OPTS java -jar backend.jar
diff --git a/docker_push.sh b/docker_push.sh
deleted file mode 100755
index 7fa7eedb6..000000000
--- a/docker_push.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env bash
-set -e
-
-get_script_dir () {
- SOURCE="${BASH_SOURCE[0]}"
-
- while [ -h "$SOURCE" ]; do
- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
- SOURCE="$( readlink "$SOURCE" )"
- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
- done
- cd -P "$( dirname "$SOURCE" )"
- pwd
-}
-
-export WORKSPACE=$(get_script_dir)
-
-if pgrep -lf sshuttle > /dev/null ; then
- echo "sshuttle detected. Please close this program as it messes with networking and prevents builds inside Docker to work"
- exit 1
-fi
-
-if groups $USER | grep &>/dev/null '\bdocker\b'; then
- CAPTAIN="captain"
-else
- CAPTAIN="sudo captain"
-fi
-
-$CAPTAIN push --branch-tags=false --commit-tags=true portal-backend
-sed "s/USER/${USER^}/" $WORKSPACE/docker/runner/slack.json > $WORKSPACE/target/slack.json
-curl -k -X POST --data-urlencode payload@$WORKSPACE/target/slack.json https://hbps1.chuv.ch/slack/dev-activity
-rm -f $WORKSPACE/target/slack.json
diff --git a/hbp.yml b/hbp.yml
new file mode 100644
index 000000000..32c424582
--- /dev/null
+++ b/hbp.yml
@@ -0,0 +1,94 @@
+description: "Backend for the MIP portal"
+
+long_description: |
+ Backend for the MIP portal
+
+authors:
+ - author: Mirco Nasuti
+ author_email:
+ - mirco.nasuti@chuv.ch
+ organisation: LREN-CHUV
+ organisation_badge: https://img.shields.io/badge/CHUV-LREN-AF4C64.svg
+ - author: Ludovic Claude
+ author_email:
+ - ludovic.claude@chuv.ch
+ - ludovic.claude54@gmail.com
+ - ludovic.claude54@googlemail.com
+ - ludovic.claude@laposte.net
+ organisation: LREN-CHUV
+ organisation_badge: https://img.shields.io/badge/CHUV-LREN-AF4C64.svg
+ - author: Than Luu-tho
+ author_email:
+ - Thanh.Luu-Tho@chuv.ch
+ organisation: LREN-CHUV
+ organisation_badge: https://img.shields.io/badge/CHUV-LREN-AF4C64.svg
+
+platform: MIP
+component:
+ mip_building_block: web-analytics
+ nature: server
+
+license:
+ name: GNU Affero General Public License, Version 3.0
+ badge: https://img.shields.io/badge/license-AGPL--3.0-blue.svg
+ url: https://github.com/LREN-CHUV/portal-backend/blob/master/LICENSE
+
+code_repositories:
+ - name: chuv-gitlab
+ visibility: private
+ url: https://___.chuv.ch/web-analytics/portal-backend/
+ git_clone: https://___.chuv.ch/web-analytics/portal-backend.git
+ - name: github/LREN-CHUV
+ visibility: public
+ url: https://github.io/LREN-CHUV/portal-backend/
+ git_clone: https://github.io/LREN-CHUV/portal-backend.git
+ - name: github/HBPMedical
+ visibility: public
+ url: https://github.io/HBPMedical/portal-backend/
+ git_clone: https://github.io/HBPMedical/portal-backend.git
+
+code_quality_checks:
+ codacy:
+ badge: https://api.codacy.com/project/badge/Grade/05ba08087da24b3980475f88e1a591b7
+ url: "https://www.codacy.com/app/hbp-mip/portal-backend?utm_source=github.com&utm_medium=referral&utm_content=LREN-CHUV/portal-backend&utm_campaign=Badge_Grade"
+
+testing:
+ unit_testing:
+ source: src/test/java
+ command: ./test.sh
+
+release_management:
+ current_version: 2.0.0
+ current_code_release: https://github.com/HBPMedical/portal-backend/archive/2.0.0.zip
+ current_binary_release: https://pypi.python.org/pypi/portal-backend/2.0.0
+ release_script: 'publish.sh'
+
+continuous_integration:
+ - name: CircleCI
+ description: "Check style and execute unit tests"
+ url: https://circleci.com/gh/LREN-CHUV/portal-backend/tree/master
+ badge: https://circleci.com/gh/LREN-CHUV/portal-backend/tree/master.svg?style=svg
+ actions:
+ - build
+ - unit_tests
+
+distribution:
+ docker_hub:
+ name: hbpmip/portal-backend
+ current_tag: 2.0.0
+ url: https://hub.docker.com/r/hbpmip/portal-backend/
+ badge: https://img.shields.io/badge/docker-hbpmip%2Fportal--backend-008bb8.svg
+ command: docker pull hbpmip/portal-backend:2.0.0
+
+planning:
+ github:
+ name: Issues on Github
+ url: https://github.com/LREN-CHUV/portal-backend/issues
+ trello:
+ name: "[plans] Web front end"
+ url: https://trello.com/b/lr3NS4W6/plans-web-front-end
+
+related_projects:
+ - name: portal-frontend
+ mip_building_block: web-analytics
+ relationship: other-depends-on
diff --git a/pom.xml b/pom.xml
index 5e7fa773d..34879a537 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
<groupId>eu.hbp.mip</groupId>
<artifactId>portal-backend</artifactId>
- <version>1.1</version>
+ <version>2.0.0</version><!-- BUMP_VERSION -->
<packaging>jar</packaging>
<name>portal-backend</name>
diff --git a/publish.sh b/publish.sh
new file mode 100755
index 000000000..b53435806
--- /dev/null
+++ b/publish.sh
@@ -0,0 +1,89 @@
+#!/usr/bin/env bash
+set -e
+
+get_script_dir () {
+ SOURCE="${BASH_SOURCE[0]}"
+
+ while [ -h "$SOURCE" ]; do
+ DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+ SOURCE="$( readlink "$SOURCE" )"
+ [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+ done
+ cd -P "$( dirname "$SOURCE" )"
+ pwd
+}
+
+export WORKSPACE=$(get_script_dir)
+
+if pgrep -lf sshuttle > /dev/null ; then
+ echo "sshuttle detected. Please close this program as it messes with networking and prevents builds inside Docker to work"
+ exit 1
+fi
+
+if groups $USER | grep &>/dev/null '\bdocker\b'; then
+ CAPTAIN="captain"
+else
+ CAPTAIN="sudo captain"
+fi
+
+count=$(git status --porcelain | wc -l)
+if test $count -gt 0; then
+ git status
+ echo "Not all files have been committed in Git. Release aborted"
+ exit 1
+fi
+
+select_part() {
+ local choice=$1
+ case "$choice" in
+ "Patch release")
+ bumpversion patch
+ ;;
+ "Minor release")
+ bumpversion minor
+ ;;
+ "Major release")
+ bumpversion major
+ ;;
+ *)
+ read -p "Version > " version
+ bumpversion --new-version=$version all
+ ;;
+ esac
+}
+
+git pull --tags
+# Look for a version tag in Git. If not found, ask the user to provide one
+[ $(git tag --points-at HEAD | wc -l) == 1 ] || (
+ latest_version=$(git describe --abbrev=00 || \
+ (bumpversion --dry-run --list patch | grep current_version | sed -r s,"^.*=",,) || echo '0.0.1')
+ echo
+ echo "Current commit has not been tagged with a version. Latest known version is $latest_version."
+ echo
+ echo 'What do you want to release?'
+ PS3='Select the version increment> '
+ options=("Patch release" "Minor release" "Major release" "Release with a custom version")
+ select choice in "${options[@]}";
+ do
+ select_part "$choice"
+ break
+ done
+ updated_version=$(bumpversion --dry-run --list patch | grep current_version | sed -r s,"^.*=",,)
+ read -p "Release version $updated_version? [y/N] > " ok
+ if [ "$ok" != "y" ]; then
+ echo "Release aborted"
+ exit 1
+ fi
+)
+
+git push
+git push --tags
+updated_version=$(bumpversion --dry-run --list patch | grep current_version | sed -r s,"^.*=",,)
+
+# WARNING: Requires captain 1.1.0 to push user tags
+BUILD_DATE=$(date --iso-8601=seconds) VCS_REF=$updated_version VERSION=$updated_version \
+ $CAPTAIN push portal-backend --branch-tags=false --commit-tags=false --tag $updated_version
+sed "s/USER/${USER^}/" $WORKSPACE/docker/runner/slack.json > $WORKSPACE/target/slack.json
+sed -i.bak "s/VERSION/$updated_version/" $WORKSPACE/target/slack.json
+curl -k -X POST --data-urlencode payload@$WORKSPACE/target/slack.json https://hbps1.chuv.ch/slack/dev-activity
+rm -f $WORKSPACE/target/slack.json
diff --git a/slack.json b/slack.json
new file mode 100644
index 000000000..8f25bd423
--- /dev/null
+++ b/slack.json
@@ -0,0 +1 @@
+{"channel": "#dev-activity", "username": "webhookbot", "text": "USER pushed a new version of hbpmip/portal-backend:VERSION to Docker hub", "icon_emoji": ":whale:"}
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index 64c5ce3ad..804444e0e 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -26,8 +26,8 @@ import javax.sql.DataSource;
@EntityScan(basePackages = "eu.hbp.mip.model")
public class PersistenceConfiguration {
- @Value("#{'${spring.scienceDatasource.main-table:adni_merge}'}")
- private String scienceMainTable;
+ @Value("#{'${spring.featuresDatasource.main-table:adni_merge}'}")
+ private String featuresMainTable;
@Primary
@Bean(name = "portalDatasource")
@@ -42,9 +42,9 @@ public class PersistenceConfiguration {
return DataSourceBuilder.create().build();
}
- @Bean(name = "scienceDatasource")
- @ConfigurationProperties(prefix="spring.scienceDatasource")
- public DataSource scienceDataSource() {
+ @Bean(name = "featuresDatasource")
+ @ConfigurationProperties(prefix="spring.featuresDatasource")
+ public DataSource featuresDataSource() {
return DataSourceBuilder.create().build();
}
@@ -57,9 +57,9 @@ public class PersistenceConfiguration {
@Bean
@Autowired
- @Qualifier("scienceJdbcTemplate")
- public JdbcTemplate scienceJdbcTemplate() {
- return new JdbcTemplate(scienceDataSource());
+ @Qualifier("featuresJdbcTemplate")
+ public JdbcTemplate featuresJdbcTemplate() {
+ return new JdbcTemplate(featuresDataSource());
}
@Bean(name = "entityManagerFactory")
@@ -83,7 +83,7 @@ public class PersistenceConfiguration {
@Bean(name = "dataUtil")
@Scope("singleton")
public DataUtil dataUtil() {
- return new DataUtil(scienceJdbcTemplate(), scienceMainTable);
+ return new DataUtil(featuresJdbcTemplate(), featuresMainTable);
}
}
diff --git a/src/main/java/eu/hbp/mip/utils/DataUtil.java b/src/main/java/eu/hbp/mip/utils/DataUtil.java
index a99a9b963..87ff932f8 100644
--- a/src/main/java/eu/hbp/mip/utils/DataUtil.java
+++ b/src/main/java/eu/hbp/mip/utils/DataUtil.java
@@ -17,12 +17,12 @@ public class DataUtil {
private static final int TABLESAMPLE_SEED = 42;
private JdbcTemplate jdbcTemplate;
- private String scienceMainTable;
+ private String featuresMainTable;
- public DataUtil(JdbcTemplate jdbcTemplate, String scienceMainTable)
+ public DataUtil(JdbcTemplate jdbcTemplate, String featuresMainTable)
{
this.jdbcTemplate = jdbcTemplate;
- this.scienceMainTable = scienceMainTable;
+ this.featuresMainTable = featuresMainTable;
}
@Cacheable("varsdata")
@@ -39,7 +39,7 @@ public class DataUtil {
int nb_samples = Math.min(nbRows, MAX_NB_SAMPLES);
int samplingPercentage = 100 * nb_samples / nbRows;
List<Object> queryResult = jdbcTemplate.queryForList(
- "SELECT " + var + " FROM "+scienceMainTable+" " +
+ "SELECT " + var + " FROM "+featuresMainTable+" " +
"TABLESAMPLE SYSTEM ("+ samplingPercentage +") REPEATABLE ( "+ TABLESAMPLE_SEED +" )", Object.class);
for (Object value : queryResult)
{
@@ -62,14 +62,14 @@ public class DataUtil {
{
return jdbcTemplate.queryForObject(
"SELECT COUNT(*) FROM INFORMATION_SCHEMA.COLUMNS " +
- "WHERE table_name = '"+scienceMainTable+"'", Long.class);
+ "WHERE table_name = '"+featuresMainTable+"'", Long.class);
}
@Cacheable("rowscount")
public long countDatasetRows()
{
return jdbcTemplate.queryForObject(
- "SELECT COUNT(*) FROM "+scienceMainTable, Long.class);
+ "SELECT COUNT(*) FROM "+featuresMainTable, Long.class);
}
}
diff --git a/src/main/resources/data/exareme_algorithms.json b/src/main/resources/data/exareme_algorithms.json
index 3fc6a3471..e885b6200 100644
--- a/src/main/resources/data/exareme_algorithms.json
+++ b/src/main/resources/data/exareme_algorithms.json
@@ -11,4 +11,4 @@
"polynominal": false
}
}
-}
\ No newline at end of file
+}
diff --git a/tests/integration/algorithmsFactory/test.sh b/tests/integration/algorithmsFactory/test.sh
index 6e21e6285..b8d0c939b 100755
--- a/tests/integration/algorithmsFactory/test.sh
+++ b/tests/integration/algorithmsFactory/test.sh
@@ -14,4 +14,4 @@ echo "exp1: $response"
response=$(curl -s http://backend:8080/services/experiments -X POST -H "Content-Type: application/json" -d @expQuery2.json)
echo "exp2: $response"
response=$(curl -s http://backend:8080/services/experiments -X POST -H "Content-Type: application/json" -d @expQuery3.json)
-echo "exp3: $response"
\ No newline at end of file
+echo "exp3: $response"
diff --git a/tests/post-test-run.sh b/tests/post-test-run.sh
index fffdd77f5..cd30147d6 100755
--- a/tests/post-test-run.sh
+++ b/tests/post-test-run.sh
@@ -9,8 +9,8 @@ fi
if [ $(docker ps | grep portal-db-test | wc -l) -gt 0 ]; then
docker kill portal-db-test
fi
-if [ $(docker ps | grep science-db-test | wc -l) -gt 0 ]; then
- docker kill science-db-test
+if [ $(docker ps | grep features-db-test | wc -l) -gt 0 ]; then
+ docker kill features-db-test
fi
if [ $(docker ps | grep meta-db-test | wc -l) -gt 0 ]; then
docker kill meta-db-test
@@ -25,8 +25,8 @@ fi
if [ $(docker ps -a | grep portal-db-test | wc -l) -gt 0 ]; then
docker rm -f portal-db-test
fi
-if [ $(docker ps -a | grep science-db-test | wc -l) -gt 0 ]; then
- docker rm -f science-db-test
+if [ $(docker ps -a | grep features-db-test | wc -l) -gt 0 ]; then
+ docker rm -f features-db-test
fi
if [ $(docker ps -a | grep meta-db-test | wc -l) -gt 0 ]; then
docker rm -f meta-db-test
diff --git a/tests/pre-test-run.sh b/tests/pre-test-run.sh
index ee10e2488..01e97cc7e 100755
--- a/tests/pre-test-run.sh
+++ b/tests/pre-test-run.sh
@@ -10,8 +10,8 @@ fi
if [ $(docker ps | grep portal-db-test | wc -l) -gt 0 ]; then
docker kill portal-db-test
fi
-if [ $(docker ps | grep science-db-test | wc -l) -gt 0 ]; then
- docker kill science-db-test
+if [ $(docker ps | grep features-db-test | wc -l) -gt 0 ]; then
+ docker kill features-db-test
fi
@@ -24,15 +24,15 @@ fi
if [ $(docker ps -a | grep portal-db-test | wc -l) -gt 0 ]; then
docker rm -f portal-db-test
fi
-if [ $(docker ps -a | grep science-db-test | wc -l) -gt 0 ]; then
- docker rm -f science-db-test
+if [ $(docker ps -a | grep features-db-test | wc -l) -gt 0 ]; then
+ docker rm -f features-db-test
fi
# Run databases containers
echo "Running databases containers..."
-docker run --name science-db-test -p 65432:5432 -v $(pwd)/tests/science-db/sql:/docker-entrypoint-initdb.d/ -e POSTGRES_USER=postgres -d postgres:9.5.3
+docker run --name features-db-test -p 65432:5432 -v $(pwd)/tests/features-db/sql:/docker-entrypoint-initdb.d/ -e POSTGRES_USER=postgres -d postgres:9.5.3
docker run --name meta-db-test -p 65433:5432 -v $(pwd)/tests/meta-db/sql:/docker-entrypoint-initdb.d/ -e POSTGRES_USER=postgres -d postgres:9.5.3
docker run --name portal-db-test -p 65434:5432 -e POSTGRES_USER=postgres -d postgres:9.5.3
@@ -40,17 +40,17 @@ docker run --name portal-db-test -p 65434:5432 -e POSTGRES_USER=postgres -d post
# Get gateway IP
echo "Searching gateway IP..."
-GATEWAY_IP=$(docker inspect science-db-test | grep \"Gateway\":\ \" | sed 's/.*Gateway\":\ \"\([^-]*\)\",/\1/' | head -n 1)
+GATEWAY_IP=$(docker inspect features-db-test | grep \"Gateway\":\ \" | sed 's/.*Gateway\":\ \"\([^-]*\)\",/\1/' | head -n 1)
echo "Gateway IP: $GATEWAY_IP"
# Wait for databases to be ready
-echo "Waiting for science-db to start..."
+echo "Waiting for features-db to start..."
if [ "$CIRCLECI" = true ] ; then
sleep 10
else
- until [ $(docker exec science-db-test psql -U postgres -c "\q" 2>&1 | wc -l) -eq 0 ]; do
+ until [ $(docker exec features-db-test psql -U postgres -c "\q" 2>&1 | wc -l) -eq 0 ]; do
printf '.'
sleep 1
done
@@ -90,9 +90,9 @@ docker run --name backend-test -p 65440:8080 \
-e "META_DB_URL=jdbc:postgresql://$GATEWAY_IP:65433/postgres" \
-e "META_DB_SERVER=$GATEWAY_IP:65433/postgres" \
-e "META_DB_USER=postgres" \
--e "SCIENCE_DB_URL=jdbc:postgresql://$GATEWAY_IP:65432/postgres" \
--e "SCIENCE_DB_SERVER=$GATEWAY_IP:65432/postgres" \
--e "SCIENCE_DB_USER=postgres" \
+-e "FEATURES_DB_URL=jdbc:postgresql://$GATEWAY_IP:65432/postgres" \
+-e "FEATURES_DB_SERVER=$GATEWAY_IP:65432/postgres" \
+-e "FEATURES_DB_USER=postgres" \
-e "CONTEXT_PATH=/services" \
-e "AUTHENTICATION=0" \
-d hbpmip/portal-backend:latest
--
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