From ee235653ee6cef20afe512b4c71bb9b5bfa6054a Mon Sep 17 00:00:00 2001
From: BaranekD <0Baranek.dominik0@gmail.com>
Date: Wed, 13 Jul 2022 11:07:28 +0200
Subject: [PATCH] Initial commit
---
.github/workflows/main.yml | 41 +
.gitignore | 6 +-
.mvn/wrapper/maven-wrapper.jar | Bin 0 -> 59925 bytes
.mvn/wrapper/maven-wrapper.properties | 18 +
.releaserc | 20 +
README.md | 0
mvnw | 287 ++
mvnw.cmd | 187 +
package-lock.json | 4423 +++++++++++++++++
package.json | 10 +
pom.xml | 73 +-
renovate.json | 17 +
.../java/cz/muni/ics/ga4gh/Application.java | 3 +-
.../cz/muni/ics/ga4gh/ApplicationContext.java | 44 +
.../muni/ics/ga4gh/adapters/PerunAdapter.java | 39 +
.../ga4gh/adapters/PerunAdapterMethods.java | 23 +
.../adapters/PerunAdapterMethodsLdap.java | 4 +
.../adapters/PerunAdapterMethodsRpc.java | 12 +
.../ga4gh/adapters/impl/PerunAdapterImpl.java | 72 +
.../ga4gh/adapters/impl/PerunAdapterLdap.java | 199 +
.../ga4gh/adapters/impl/PerunAdapterRpc.java | 283 ++
.../java/cz/muni/ics/ga4gh/aop/LogTimes.java | 11 +
.../muni/ics/ga4gh/config/AdapterConfig.java | 19 +
.../ics/ga4gh/config/AttributesConfig.java | 20 +
.../ics/ga4gh/config/BasicAuthConfig.java | 19 +
.../muni/ics/ga4gh/config/BrokerConfig.java | 37 +
.../cz/muni/ics/ga4gh/config/Ga4ghConfig.java | 20 +
.../cz/muni/ics/ga4gh/config/LdapConfig.java | 33 +
.../cz/muni/ics/ga4gh/config/RpcConfig.java | 25 +
.../ga4gh/connectors/PerunConnectorLdap.java | 154 +
.../ga4gh/connectors/PerunConnectorRpc.java | 188 +
.../controllers/Ga4ghBrokerController.java | 35 +
.../controllers/JwkSetPublishingEndpoint.java | 40 +
.../cz/muni/ics/ga4gh/enums/MemberStatus.java | 31 +
.../InconvertibleValueException.java | 24 +
.../exceptions/MissingFieldException.java | 24 +
.../exceptions/UserNotUniqueException.java | 24 +
.../ics/ga4gh/facade/Ga4ghBrokerFacade.java | 8 +
.../facade/impl/Ga4GhBrokerFacadeImpl.java | 23 +
.../ga4gh/jose/keystore/JWKSetKeyStore.java | 79 +
.../cz/muni/ics/ga4gh/mappers/RpcMapper.java | 277 ++
.../cz/muni/ics/ga4gh/model/Affiliation.java | 19 +
.../ics/ga4gh/model/AttributeMapping.java | 23 +
.../cz/muni/ics/ga4gh/model/ExtSource.java | 40 +
.../ics/ga4gh/model/Ga4ghClaimRepository.java | 20 +
.../ics/ga4gh/model/Ga4ghPassportVisa.java | 59 +
.../java/cz/muni/ics/ga4gh/model/Group.java | 45 +
.../java/cz/muni/ics/ga4gh/model/Member.java | 26 +
.../ics/ga4gh/model/PerunAttributeValue.java | 173 +
.../java/cz/muni/ics/ga4gh/model/Repo.java | 27 +
.../cz/muni/ics/ga4gh/model/RepoHeader.java | 30 +
.../muni/ics/ga4gh/model/UserExtSource.java | 56 +
.../ga4gh/security/WebSecurityConfigurer.java | 50 +
.../ics/ga4gh/service/Ga4ghBrokerService.java | 8 +
.../JWTSigningAndValidationService.java | 37 +
.../impl/Ga4GhBrokerBrokerServiceImpl.java | 61 +
.../JWTSigningAndValidationServiceImpl.java | 227 +
.../impl/brokers/BbmriGa4ghBroker.java | 204 +
.../impl/brokers/ElixirGa4ghBroker.java | 201 +
.../service/impl/brokers/Ga4ghBroker.java | 223 +
.../java/cz/muni/ics/ga4gh/utils/Utils.java | 218 +
src/main/resources/application-bbmri.yml | 77 +
src/main/resources/application-elixir.yml | 92 +
src/main/resources/application.yml | 13 +
update-versions.sh | 2 +
65 files changed, 8766 insertions(+), 17 deletions(-)
create mode 100644 .github/workflows/main.yml
create mode 100644 .mvn/wrapper/maven-wrapper.jar
create mode 100644 .mvn/wrapper/maven-wrapper.properties
create mode 100644 .releaserc
create mode 100644 README.md
create mode 100755 mvnw
create mode 100644 mvnw.cmd
create mode 100644 package-lock.json
create mode 100644 package.json
create mode 100644 renovate.json
create mode 100644 src/main/java/cz/muni/ics/ga4gh/ApplicationContext.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapter.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethods.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsLdap.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsRpc.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterImpl.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterLdap.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterRpc.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/aop/LogTimes.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/config/AdapterConfig.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/config/AttributesConfig.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/config/BasicAuthConfig.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/config/BrokerConfig.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/config/Ga4ghConfig.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/config/LdapConfig.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/config/RpcConfig.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorLdap.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorRpc.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/controllers/Ga4ghBrokerController.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/controllers/JwkSetPublishingEndpoint.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/enums/MemberStatus.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/exceptions/InconvertibleValueException.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/exceptions/MissingFieldException.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/exceptions/UserNotUniqueException.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/facade/Ga4ghBrokerFacade.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/facade/impl/Ga4GhBrokerFacadeImpl.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/jose/keystore/JWKSetKeyStore.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/mappers/RpcMapper.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/Affiliation.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/AttributeMapping.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/ExtSource.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/Ga4ghClaimRepository.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/Ga4ghPassportVisa.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/Group.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/Member.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/PerunAttributeValue.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/Repo.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/RepoHeader.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/model/UserExtSource.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/security/WebSecurityConfigurer.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/service/Ga4ghBrokerService.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/service/JWTSigningAndValidationService.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/service/impl/Ga4GhBrokerBrokerServiceImpl.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/service/impl/JWTSigningAndValidationServiceImpl.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/BbmriGa4ghBroker.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/ElixirGa4ghBroker.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/Ga4ghBroker.java
create mode 100644 src/main/java/cz/muni/ics/ga4gh/utils/Utils.java
create mode 100644 src/main/resources/application-bbmri.yml
create mode 100644 src/main/resources/application-elixir.yml
create mode 100644 src/main/resources/application.yml
create mode 100755 update-versions.sh
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 0000000..79bc9f5
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,41 @@
+name: Maven build with tests
+on: [ push, pull_request ]
+jobs:
+ build:
+ name: JDK ${{ matrix.java }}
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ java: [ '11', '17' ]
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up JDK ${{ matrix.java }}
+ uses: actions/setup-java@v3
+ with:
+ distribution: 'zulu'
+ java-version: ${{ matrix.java }}
+ - uses: actions/cache@v3
+ with:
+ path: ~/.m2/repository
+ key: ${{ runner.os }}-maven-jdk${{ matrix.java }}-${{ hashFiles('**/pom.xml') }}
+ restore-keys: |
+ ${{ runner.os }}-maven-jdk${{ matrix.java }}-
+ - name: Build with Maven
+ run: mvn -B clean install -Djava.version=${{matrix.java}}
+ release:
+ name: Release
+ needs: [build]
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+ - name: Setup Node.js
+ uses: actions/setup-node@v3
+ with:
+ node-version: 16
+ - name: Release
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ run: npm install && npx semantic-release
diff --git a/.gitignore b/.gitignore
index 5ff6309..946c634 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,11 +3,15 @@ target/
!**/src/main/**/target/
!**/src/test/**/target/
+# semantic
+node_modules
+
### IntelliJ IDEA ###
.idea/modules.xml
.idea/jarRepositories.xml
.idea/compiler.xml
.idea/libraries/
+.idea
*.iws
*.iml
*.ipr
@@ -35,4 +39,4 @@ build/
.vscode/
### Mac OS ###
-.DS_Store
\ No newline at end of file
+.DS_Store
diff --git a/.mvn/wrapper/maven-wrapper.jar b/.mvn/wrapper/maven-wrapper.jar
new file mode 100644
index 0000000000000000000000000000000000000000..bf82ff01c6cdae4a1bb754a6e062954d77ac5c11
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HcmV?d00001
diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties
new file mode 100644
index 0000000..996a98a
--- /dev/null
+++ b/.mvn/wrapper/maven-wrapper.properties
@@ -0,0 +1,18 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.6.0/apache-maven-3.6.0-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar
diff --git a/.releaserc b/.releaserc
new file mode 100644
index 0000000..a05f894
--- /dev/null
+++ b/.releaserc
@@ -0,0 +1,20 @@
+{
+ "branches": ["master"],
+ "plugins": [
+ "@semantic-release/commit-analyzer",
+ "@semantic-release/release-notes-generator",
+ ["@semantic-release/exec", {
+ "prepareCmd": "./update-versions.sh ${nextRelease.version} && ./mvnw clean package"
+ }],
+ "@semantic-release/changelog",
+ ["@semantic-release/git", {
+ "assets": ["CHANGELOG.md", "pom.xml"],
+ "message": "chore(release): ${nextRelease.version} [skip ci]\n\n${nextRelease.notes}"
+ }],
+ ["@semantic-release/github", {
+ "assets": [
+ {"path": "target/perun-ga4gh-broker.war"}
+ ]
+ }]
+ ]
+}
\ No newline at end of file
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/mvnw b/mvnw
new file mode 100755
index 0000000..b7f0646
--- /dev/null
+++ b/mvnw
@@ -0,0 +1,287 @@
+#!/bin/sh
+# ----------------------------------------------------------------------------
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+# ----------------------------------------------------------------------------
+
+# ----------------------------------------------------------------------------
+# Apache Maven Wrapper startup batch script, version 3.1.1
+#
+# Required ENV vars:
+# ------------------
+# JAVA_HOME - location of a JDK home dir
+#
+# Optional ENV vars
+# -----------------
+# MAVEN_OPTS - parameters passed to the Java VM when running Maven
+# e.g. to debug Maven itself, use
+# set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
+# MAVEN_SKIP_RC - flag to disable loading of mavenrc files
+# ----------------------------------------------------------------------------
+
+if [ -z "$MAVEN_SKIP_RC" ] ; then
+
+ if [ -f /usr/local/etc/mavenrc ] ; then
+ . /usr/local/etc/mavenrc
+ fi
+
+ if [ -f /etc/mavenrc ] ; then
+ . /etc/mavenrc
+ fi
+
+ if [ -f "$HOME/.mavenrc" ] ; then
+ . "$HOME/.mavenrc"
+ fi
+
+fi
+
+# OS specific support. $var _must_ be set to either true or false.
+cygwin=false;
+darwin=false;
+mingw=false
+case "`uname`" in
+ CYGWIN*) cygwin=true ;;
+ MINGW*) mingw=true;;
+ Darwin*) darwin=true
+ # Use /usr/libexec/java_home if available, otherwise fall back to /Library/Java/Home
+ # See https://developer.apple.com/library/mac/qa/qa1170/_index.html
+ if [ -z "$JAVA_HOME" ]; then
+ if [ -x "/usr/libexec/java_home" ]; then
+ JAVA_HOME="`/usr/libexec/java_home`"; export JAVA_HOME
+ else
+ JAVA_HOME="/Library/Java/Home"; export JAVA_HOME
+ fi
+ fi
+ ;;
+esac
+
+if [ -z "$JAVA_HOME" ] ; then
+ if [ -r /etc/gentoo-release ] ; then
+ JAVA_HOME=`java-config --jre-home`
+ fi
+fi
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+ [ -n "$JAVA_HOME" ] &&
+ JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+ [ -n "$CLASSPATH" ] &&
+ CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
+fi
+
+# For Mingw, ensure paths are in UNIX format before anything is touched
+if $mingw ; then
+ [ -n "$JAVA_HOME" ] &&
+ JAVA_HOME="`(cd "$JAVA_HOME"; pwd)`"
+fi
+
+if [ -z "$JAVA_HOME" ]; then
+ javaExecutable="`which javac`"
+ if [ -n "$javaExecutable" ] && ! [ "`expr \"$javaExecutable\" : '\([^ ]*\)'`" = "no" ]; then
+ # readlink(1) is not available as standard on Solaris 10.
+ readLink=`which readlink`
+ if [ ! `expr "$readLink" : '\([^ ]*\)'` = "no" ]; then
+ if $darwin ; then
+ javaHome="`dirname \"$javaExecutable\"`"
+ javaExecutable="`cd \"$javaHome\" && pwd -P`/javac"
+ else
+ javaExecutable="`readlink -f \"$javaExecutable\"`"
+ fi
+ javaHome="`dirname \"$javaExecutable\"`"
+ javaHome=`expr "$javaHome" : '\(.*\)/bin'`
+ JAVA_HOME="$javaHome"
+ export JAVA_HOME
+ fi
+ fi
+fi
+
+if [ -z "$JAVACMD" ] ; then
+ if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD="$JAVA_HOME/jre/sh/java"
+ else
+ JAVACMD="$JAVA_HOME/bin/java"
+ fi
+ else
+ JAVACMD="`\\unset -f command; \\command -v java`"
+ fi
+fi
+
+if [ ! -x "$JAVACMD" ] ; then
+ echo "Error: JAVA_HOME is not defined correctly." >&2
+ echo " We cannot execute $JAVACMD" >&2
+ exit 1
+fi
+
+if [ -z "$JAVA_HOME" ] ; then
+ echo "Warning: JAVA_HOME environment variable is not set."
+fi
+
+# traverses directory structure from process work directory to filesystem root
+# first directory with .mvn subdirectory is considered project base directory
+find_maven_basedir() {
+ if [ -z "$1" ]
+ then
+ echo "Path not specified to find_maven_basedir"
+ return 1
+ fi
+
+ basedir="$1"
+ wdir="$1"
+ while [ "$wdir" != '/' ] ; do
+ if [ -d "$wdir"/.mvn ] ; then
+ basedir=$wdir
+ break
+ fi
+ # workaround for JBEAP-8937 (on Solaris 10/Sparc)
+ if [ -d "${wdir}" ]; then
+ wdir=`cd "$wdir/.."; pwd`
+ fi
+ # end of workaround
+ done
+ printf '%s' "$(cd "$basedir"; pwd)"
+}
+
+# concatenates all lines of a file
+concat_lines() {
+ if [ -f "$1" ]; then
+ echo "$(tr -s '\n' ' ' < "$1")"
+ fi
+}
+
+BASE_DIR=$(find_maven_basedir "$(dirname $0)")
+if [ -z "$BASE_DIR" ]; then
+ exit 1;
+fi
+
+MAVEN_PROJECTBASEDIR=${MAVEN_BASEDIR:-"$BASE_DIR"}; export MAVEN_PROJECTBASEDIR
+if [ "$MVNW_VERBOSE" = true ]; then
+ echo $MAVEN_PROJECTBASEDIR
+fi
+
+##########################################################################################
+# Extension to allow automatically downloading the maven-wrapper.jar from Maven-central
+# This allows using the maven wrapper in projects that prohibit checking in binary data.
+##########################################################################################
+if [ -r "$BASE_DIR/.mvn/wrapper/maven-wrapper.jar" ]; then
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo "Found .mvn/wrapper/maven-wrapper.jar"
+ fi
+else
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo "Couldn't find .mvn/wrapper/maven-wrapper.jar, downloading it ..."
+ fi
+ if [ -n "$MVNW_REPOURL" ]; then
+ wrapperUrl="$MVNW_REPOURL/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar"
+ else
+ wrapperUrl="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar"
+ fi
+ while IFS="=" read key value; do
+ case "$key" in (wrapperUrl) wrapperUrl="$value"; break ;;
+ esac
+ done < "$BASE_DIR/.mvn/wrapper/maven-wrapper.properties"
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo "Downloading from: $wrapperUrl"
+ fi
+ wrapperJarPath="$BASE_DIR/.mvn/wrapper/maven-wrapper.jar"
+ if $cygwin; then
+ wrapperJarPath=`cygpath --path --windows "$wrapperJarPath"`
+ fi
+
+ if command -v wget > /dev/null; then
+ QUIET="--quiet"
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo "Found wget ... using wget"
+ QUIET=""
+ fi
+ if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then
+ wget $QUIET "$wrapperUrl" -O "$wrapperJarPath"
+ else
+ wget $QUIET --http-user="$MVNW_USERNAME" --http-password="$MVNW_PASSWORD" "$wrapperUrl" -O "$wrapperJarPath"
+ fi
+ [ $? -eq 0 ] || rm -f "$wrapperJarPath"
+ elif command -v curl > /dev/null; then
+ QUIET="--silent"
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo "Found curl ... using curl"
+ QUIET=""
+ fi
+ if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then
+ curl $QUIET -o "$wrapperJarPath" "$wrapperUrl" -f -L
+ else
+ curl $QUIET --user "$MVNW_USERNAME:$MVNW_PASSWORD" -o "$wrapperJarPath" "$wrapperUrl" -f -L
+ fi
+ [ $? -eq 0 ] || rm -f "$wrapperJarPath"
+ else
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo "Falling back to using Java to download"
+ fi
+ javaSource="$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.java"
+ javaClass="$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.class"
+ # For Cygwin, switch paths to Windows format before running javac
+ if $cygwin; then
+ javaSource=`cygpath --path --windows "$javaSource"`
+ javaClass=`cygpath --path --windows "$javaClass"`
+ fi
+ if [ -e "$javaSource" ]; then
+ if [ ! -e "$javaClass" ]; then
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo " - Compiling MavenWrapperDownloader.java ..."
+ fi
+ # Compiling the Java class
+ ("$JAVA_HOME/bin/javac" "$javaSource")
+ fi
+ if [ -e "$javaClass" ]; then
+ # Running the downloader
+ if [ "$MVNW_VERBOSE" = true ]; then
+ echo " - Running MavenWrapperDownloader.java ..."
+ fi
+ ("$JAVA_HOME/bin/java" -cp .mvn/wrapper MavenWrapperDownloader "$MAVEN_PROJECTBASEDIR")
+ fi
+ fi
+ fi
+fi
+##########################################################################################
+# End of extension
+##########################################################################################
+
+MAVEN_OPTS="$(concat_lines "$MAVEN_PROJECTBASEDIR/.mvn/jvm.config") $MAVEN_OPTS"
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+ [ -n "$JAVA_HOME" ] &&
+ JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
+ [ -n "$CLASSPATH" ] &&
+ CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
+ [ -n "$MAVEN_PROJECTBASEDIR" ] &&
+ MAVEN_PROJECTBASEDIR=`cygpath --path --windows "$MAVEN_PROJECTBASEDIR"`
+fi
+
+# Provide a "standardized" way to retrieve the CLI args that will
+# work with both Windows and non-Windows executions.
+MAVEN_CMD_LINE_ARGS="$MAVEN_CONFIG $@"
+export MAVEN_CMD_LINE_ARGS
+
+WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
+
+exec "$JAVACMD" \
+ $MAVEN_OPTS \
+ $MAVEN_DEBUG_OPTS \
+ -classpath "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" \
+ "-Dmaven.multiModuleProjectDirectory=${MAVEN_PROJECTBASEDIR}" \
+ ${WRAPPER_LAUNCHER} $MAVEN_CONFIG "$@"
diff --git a/mvnw.cmd b/mvnw.cmd
new file mode 100644
index 0000000..cba1f04
--- /dev/null
+++ b/mvnw.cmd
@@ -0,0 +1,187 @@
+@REM ----------------------------------------------------------------------------
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements. See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership. The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License. You may obtain a copy of the License at
+@REM
+@REM http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied. See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM ----------------------------------------------------------------------------
+
+@REM ----------------------------------------------------------------------------
+@REM Apache Maven Wrapper startup batch script, version 3.1.1
+@REM
+@REM Required ENV vars:
+@REM JAVA_HOME - location of a JDK home dir
+@REM
+@REM Optional ENV vars
+@REM MAVEN_BATCH_ECHO - set to 'on' to enable the echoing of the batch commands
+@REM MAVEN_BATCH_PAUSE - set to 'on' to wait for a keystroke before ending
+@REM MAVEN_OPTS - parameters passed to the Java VM when running Maven
+@REM e.g. to debug Maven itself, use
+@REM set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
+@REM MAVEN_SKIP_RC - flag to disable loading of mavenrc files
+@REM ----------------------------------------------------------------------------
+
+@REM Begin all REM lines with '@' in case MAVEN_BATCH_ECHO is 'on'
+@echo off
+@REM set title of command window
+title %0
+@REM enable echoing by setting MAVEN_BATCH_ECHO to 'on'
+@if "%MAVEN_BATCH_ECHO%" == "on" echo %MAVEN_BATCH_ECHO%
+
+@REM set %HOME% to equivalent of $HOME
+if "%HOME%" == "" (set "HOME=%HOMEDRIVE%%HOMEPATH%")
+
+@REM Execute a user defined script before this one
+if not "%MAVEN_SKIP_RC%" == "" goto skipRcPre
+@REM check for pre script, once with legacy .bat ending and once with .cmd ending
+if exist "%USERPROFILE%\mavenrc_pre.bat" call "%USERPROFILE%\mavenrc_pre.bat" %*
+if exist "%USERPROFILE%\mavenrc_pre.cmd" call "%USERPROFILE%\mavenrc_pre.cmd" %*
+:skipRcPre
+
+@setlocal
+
+set ERROR_CODE=0
+
+@REM To isolate internal variables from possible post scripts, we use another setlocal
+@setlocal
+
+@REM ==== START VALIDATION ====
+if not "%JAVA_HOME%" == "" goto OkJHome
+
+echo.
+echo Error: JAVA_HOME not found in your environment. >&2
+echo Please set the JAVA_HOME variable in your environment to match the >&2
+echo location of your Java installation. >&2
+echo.
+goto error
+
+:OkJHome
+if exist "%JAVA_HOME%\bin\java.exe" goto init
+
+echo.
+echo Error: JAVA_HOME is set to an invalid directory. >&2
+echo JAVA_HOME = "%JAVA_HOME%" >&2
+echo Please set the JAVA_HOME variable in your environment to match the >&2
+echo location of your Java installation. >&2
+echo.
+goto error
+
+@REM ==== END VALIDATION ====
+
+:init
+
+@REM Find the project base dir, i.e. the directory that contains the folder ".mvn".
+@REM Fallback to current working directory if not found.
+
+set MAVEN_PROJECTBASEDIR=%MAVEN_BASEDIR%
+IF NOT "%MAVEN_PROJECTBASEDIR%"=="" goto endDetectBaseDir
+
+set EXEC_DIR=%CD%
+set WDIR=%EXEC_DIR%
+:findBaseDir
+IF EXIST "%WDIR%"\.mvn goto baseDirFound
+cd ..
+IF "%WDIR%"=="%CD%" goto baseDirNotFound
+set WDIR=%CD%
+goto findBaseDir
+
+:baseDirFound
+set MAVEN_PROJECTBASEDIR=%WDIR%
+cd "%EXEC_DIR%"
+goto endDetectBaseDir
+
+:baseDirNotFound
+set MAVEN_PROJECTBASEDIR=%EXEC_DIR%
+cd "%EXEC_DIR%"
+
+:endDetectBaseDir
+
+IF NOT EXIST "%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config" goto endReadAdditionalConfig
+
+@setlocal EnableExtensions EnableDelayedExpansion
+for /F "usebackq delims=" %%a in ("%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config") do set JVM_CONFIG_MAVEN_PROPS=!JVM_CONFIG_MAVEN_PROPS! %%a
+@endlocal & set JVM_CONFIG_MAVEN_PROPS=%JVM_CONFIG_MAVEN_PROPS%
+
+:endReadAdditionalConfig
+
+SET MAVEN_JAVA_EXE="%JAVA_HOME%\bin\java.exe"
+set WRAPPER_JAR="%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.jar"
+set WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
+
+set WRAPPER_URL="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar"
+
+FOR /F "usebackq tokens=1,2 delims==" %%A IN ("%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties") DO (
+ IF "%%A"=="wrapperUrl" SET WRAPPER_URL=%%B
+)
+
+@REM Extension to allow automatically downloading the maven-wrapper.jar from Maven-central
+@REM This allows using the maven wrapper in projects that prohibit checking in binary data.
+if exist %WRAPPER_JAR% (
+ if "%MVNW_VERBOSE%" == "true" (
+ echo Found %WRAPPER_JAR%
+ )
+) else (
+ if not "%MVNW_REPOURL%" == "" (
+ SET WRAPPER_URL="%MVNW_REPOURL%/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar"
+ )
+ if "%MVNW_VERBOSE%" == "true" (
+ echo Couldn't find %WRAPPER_JAR%, downloading it ...
+ echo Downloading from: %WRAPPER_URL%
+ )
+
+ powershell -Command "&{"^
+ "$webclient = new-object System.Net.WebClient;"^
+ "if (-not ([string]::IsNullOrEmpty('%MVNW_USERNAME%') -and [string]::IsNullOrEmpty('%MVNW_PASSWORD%'))) {"^
+ "$webclient.Credentials = new-object System.Net.NetworkCredential('%MVNW_USERNAME%', '%MVNW_PASSWORD%');"^
+ "}"^
+ "[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12; $webclient.DownloadFile('%WRAPPER_URL%', '%WRAPPER_JAR%')"^
+ "}"
+ if "%MVNW_VERBOSE%" == "true" (
+ echo Finished downloading %WRAPPER_JAR%
+ )
+)
+@REM End of extension
+
+@REM Provide a "standardized" way to retrieve the CLI args that will
+@REM work with both Windows and non-Windows executions.
+set MAVEN_CMD_LINE_ARGS=%*
+
+%MAVEN_JAVA_EXE% ^
+ %JVM_CONFIG_MAVEN_PROPS% ^
+ %MAVEN_OPTS% ^
+ %MAVEN_DEBUG_OPTS% ^
+ -classpath %WRAPPER_JAR% ^
+ "-Dmaven.multiModuleProjectDirectory=%MAVEN_PROJECTBASEDIR%" ^
+ %WRAPPER_LAUNCHER% %MAVEN_CONFIG% %*
+if ERRORLEVEL 1 goto error
+goto end
+
+:error
+set ERROR_CODE=1
+
+:end
+@endlocal & set ERROR_CODE=%ERROR_CODE%
+
+if not "%MAVEN_SKIP_RC%"=="" goto skipRcPost
+@REM check for post script, once with legacy .bat ending and once with .cmd ending
+if exist "%USERPROFILE%\mavenrc_post.bat" call "%USERPROFILE%\mavenrc_post.bat"
+if exist "%USERPROFILE%\mavenrc_post.cmd" call "%USERPROFILE%\mavenrc_post.cmd"
+:skipRcPost
+
+@REM pause the script if MAVEN_BATCH_PAUSE is set to 'on'
+if "%MAVEN_BATCH_PAUSE%"=="on" pause
+
+if "%MAVEN_TERMINATE_CMD%"=="on" exit %ERROR_CODE%
+
+cmd /C exit /B %ERROR_CODE%
diff --git a/package-lock.json b/package-lock.json
new file mode 100644
index 0000000..dc43bd3
--- /dev/null
+++ b/package-lock.json
@@ -0,0 +1,4423 @@
+{
+ "name": "perun-ga4gh-broker",
+ "requires": true,
+ "lockfileVersion": 1,
+ "dependencies": {
+ "@babel/code-frame": {
+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz",
+ "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==",
+ "dev": true,
+ "requires": {
+ "@babel/highlight": "^7.18.6"
+ }
+ },
+ "@babel/helper-validator-identifier": {
+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.18.6.tgz",
+ "integrity": "sha512-MmetCkz9ej86nJQV+sFCxoGGrUbU3q02kgLciwkrt9QqEB7cP39oKEY0PakknEO0Gu20SskMRi+AYZ3b1TpN9g==",
+ "dev": true
+ },
+ "@babel/highlight": {
+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.18.6.tgz",
+ "integrity": "sha512-u7stbOuYjaPezCuLj29hNW1v64M2Md2qupEKP1fHc7WdOA3DgLh37suiSrZYY7haUB7iBeQZ9P1uiRF359do3g==",
+ "dev": true,
+ "requires": {
+ "@babel/helper-validator-identifier": "^7.18.6",
+ "chalk": "^2.0.0",
+ "js-tokens": "^4.0.0"
+ }
+ },
+ "@colors/colors": {
+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/@colors/colors/-/colors-1.5.0.tgz",
+ "integrity": "sha512-ooWCrlZP11i8GImSjTHYHLkvFDP48nS4+204nGb1RiX/WXYHmJA2III9/e2DWVabCESdW7hBAEzHRqUn9OUVvQ==",
+ "dev": true,
+ "optional": true
+ },
+ "@nodelib/fs.scandir": {
+ "version": "2.1.5",
+ "resolved": "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.5.tgz",
+ "integrity": "sha512-vq24Bq3ym5HEQm2NKCr3yXDwjc7vTsEThRDnkp2DK9p1uqLR+DHurm/NOTo0KG7HYHU7eppKZj3MyqYuMBf62g==",
+ "dev": true,
+ "requires": {
+ "@nodelib/fs.stat": "2.0.5",
+ "run-parallel": "^1.1.9"
+ }
+ },
+ "@nodelib/fs.stat": {
+ "version": "2.0.5",
+ "resolved": "https://registry.npmjs.org/@nodelib/fs.stat/-/fs.stat-2.0.5.tgz",
+ "integrity": "sha512-RkhPPp2zrqDAQA/2jNhnztcPAlv64XdhIp7a7454A5ovI7Bukxgt7MX7udwAu3zg1DcpPU0rz3VV1SeaqvY4+A==",
+ "dev": true
+ },
+ "@nodelib/fs.walk": {
+ "version": "1.2.8",
+ "resolved": "https://registry.npmjs.org/@nodelib/fs.walk/-/fs.walk-1.2.8.tgz",
+ "integrity": "sha512-oGB+UxlgWcgQkgwo8GcEGwemoTFt3FIO9ababBmaGwXIoBKZ+GTy0pP185beGg7Llih/NSHSV2XAs1lnznocSg==",
+ "dev": true,
+ "requires": {
+ "@nodelib/fs.scandir": "2.1.5",
+ "fastq": "^1.6.0"
+ }
+ },
+ "@octokit/auth-token": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/@octokit/auth-token/-/auth-token-3.0.0.tgz",
+ "integrity": "sha512-MDNFUBcJIptB9At7HiV7VCvU3NcL4GnfCQaP8C5lrxWrRPMJBnemYtehaKSOlaM7AYxeRyj9etenu8LVpSpVaQ==",
+ "dev": true,
+ "requires": {
+ "@octokit/types": "^6.0.3"
+ }
+ },
+ "@octokit/core": {
+ "version": "4.0.4",
+ "resolved": "https://registry.npmjs.org/@octokit/core/-/core-4.0.4.tgz",
+ "integrity": "sha512-sUpR/hc4Gc7K34o60bWC7WUH6Q7T6ftZ2dUmepSyJr9PRF76/qqkWjE2SOEzCqLA5W83SaISymwKtxks+96hPQ==",
+ "dev": true,
+ "requires": {
+ "@octokit/auth-token": "^3.0.0",
+ "@octokit/graphql": "^5.0.0",
+ "@octokit/request": "^6.0.0",
+ "@octokit/request-error": "^3.0.0",
+ "@octokit/types": "^6.0.3",
+ "before-after-hook": "^2.2.0",
+ "universal-user-agent": "^6.0.0"
+ }
+ },
+ "@octokit/endpoint": {
+ "version": "7.0.0",
+ "resolved": "https://registry.npmjs.org/@octokit/endpoint/-/endpoint-7.0.0.tgz",
+ "integrity": "sha512-Kz/mIkOTjs9rV50hf/JK9pIDl4aGwAtT8pry6Rpy+hVXkAPhXanNQRxMoq6AeRgDCZR6t/A1zKniY2V1YhrzlQ==",
+ "dev": true,
+ "requires": {
+ "@octokit/types": "^6.0.3",
+ "is-plain-object": "^5.0.0",
+ "universal-user-agent": "^6.0.0"
+ }
+ },
+ "@octokit/graphql": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/@octokit/graphql/-/graphql-5.0.0.tgz",
+ "integrity": "sha512-1ZZ8tX4lUEcLPvHagfIVu5S2xpHYXAmgN0+95eAOPoaVPzCfUXJtA5vASafcpWcO86ze0Pzn30TAx72aB2aguQ==",
+ "dev": true,
+ "requires": {
+ "@octokit/request": "^6.0.0",
+ "@octokit/types": "^6.0.3",
+ "universal-user-agent": "^6.0.0"
+ }
+ },
+ "@octokit/openapi-types": {
+ "version": "12.10.1",
+ "resolved": "https://registry.npmjs.org/@octokit/openapi-types/-/openapi-types-12.10.1.tgz",
+ "integrity": "sha512-P+SukKanjFY0ZhsK6wSVnQmxTP2eVPPE8OPSNuxaMYtgVzwJZgfGdwlYjf4RlRU4vLEw4ts2fsE2icG4nZ5ddQ==",
+ "dev": true
+ },
+ "@octokit/plugin-paginate-rest": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/@octokit/plugin-paginate-rest/-/plugin-paginate-rest-3.0.0.tgz",
+ "integrity": "sha512-fvw0Q5IXnn60D32sKeLIxgXCEZ7BTSAjJd8cFAE6QU5qUp0xo7LjFUjjX1J5D7HgN355CN4EXE4+Q1/96JaNUA==",
+ "dev": true,
+ "requires": {
+ "@octokit/types": "^6.39.0"
+ }
+ },
+ "@octokit/plugin-request-log": {
+ "version": "1.0.4",
+ "resolved": "https://registry.npmjs.org/@octokit/plugin-request-log/-/plugin-request-log-1.0.4.tgz",
+ "integrity": "sha512-mLUsMkgP7K/cnFEw07kWqXGF5LKrOkD+lhCrKvPHXWDywAwuDUeDwWBpc69XK3pNX0uKiVt8g5z96PJ6z9xCFA==",
+ "dev": true
+ },
+ "@octokit/plugin-rest-endpoint-methods": {
+ "version": "6.1.2",
+ "resolved": "https://registry.npmjs.org/@octokit/plugin-rest-endpoint-methods/-/plugin-rest-endpoint-methods-6.1.2.tgz",
+ "integrity": "sha512-sAfSKtLHNq0UQ2iFuI41I6m5SK6bnKFRJ5kUjDRVbmQXiRVi4aQiIcgG4cM7bt+bhSiWL4HwnTxDkWFlKeKClA==",
+ "dev": true,
+ "requires": {
+ "@octokit/types": "^6.40.0",
+ "deprecation": "^2.3.1"
+ }
+ },
+ "@octokit/request": {
+ "version": "6.2.0",
+ "resolved": "https://registry.npmjs.org/@octokit/request/-/request-6.2.0.tgz",
+ "integrity": "sha512-7IAmHnaezZrgUqtRShMlByJK33MT9ZDnMRgZjnRrRV9a/jzzFwKGz0vxhFU6i7VMLraYcQ1qmcAOin37Kryq+Q==",
+ "dev": true,
+ "requires": {
+ "@octokit/endpoint": "^7.0.0",
+ "@octokit/request-error": "^3.0.0",
+ "@octokit/types": "^6.16.1",
+ "is-plain-object": "^5.0.0",
+ "node-fetch": "^2.6.7",
+ "universal-user-agent": "^6.0.0"
+ }
+ },
+ "@octokit/request-error": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/@octokit/request-error/-/request-error-3.0.0.tgz",
+ "integrity": "sha512-WBtpzm9lR8z4IHIMtOqr6XwfkGvMOOILNLxsWvDwtzm/n7f5AWuqJTXQXdDtOvPfTDrH4TPhEvW2qMlR4JFA2w==",
+ "dev": true,
+ "requires": {
+ "@octokit/types": "^6.0.3",
+ "deprecation": "^2.0.0",
+ "once": "^1.4.0"
+ }
+ },
+ "@octokit/rest": {
+ "version": "19.0.3",
+ "resolved": "https://registry.npmjs.org/@octokit/rest/-/rest-19.0.3.tgz",
+ "integrity": "sha512-5arkTsnnRT7/sbI4fqgSJ35KiFaN7zQm0uQiQtivNQLI8RQx8EHwJCajcTUwmaCMNDg7tdCvqAnc7uvHHPxrtQ==",
+ "dev": true,
+ "requires": {
+ "@octokit/core": "^4.0.0",
+ "@octokit/plugin-paginate-rest": "^3.0.0",
+ "@octokit/plugin-request-log": "^1.0.4",
+ "@octokit/plugin-rest-endpoint-methods": "^6.0.0"
+ }
+ },
+ "@octokit/types": {
+ "version": "6.40.0",
+ "resolved": "https://registry.npmjs.org/@octokit/types/-/types-6.40.0.tgz",
+ "integrity": "sha512-MFZOU5r8SwgJWDMhrLUSvyJPtVsqA6VnbVI3TNbsmw+Jnvrktzvq2fYES/6RiJA/5Ykdwq4mJmtlYUfW7CGjmw==",
+ "dev": true,
+ "requires": {
+ "@octokit/openapi-types": "^12.10.0"
+ }
+ },
+ "@semantic-release/changelog": {
+ "version": "6.0.1",
+ "resolved": "https://registry.npmjs.org/@semantic-release/changelog/-/changelog-6.0.1.tgz",
+ "integrity": "sha512-FT+tAGdWHr0RCM3EpWegWnvXJ05LQtBkQUaQRIExONoXjVjLuOILNm4DEKNaV+GAQyJjbLRVs57ti//GypH6PA==",
+ "dev": true,
+ "requires": {
+ "@semantic-release/error": "^3.0.0",
+ "aggregate-error": "^3.0.0",
+ "fs-extra": "^9.0.0",
+ "lodash": "^4.17.4"
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+ "dev": true
+ },
+ "util-deprecate": {
+ "version": "1.0.2",
+ "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
+ "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==",
+ "dev": true
+ },
+ "validate-npm-package-license": {
+ "version": "3.0.4",
+ "resolved": "https://registry.npmjs.org/validate-npm-package-license/-/validate-npm-package-license-3.0.4.tgz",
+ "integrity": "sha512-DpKm2Ui/xN7/HQKCtpZxoRWBhZ9Z0kqtygG8XCgNQ8ZlDnxuQmWhj566j8fN4Cu3/JmbhsDo7fcAJq4s9h27Ew==",
+ "dev": true,
+ "requires": {
+ "spdx-correct": "^3.0.0",
+ "spdx-expression-parse": "^3.0.0"
+ }
+ },
+ "webidl-conversions": {
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
+ "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ==",
+ "dev": true
+ },
+ "whatwg-url": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
+ "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
+ "dev": true,
+ "requires": {
+ "tr46": "~0.0.3",
+ "webidl-conversions": "^3.0.0"
+ }
+ },
+ "which": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
+ "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
+ "dev": true,
+ "requires": {
+ "isexe": "^2.0.0"
+ }
+ },
+ "wordwrap": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-1.0.0.tgz",
+ "integrity": "sha512-gvVzJFlPycKc5dZN4yPkP8w7Dc37BtP1yczEneOb4uq34pXZcvrtRTmWV8W+Ume+XCxKgbjM+nevkyFPMybd4Q==",
+ "dev": true
+ },
+ "wrap-ansi": {
+ "version": "7.0.0",
+ "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
+ "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
+ "dev": true,
+ "requires": {
+ "ansi-styles": "^4.0.0",
+ "string-width": "^4.1.0",
+ "strip-ansi": "^6.0.0"
+ },
+ "dependencies": {
+ "ansi-styles": {
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
+ "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
+ "dev": true,
+ "requires": {
+ "color-convert": "^2.0.1"
+ }
+ },
+ "color-convert": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
+ "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
+ "dev": true,
+ "requires": {
+ "color-name": "~1.1.4"
+ }
+ },
+ "color-name": {
+ "version": "1.1.4",
+ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
+ "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
+ "dev": true
+ }
+ }
+ },
+ "wrappy": {
+ "version": "1.0.2",
+ "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
+ "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==",
+ "dev": true
+ },
+ "xtend": {
+ "version": "4.0.2",
+ "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
+ "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==",
+ "dev": true
+ },
+ "y18n": {
+ "version": "5.0.8",
+ "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz",
+ "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==",
+ "dev": true
+ },
+ "yallist": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
+ "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
+ "dev": true
+ },
+ "yaml": {
+ "version": "1.10.2",
+ "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.2.tgz",
+ "integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==",
+ "dev": true
+ },
+ "yargs": {
+ "version": "16.2.0",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz",
+ "integrity": "sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw==",
+ "dev": true,
+ "requires": {
+ "cliui": "^7.0.2",
+ "escalade": "^3.1.1",
+ "get-caller-file": "^2.0.5",
+ "require-directory": "^2.1.1",
+ "string-width": "^4.2.0",
+ "y18n": "^5.0.5",
+ "yargs-parser": "^20.2.2"
+ }
+ },
+ "yargs-parser": {
+ "version": "20.2.9",
+ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz",
+ "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==",
+ "dev": true
+ }
+ }
+}
diff --git a/package.json b/package.json
new file mode 100644
index 0000000..37434d5
--- /dev/null
+++ b/package.json
@@ -0,0 +1,10 @@
+{
+ "name": "perun-ga4gh-broker",
+ "private": true,
+ "devDependencies": {
+ "@semantic-release/changelog": "6.0.1",
+ "@semantic-release/git": "10.0.1",
+ "@semantic-release/exec": "6.0.3",
+ "semantic-release": "19.0.3"
+ }
+}
diff --git a/pom.xml b/pom.xml
index afebcd7..4544eee 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,24 +4,32 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
- <groupId>org.example</groupId>
- <artifactId>Perun-GA4GH</artifactId>
- <version>1.0-SNAPSHOT</version>
-
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
- <version>2.4.0</version>
+ <version>2.7.2</version>
<relativePath />
</parent>
+ <groupId>cz.muni.ics</groupId>
+ <artifactId>Perun-GA4GH</artifactId>
+ <version>1.0.0</version>
+
+ <name>perun-ga4gh-broker</name>
+ <description>GA4GH broker</description>
+ <packaging>war</packaging>
+
<properties>
- <java.version>16</java.version>
- <maven.compiler.source>16</maven.compiler.source>
- <maven.compiler.target>16</maven.compiler.target>
+ <java.version>11</java.version>
+ <maven.compiler.source>${java.version}</maven.compiler.source>
+ <maven.compiler.target>${java.version}</maven.compiler.target>
<version.springfox>3.0.0</version.springfox>
<version.swagger>3.0.0</version.swagger>
+ <version.apache-directory-api>2.1.0</version.apache-directory-api>
+ <version.nimbus-jose-jwt>9.23</version.nimbus-jose-jwt>
+ <version.guava>31.1-jre</version.guava>
+ <version.bouncy-castle>1.70</version.bouncy-castle>
</properties>
<dependencies>
@@ -30,17 +38,22 @@
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-core</artifactId>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-configuration-processor</artifactId>
+ <optional>true</optional>
+ </dependency>
+ <dependency>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-oauth2-client</artifactId>
</dependency>
<dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-context</artifactId>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-configuration-processor</artifactId>
- <optional>true</optional>
+ <artifactId>spring-boot-starter-tomcat</artifactId>
+ <scope>provided</scope>
</dependency>
<dependency>
@@ -59,9 +72,39 @@
<artifactId>springfox-swagger-ui</artifactId>
<version>${version.swagger}</version>
</dependency>
+
+ <dependency>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.directory.api</groupId>
+ <artifactId>api-all</artifactId>
+ <version>${version.apache-directory-api}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bouncycastle</groupId>
+ <artifactId>bcpkix-jdk15on</artifactId>
+ <version>${version.bouncy-castle}</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.bouncycastle</groupId>
+ <artifactId>bcprov-jdk15on</artifactId>
+ <version>${version.bouncy-castle}</version>
+ <scope>compile</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ <version>${version.guava}</version>
+ </dependency>
</dependencies>
<build>
+ <finalName>perun-ga4gh-broker</finalName>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
@@ -78,4 +121,4 @@
</plugins>
</build>
-</project>
\ No newline at end of file
+</project>
diff --git a/renovate.json b/renovate.json
new file mode 100644
index 0000000..820b73b
--- /dev/null
+++ b/renovate.json
@@ -0,0 +1,17 @@
+{
+ "extends": [
+ "config:base",
+ ":automergeBranch",
+ ":automergeLinters",
+ ":automergeTesters",
+ ":enableVulnerabilityAlertsWithLabel(security)",
+ ":maintainLockFilesWeekly",
+ ":pinOnlyDevDependencies",
+ ":prNotPending",
+ ":rebaseStalePrs",
+ ":semanticCommits",
+ "npm:unpublishSafe"
+ ],
+ "stabilityDays": 3,
+ "transitiveRemediation": true
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/Application.java b/src/main/java/cz/muni/ics/ga4gh/Application.java
index 8627f5e..efc5f3c 100644
--- a/src/main/java/cz/muni/ics/ga4gh/Application.java
+++ b/src/main/java/cz/muni/ics/ga4gh/Application.java
@@ -2,9 +2,10 @@ package cz.muni.ics.ga4gh;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
@SpringBootApplication
-public class Application {
+public class Application extends SpringBootServletInitializer {
public static void main(String[] args) {
SpringApplication.run(Application.class, args);
diff --git a/src/main/java/cz/muni/ics/ga4gh/ApplicationContext.java b/src/main/java/cz/muni/ics/ga4gh/ApplicationContext.java
new file mode 100644
index 0000000..13e6043
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/ApplicationContext.java
@@ -0,0 +1,44 @@
+package cz.muni.ics.ga4gh;
+
+import cz.muni.ics.ga4gh.config.BrokerConfig;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.core.io.FileUrlResource;
+import org.springframework.core.io.Resource;
+import org.springframework.security.crypto.bcrypt.BCryptPasswordEncoder;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import springfox.documentation.builders.PathSelectors;
+import springfox.documentation.builders.RequestHandlerSelectors;
+import springfox.documentation.spi.DocumentationType;
+import springfox.documentation.spring.web.plugins.Docket;
+
+import java.net.MalformedURLException;
+
+@Configuration
+public class ApplicationContext {
+
+ private final String pathToJwkFile;
+
+ public ApplicationContext(BrokerConfig config) {
+ this.pathToJwkFile = config.getPathToJwkFile();
+ }
+
+ @Bean
+ public Docket api() {
+ return new Docket(DocumentationType.SWAGGER_2)
+ .select()
+ .apis(RequestHandlerSelectors.any())
+ .paths(PathSelectors.any())
+ .build();
+ }
+
+ @Bean
+ public PasswordEncoder passwordEncoder() {
+ return new BCryptPasswordEncoder();
+ }
+
+ @Bean
+ public Resource jwks() throws MalformedURLException {
+ return new FileUrlResource(pathToJwkFile);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapter.java b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapter.java
new file mode 100644
index 0000000..7358f9a
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapter.java
@@ -0,0 +1,39 @@
+package cz.muni.ics.ga4gh.adapters;
+
+import cz.muni.ics.ga4gh.adapters.impl.PerunAdapterLdap;
+import cz.muni.ics.ga4gh.adapters.impl.PerunAdapterRpc;
+import cz.muni.ics.ga4gh.config.AdapterConfig;
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.Objects;
+
+@Getter
+@Setter
+public abstract class PerunAdapter implements PerunAdapterMethods {
+
+ private final String RPC = "rpc";
+
+ private PerunAdapterMethods adapterPrimary;
+ private PerunAdapterMethods adapterFallback;
+
+ private PerunAdapterMethodsRpc adapterRpc;
+ private PerunAdapterMethodsLdap adapterLdap;
+
+ private boolean callFallback;
+
+ public PerunAdapter(AdapterConfig config, PerunAdapterRpc adapterRpc, PerunAdapterLdap adapterLdap) {
+ if (config.getAdapterPrimary() != null && config.getAdapterPrimary().equalsIgnoreCase(RPC)) {
+ this.adapterPrimary = adapterRpc;
+ this.adapterFallback = adapterLdap;
+ } else {
+ this.adapterPrimary = adapterLdap;
+ this.adapterFallback = adapterRpc;
+ }
+
+ this.adapterRpc = adapterRpc;
+ this.adapterLdap = adapterLdap;
+
+ this.callFallback = Objects.requireNonNullElse(config.getCallFallback(), false);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethods.java b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethods.java
new file mode 100644
index 0000000..85485da
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethods.java
@@ -0,0 +1,23 @@
+package cz.muni.ics.ga4gh.adapters;
+
+import cz.muni.ics.ga4gh.model.Affiliation;
+import cz.muni.ics.ga4gh.model.AttributeMapping;
+
+import java.util.List;
+import java.util.Set;
+
+public interface PerunAdapterMethods {
+
+ /**
+ * Fetch user based on his principal (extLogin and extSource) from Perun
+ *
+ * @return PerunUser with id of found user
+ */
+ Long getPreauthenticatedUserId(String extLogin, String extSourceName);
+
+ boolean isUserInGroup(Long userId, Long groupId);
+
+ List<Affiliation> getGroupAffiliations(Long userId, String groupAffiliationsAttr);
+
+ Set<Long> getUserIdsByAttributeValue(AttributeMapping attrName, String attrValue);
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsLdap.java b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsLdap.java
new file mode 100644
index 0000000..70c67cd
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsLdap.java
@@ -0,0 +1,4 @@
+package cz.muni.ics.ga4gh.adapters;
+
+public interface PerunAdapterMethodsLdap {
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsRpc.java b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsRpc.java
new file mode 100644
index 0000000..f2c4d5e
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/adapters/PerunAdapterMethodsRpc.java
@@ -0,0 +1,12 @@
+package cz.muni.ics.ga4gh.adapters;
+
+import cz.muni.ics.ga4gh.model.Affiliation;
+
+import java.util.List;
+
+public interface PerunAdapterMethodsRpc {
+
+ String getUserAttributeCreatedAt(Long userId, String attrName);
+
+ List<Affiliation> getUserExtSourcesAffiliations(Long userId, String affiliationsAttr, String orgUrlAttr);
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterImpl.java b/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterImpl.java
new file mode 100644
index 0000000..fd5553b
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterImpl.java
@@ -0,0 +1,72 @@
+package cz.muni.ics.ga4gh.adapters.impl;
+
+import cz.muni.ics.ga4gh.adapters.PerunAdapter;
+import cz.muni.ics.ga4gh.config.AdapterConfig;
+import cz.muni.ics.ga4gh.model.Affiliation;
+import cz.muni.ics.ga4gh.model.AttributeMapping;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.util.List;
+import java.util.Set;
+
+@Component
+public class PerunAdapterImpl extends PerunAdapter {
+
+ @Autowired
+ public PerunAdapterImpl(AdapterConfig config, PerunAdapterRpc adapterRpc, PerunAdapterLdap adapterLdap) {
+ super(config, adapterRpc, adapterLdap);
+ }
+
+ @Override
+ public Long getPreauthenticatedUserId(String extLogin, String extSourceName) {
+ try {
+ return this.getAdapterPrimary().getPreauthenticatedUserId(extLogin, extSourceName);
+ } catch (UnsupportedOperationException e) {
+ if (this.isCallFallback()) {
+ return this.getAdapterFallback().getPreauthenticatedUserId(extLogin, extSourceName);
+ } else {
+ throw e;
+ }
+ }
+ }
+
+ @Override
+ public boolean isUserInGroup(Long userId, Long groupId) {
+ try {
+ return this.getAdapterPrimary().isUserInGroup(userId, groupId);
+ } catch (UnsupportedOperationException e) {
+ if (this.isCallFallback()) {
+ return this.getAdapterFallback().isUserInGroup(userId, groupId);
+ } else {
+ throw e;
+ }
+ }
+ }
+
+ @Override
+ public List<Affiliation> getGroupAffiliations(Long userId, String groupAffiliationsAttr) {
+ try {
+ return this.getAdapterPrimary().getGroupAffiliations(userId, groupAffiliationsAttr);
+ } catch (UnsupportedOperationException e) {
+ if (this.isCallFallback()) {
+ return this.getAdapterFallback().getGroupAffiliations(userId, groupAffiliationsAttr);
+ } else {
+ throw e;
+ }
+ }
+ }
+
+ @Override
+ public Set<Long> getUserIdsByAttributeValue(AttributeMapping attrName, String attrValue) {
+ try {
+ return this.getAdapterPrimary().getUserIdsByAttributeValue(attrName, attrValue);
+ } catch (UnsupportedOperationException e) {
+ if (this.isCallFallback()) {
+ return this.getAdapterFallback().getUserIdsByAttributeValue(attrName, attrValue);
+ } else {
+ throw e;
+ }
+ }
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterLdap.java b/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterLdap.java
new file mode 100644
index 0000000..2c68d7e
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterLdap.java
@@ -0,0 +1,199 @@
+package cz.muni.ics.ga4gh.adapters.impl;
+
+import cz.muni.ics.ga4gh.adapters.PerunAdapterMethods;
+import cz.muni.ics.ga4gh.adapters.PerunAdapterMethodsLdap;
+import cz.muni.ics.ga4gh.config.AttributesConfig;
+import cz.muni.ics.ga4gh.connectors.PerunConnectorLdap;
+import cz.muni.ics.ga4gh.model.Affiliation;
+import cz.muni.ics.ga4gh.model.AttributeMapping;
+import org.apache.directory.api.ldap.model.entry.Attribute;
+import org.apache.directory.api.ldap.model.entry.Entry;
+import org.apache.directory.api.ldap.model.message.SearchScope;
+import org.apache.directory.ldap.client.api.search.FilterBuilder;
+import org.apache.directory.ldap.client.template.EntryMapper;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import org.springframework.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static org.apache.directory.ldap.client.api.search.FilterBuilder.and;
+import static org.apache.directory.ldap.client.api.search.FilterBuilder.equal;
+import static org.apache.directory.ldap.client.api.search.FilterBuilder.or;
+
+@Component
+public class PerunAdapterLdap implements PerunAdapterMethods, PerunAdapterMethodsLdap {
+
+ public static final String OBJECT_CLASS = "objectClass";
+ public static final String OU_PEOPLE = "ou=People";
+
+ public static final String PERUN_USER_ID = "perunUserId";
+ public static final String MEMBER_OF = "memberOf";
+
+ public static final String PERUN_GROUP = "perunGroup";
+ public static final String PERUN_USER = "perunUser";
+ public static final String PERUN_GROUP_ID = "perunGroupId";
+ public static final String UNIQUE_MEMBER = "uniqueMember";
+
+ public static final String PERUN_VO_ID = "perunVoId";
+ public static final String EDU_PERSON_PRINCIPAL_NAMES = "eduPersonPrincipalNames";
+
+ private final PerunConnectorLdap connectorLdap;
+ private final Map<String, AttributeMapping> attributeMappings;
+
+ @Autowired
+ PerunAdapterLdap(PerunConnectorLdap connectorLdap, AttributesConfig attributesConfig) {
+ this.connectorLdap = connectorLdap;
+ this.attributeMappings = attributesConfig.getAttributeMappings();
+ }
+
+ @Override
+ public Long getPreauthenticatedUserId(String extLogin, String extSourceName) {
+ FilterBuilder filter = and(
+ equal(OBJECT_CLASS, PERUN_USER), equal(EDU_PERSON_PRINCIPAL_NAMES, extLogin)
+ );
+
+ return getPerunUserId(filter);
+ }
+
+ @Override
+ public boolean isUserInGroup(Long userId, Long groupId) {
+ String uniqueMemberValue = PERUN_USER_ID + '=' + userId + ',' + OU_PEOPLE + ',' + connectorLdap.getBaseDN();
+
+ FilterBuilder filter = and(
+ equal(OBJECT_CLASS, PERUN_GROUP),
+ equal(PERUN_GROUP_ID, String.valueOf(groupId)),
+ equal(UNIQUE_MEMBER, uniqueMemberValue)
+ );
+
+ EntryMapper<Long> mapper = e -> Long.parseLong(e.get(PERUN_GROUP_ID).getString());
+ String[] attributes = new String[] { PERUN_GROUP_ID };
+ List<Long> ids = connectorLdap.search(null, filter, SearchScope.SUBTREE, attributes, mapper);
+
+ return ids.stream().filter(groupId::equals).count() == 1L;
+ }
+
+ @Override
+ public List<Affiliation> getGroupAffiliations(Long userId, String groupAffiliationsAttr) {
+ Set<Long> userGroupIds = getGroupIdsWhereUserIsMember(userId, null);
+ if (userGroupIds.isEmpty()) {
+ return new ArrayList<>();
+ }
+
+ FilterBuilder[] groupIdFilters = new FilterBuilder[userGroupIds.size()];
+ int i = 0;
+
+ for (Long id: userGroupIds) {
+ groupIdFilters[i++] = equal(PERUN_GROUP_ID, String.valueOf(id));
+ }
+
+ AttributeMapping affiliationsMapping = attributeMappings.get(groupAffiliationsAttr);
+ FilterBuilder filterBuilder = and(equal(OBJECT_CLASS, PERUN_GROUP), or(groupIdFilters));
+ String[] attributes = new String[] { affiliationsMapping.getLdapName() };
+
+ EntryMapper<Set<Affiliation>> mapper = e -> {
+ Set<Affiliation> affiliations = new HashSet<>();
+ if (!checkHasAttributes(e, attributes)) {
+ return affiliations;
+ }
+
+ Attribute a = e.get(affiliationsMapping.getLdapName());
+ long linuxTime = System.currentTimeMillis() / 1000L;
+ a.iterator().forEachRemaining(v -> affiliations.add(new Affiliation(null, v.getString(), linuxTime)));
+
+ return affiliations;
+ };
+
+ List<Set<Affiliation>> affiliationSets = connectorLdap.search(null, filterBuilder, SearchScope.SUBTREE, attributes, mapper);
+
+ return affiliationSets.stream().flatMap(Set::stream).distinct().collect(Collectors.toList());
+ }
+
+ @Override
+ public Set<Long> getUserIdsByAttributeValue(AttributeMapping attrName, String attrValue) {
+ if (!StringUtils.hasText(attrName.getLdapName())) {
+ return new HashSet<>();
+ }
+
+ FilterBuilder filter = and(
+ equal(OBJECT_CLASS, PERUN_USER),
+ equal(attrName.getLdapName(), attrValue)
+ );
+
+ SearchScope scope = SearchScope.ONELEVEL;
+ String[] attributes = new String[]{PERUN_USER_ID};
+ EntryMapper<Long> mapper = e -> Long.parseLong(e.get(PERUN_USER_ID).getString());
+
+ List<Long> result = connectorLdap.search(OU_PEOPLE, filter, scope, attributes, mapper);
+
+ return Set.copyOf(result);
+ }
+
+ private Set<Long> getGroupIdsWhereUserIsMember(Long userId, Long voId) {
+ String dnPrefix = getDnPrefixForUserId(userId);
+ String[] attributes = new String[] { MEMBER_OF };
+
+ EntryMapper<Set<Long>> mapper = e -> {
+ Set<Long> ids = new HashSet<>();
+ if (checkHasAttributes(e, attributes)) {
+ Attribute a = e.get(MEMBER_OF);
+ a.iterator().forEachRemaining(id -> {
+ String fullVal = id.getString();
+ String[] parts = fullVal.split(",", 3);
+
+ String groupId = parts[0];
+ groupId = groupId.replace(PERUN_GROUP_ID + '=', "");
+
+ String voIdStr = parts[1];
+ voIdStr = voIdStr.replace(PERUN_VO_ID + '=', "");
+
+ if (voId == null || voId.equals(Long.parseLong(voIdStr))) {
+ ids.add(Long.parseLong(groupId));
+ }
+ });
+ }
+
+ return ids;
+ };
+
+ Set<Long> res = connectorLdap.lookup(dnPrefix, attributes, mapper);
+ if (res == null) {
+ res = new HashSet<>();
+ }
+
+ return res;
+ }
+
+ private String getDnPrefixForUserId(Long userId) {
+ return PERUN_USER_ID + '=' + userId + ',' + OU_PEOPLE;
+ }
+
+ private boolean checkHasAttributes(Entry e, String[] attributes) {
+ if (e == null) {
+ return false;
+ } else if (attributes == null) {
+ return true;
+ }
+
+ for (String attr: attributes) {
+ if (e.get(attr) == null) {
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ private Long getPerunUserId(FilterBuilder filter) {
+ SearchScope scope = SearchScope.ONELEVEL;
+ String[] attributes = new String[]{PERUN_USER_ID};
+ EntryMapper<Long> mapper = e -> Long.parseLong(e.get(PERUN_USER_ID).getString());
+
+ return connectorLdap.searchFirst(OU_PEOPLE, filter, scope, attributes, mapper);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterRpc.java b/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterRpc.java
new file mode 100644
index 0000000..7747579
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/adapters/impl/PerunAdapterRpc.java
@@ -0,0 +1,283 @@
+package cz.muni.ics.ga4gh.adapters.impl;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import cz.muni.ics.ga4gh.adapters.PerunAdapterMethods;
+import cz.muni.ics.ga4gh.adapters.PerunAdapterMethodsRpc;
+import cz.muni.ics.ga4gh.config.AttributesConfig;
+import cz.muni.ics.ga4gh.config.RpcConfig;
+import cz.muni.ics.ga4gh.connectors.PerunConnectorRpc;
+import cz.muni.ics.ga4gh.mappers.RpcMapper;
+import cz.muni.ics.ga4gh.model.Affiliation;
+import cz.muni.ics.ga4gh.model.AttributeMapping;
+import cz.muni.ics.ga4gh.model.Group;
+import cz.muni.ics.ga4gh.model.Member;
+import cz.muni.ics.ga4gh.model.PerunAttributeValue;
+import cz.muni.ics.ga4gh.model.UserExtSource;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import org.springframework.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static cz.muni.ics.ga4gh.enums.MemberStatus.VALID;
+
+@Component
+@Slf4j
+public class PerunAdapterRpc implements PerunAdapterMethods, PerunAdapterMethodsRpc {
+
+ public static final String EXT_LOGIN = "extLogin";
+ public static final String EXT_SOURCE_NAME = "extSourceName";
+ public static final String USER_EXT_SOURCE = "userExtSource";
+ public static final String ATTR_NAMES = "attrNames";
+ public static final String VALUE_CREATED_AT = "valueCreatedAt";
+
+ public static final String ID = "id";
+ public static final String VO = "vo";
+ public static final String USER = "user";
+ public static final String MEMBER = "member";
+ public static final String GROUP = "group";
+
+ public static final String ATTRIBUTE_NAME = "attributeName";
+ public static final String ATTRIBUTE_VALUE = "attributeValue";
+
+ public static final String ATTRIBUTES_MANAGER = "attributesManager";
+ public static final String GROUPS_MANAGER = "groupsManager";
+ public static final String MEMBERS_MANAGER = "membersManager";
+ public static final String USERS_MANAGER = "usersManager";
+
+ public static final String GET_USER_BY_EXT_SOURCE_NAME_AND_EXT_LOGIN = "getUserByExtSourceNameAndExtLogin";
+ public static final String GET_USER_EXT_SOURCES = "getUserExtSources";
+ public static final String GET_GROUP_BY_ID = "getGroupById";
+ public static final String GET_MEMBER_BY_USER = "getMemberByUser";
+ public static final String GET_MEMBERS_BY_USER = "getMembersByUser";
+ public static final String GET_MEMBER_GROUPS = "getMemberGroups";
+ public static final String IS_GROUP_MEMBER = "isGroupMember";
+ public static final String GET_ATTRIBUTE = "getAttribute";
+ public static final String GET_ATTRIBUTES = "getAttributes";
+ public static final String GET_USERS_BY_ATTRIBUTE_VALUE = "getUsersByAttributeValue";
+
+ private final PerunConnectorRpc connectorRpc;
+ private final Map<String, AttributeMapping> attributeMappings;
+
+ @Autowired
+ PerunAdapterRpc(PerunConnectorRpc connectorRpc, AttributesConfig attributesConfig) {
+ this.connectorRpc = connectorRpc;
+ this.attributeMappings = attributesConfig.getAttributeMappings();
+ }
+
+ @Override
+ public Long getPreauthenticatedUserId(String extLogin, String extSourceName) {
+ if (!connectorRpc.isEnabled()) {
+ return null;
+ }
+
+ Map<String, Object> map = new LinkedHashMap<>();
+ map.put(EXT_LOGIN, extLogin);
+ map.put(EXT_SOURCE_NAME, extSourceName);
+
+ JsonNode response = connectorRpc.post(USERS_MANAGER, GET_USER_BY_EXT_SOURCE_NAME_AND_EXT_LOGIN, map);
+
+ return response.get(ID) == null ? null : response.get(ID).asLong();
+ }
+
+ @Override
+ public boolean isUserInGroup(Long userId, Long groupId) {
+ if (!connectorRpc.isEnabled()) {
+ return false;
+ }
+
+ Map<String, Object> groupParams = new LinkedHashMap<>();
+ groupParams.put(ID, groupId);
+ JsonNode groupResponse = connectorRpc.post(GROUPS_MANAGER, GET_GROUP_BY_ID, groupParams);
+ Group group = RpcMapper.mapGroup(groupResponse);
+
+ Map<String, Object> memberParams = new LinkedHashMap<>();
+ memberParams.put(VO, group.getVoId());
+ memberParams.put(USER, userId);
+ JsonNode memberResponse = connectorRpc.post(MEMBERS_MANAGER, GET_MEMBER_BY_USER, memberParams);
+ Member member = RpcMapper.mapMember(memberResponse);
+
+ Map<String, Object> isGroupMemberParams = new LinkedHashMap<>();
+ isGroupMemberParams.put(GROUP, groupId);
+ isGroupMemberParams.put(MEMBER, member.getId());
+ JsonNode res = connectorRpc.post(GROUPS_MANAGER, IS_GROUP_MEMBER, isGroupMemberParams);
+
+ return res.asBoolean(false);
+ }
+
+ @Override
+ public List<Affiliation> getGroupAffiliations(Long userId, String groupAffiliationsAttr) {
+ if (!connectorRpc.isEnabled()) {
+ return new ArrayList<>();
+ }
+
+ List<Affiliation> affiliations = new ArrayList<>();
+ List<Member> userMembers = getMembersByUser(userId);
+
+ for (Member member : userMembers) {
+ if (VALID.equals(member.getStatus())) {
+ List<Group> memberGroups = getMemberGroups(member.getId());
+ for (Group group : memberGroups) {
+ PerunAttributeValue attrValue = this.getGroupAttributeValue(group, groupAffiliationsAttr);
+ if (attrValue != null && attrValue.valueAsList() != null) {
+ long linuxTime = System.currentTimeMillis() / 1000L;
+
+ for (String value : attrValue.valueAsList()) {
+ Affiliation affiliation = new Affiliation(null, value, linuxTime);
+ log.debug("found {} on group {}", value, group.getName());
+ affiliations.add(affiliation);
+ }
+ }
+ }
+ }
+ }
+
+ return affiliations;
+ }
+
+ @Override
+ public String getUserAttributeCreatedAt(Long userId, String attrName) {
+ if (!connectorRpc.isEnabled() || attributeMappings.get(attrName) == null) {
+ return null;
+ }
+
+ Map<String, Object> map = new LinkedHashMap<>();
+ map.put(USER, userId);
+ map.put(ATTRIBUTE_NAME, attributeMappings.get(attrName).getRpcName());
+
+ JsonNode res = connectorRpc.post(ATTRIBUTES_MANAGER, GET_ATTRIBUTE, map);
+
+ if (res == null || !res.hasNonNull(VALUE_CREATED_AT)) {
+ return null;
+ }
+
+ return res.get(VALUE_CREATED_AT).asText();
+ }
+
+ @Override
+ public List<Affiliation> getUserExtSourcesAffiliations(Long userId, String affiliationsAttr, String orgUrlAttr) {
+ if (!connectorRpc.isEnabled()) {
+ return new ArrayList<>();
+ }
+
+ List<UserExtSource> userExtSources = getUserExtSources(userId);
+ List<Affiliation> affiliations = new ArrayList<>();
+
+ Map<String, AttributeMapping> attrMappings = new HashMap<>();
+ attrMappings.put(affiliationsAttr, attributeMappings.get(affiliationsAttr));
+ attrMappings.put(orgUrlAttr, attributeMappings.get(orgUrlAttr));
+
+ for (UserExtSource ues : userExtSources) {
+ if ("cz.metacentrum.perun.core.impl.ExtSourceIdp".equals(ues.getExtSource().getType())) {
+ Map<String, PerunAttributeValue> uesAttrValues = getUserExtSourceAttributeValues(ues.getId(), attrMappings);
+
+ long asserted = ues.getLastAccess().getTime() / 1000L;
+
+ String orgUrl = uesAttrValues.get(affiliationsAttr).valueAsString();
+ String affs = uesAttrValues.get(orgUrlAttr).valueAsString();
+
+ if (affs != null) {
+ for (String aff : affs.split(";")) {
+ String source = ( (orgUrl != null) ? orgUrl : ues.getExtSource().getName() );
+ Affiliation affiliation = new Affiliation(source, aff, asserted);
+ log.debug("found {} from IdP {} with orgURL {} asserted at {}", aff, ues.getExtSource().getName(),
+ orgUrl, asserted);
+ affiliations.add(affiliation);
+ }
+ }
+ }
+ }
+
+ return affiliations;
+ }
+
+ @Override
+ public Set<Long> getUserIdsByAttributeValue(AttributeMapping attrName, String attrValue) {
+ if (!connectorRpc.isEnabled()) {
+ return new HashSet<>();
+ }
+
+ Set<Long> result = new HashSet<>();
+
+ if (!StringUtils.hasText(attrName.getRpcName())) {
+ return result;
+ }
+
+ Map<String, Object> map = new LinkedHashMap<>();
+ map.put(ATTRIBUTE_NAME, attrName.getRpcName());
+ map.put(ATTRIBUTE_VALUE, attrValue);
+
+ JsonNode res = connectorRpc.post(USERS_MANAGER, GET_USERS_BY_ATTRIBUTE_VALUE, map);
+
+ if (res != null) {
+ for (int i = 0; i < res.size(); i++) {
+ result.add(res.get(i).get(ID).asLong());
+ }
+ }
+
+ return result;
+ }
+
+ private List<Member> getMembersByUser(Long userId) {
+ if (!this.connectorRpc.isEnabled()) {
+ return new ArrayList<>();
+ }
+
+ Map<String, Object> params = new LinkedHashMap<>();
+ params.put(USER, userId);
+ JsonNode jsonNode = connectorRpc.post(MEMBERS_MANAGER, GET_MEMBERS_BY_USER, params);
+
+ return RpcMapper.mapMembers(jsonNode);
+ }
+
+ private List<Group> getMemberGroups(Long memberId) {
+ if (!this.connectorRpc.isEnabled()) {
+ return new ArrayList<>();
+ }
+
+ Map<String, Object> map = new LinkedHashMap<>();
+ map.put(MEMBER, memberId);
+
+ JsonNode response = connectorRpc.post(GROUPS_MANAGER, GET_MEMBER_GROUPS, map);
+ return RpcMapper.mapGroups(response);
+ }
+
+ private PerunAttributeValue getGroupAttributeValue(Group group, String attrToFetch) {
+ if (attributeMappings.get(attrToFetch) == null) {
+ return null;
+ }
+
+ Map<String, Object> map = new LinkedHashMap<>();
+ map.put(GROUP, group.getId());
+ map.put(ATTRIBUTE_NAME, attributeMappings.get(attrToFetch).getRpcName());
+ JsonNode res = connectorRpc.post(ATTRIBUTES_MANAGER, GET_ATTRIBUTE, map);
+
+ return RpcMapper.mapAttributeValue(res);
+ }
+
+ private List<UserExtSource> getUserExtSources(Long userId) {
+ Map<String, Object> map = new LinkedHashMap<>();
+ map.put(USER, userId);
+
+ JsonNode response = connectorRpc.post(USERS_MANAGER, GET_USER_EXT_SOURCES, map);
+ return RpcMapper.mapUserExtSources(response);
+ }
+
+ private Map<String, PerunAttributeValue> getUserExtSourceAttributeValues(Long uesId, Map<String, AttributeMapping> attrMappings) {
+ Map<String, Object> map = new LinkedHashMap<>();
+ map.put(USER_EXT_SOURCE, uesId);
+ map.put(ATTR_NAMES, attrMappings.values().stream().map(AttributeMapping::getRpcName).collect(Collectors.toList()));
+
+ JsonNode response = connectorRpc.post(ATTRIBUTES_MANAGER, GET_ATTRIBUTES, map);
+
+ return RpcMapper.mapAttributes(response, attrMappings);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/aop/LogTimes.java b/src/main/java/cz/muni/ics/ga4gh/aop/LogTimes.java
new file mode 100644
index 0000000..0e2e60b
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/aop/LogTimes.java
@@ -0,0 +1,11 @@
+package cz.muni.ics.ga4gh.aop;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+@Target(ElementType.METHOD)
+@Retention(RetentionPolicy.RUNTIME)
+public @interface LogTimes {
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/config/AdapterConfig.java b/src/main/java/cz/muni/ics/ga4gh/config/AdapterConfig.java
new file mode 100644
index 0000000..915582c
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/config/AdapterConfig.java
@@ -0,0 +1,19 @@
+package cz.muni.ics.ga4gh.config;
+
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@EnableConfigurationProperties
+@ConfigurationProperties(prefix = "adapter")
+@Getter
+@Setter
+public class AdapterConfig {
+
+ private String adapterPrimary;
+
+ private Boolean callFallback;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/config/AttributesConfig.java b/src/main/java/cz/muni/ics/ga4gh/config/AttributesConfig.java
new file mode 100644
index 0000000..469443e
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/config/AttributesConfig.java
@@ -0,0 +1,20 @@
+package cz.muni.ics.ga4gh.config;
+
+import cz.muni.ics.ga4gh.model.AttributeMapping;
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+import java.util.Map;
+
+@Configuration
+@EnableConfigurationProperties
+@ConfigurationProperties(prefix = "attributes")
+@Getter
+@Setter
+public class AttributesConfig {
+
+ private Map<String, AttributeMapping> attributeMappings;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/config/BasicAuthConfig.java b/src/main/java/cz/muni/ics/ga4gh/config/BasicAuthConfig.java
new file mode 100644
index 0000000..5436cdb
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/config/BasicAuthConfig.java
@@ -0,0 +1,19 @@
+package cz.muni.ics.ga4gh.config;
+
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@EnableConfigurationProperties
+@ConfigurationProperties(prefix = "basic-auth")
+@Getter
+@Setter
+public class BasicAuthConfig {
+
+ private String username;
+
+ private String password;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/config/BrokerConfig.java b/src/main/java/cz/muni/ics/ga4gh/config/BrokerConfig.java
new file mode 100644
index 0000000..ac59aaf
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/config/BrokerConfig.java
@@ -0,0 +1,37 @@
+package cz.muni.ics.ga4gh.config;
+
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+import java.util.List;
+
+@Configuration
+@EnableConfigurationProperties
+@ConfigurationProperties(prefix = "broker")
+@Getter
+@Setter
+public class BrokerConfig {
+
+ private String bonaFideStatusAttr;
+
+ private String bonaFideStatusRemsAttr;
+
+ private String groupAffiliationsAttr;
+
+ private Long termsAndPoliciesGroupId;
+
+ private String affiliationsAttr;
+
+ private String orgUrlAttr;
+
+ private List<String> attributesToSearch;
+
+ private String issuer;
+
+ private String jku;
+
+ private String pathToJwkFile;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/config/Ga4ghConfig.java b/src/main/java/cz/muni/ics/ga4gh/config/Ga4ghConfig.java
new file mode 100644
index 0000000..188a1de
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/config/Ga4ghConfig.java
@@ -0,0 +1,20 @@
+package cz.muni.ics.ga4gh.config;
+
+import cz.muni.ics.ga4gh.model.Repo;
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+import java.util.List;
+
+@Configuration
+@EnableConfigurationProperties
+@ConfigurationProperties(prefix = "ga4gh")
+@Getter
+@Setter
+public class Ga4ghConfig {
+
+ private List<Repo> repos;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/config/LdapConfig.java b/src/main/java/cz/muni/ics/ga4gh/config/LdapConfig.java
new file mode 100644
index 0000000..8a45101
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/config/LdapConfig.java
@@ -0,0 +1,33 @@
+package cz.muni.ics.ga4gh.config;
+
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@EnableConfigurationProperties
+@ConfigurationProperties(prefix = "ldap")
+@Getter
+@Setter
+public class LdapConfig {
+
+ private String host;
+
+ private String user;
+
+ private String password;
+
+ private String baseDn;
+
+ private Boolean useTls;
+
+ private Boolean useSsl;
+
+ private Boolean allowUntrustedSsl;
+
+ private Long timeoutSecs;
+
+ private int port;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/config/RpcConfig.java b/src/main/java/cz/muni/ics/ga4gh/config/RpcConfig.java
new file mode 100644
index 0000000..74f41d8
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/config/RpcConfig.java
@@ -0,0 +1,25 @@
+package cz.muni.ics.ga4gh.config;
+
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@EnableConfigurationProperties
+@ConfigurationProperties(prefix = "rpc")
+@Getter
+@Setter
+public class RpcConfig {
+
+ private Boolean enabled;
+
+ private String url;
+
+ private String username;
+
+ private String password;
+
+ private String serializer;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorLdap.java b/src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorLdap.java
new file mode 100644
index 0000000..5f4c66f
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorLdap.java
@@ -0,0 +1,154 @@
+package cz.muni.ics.ga4gh.connectors;
+
+import cz.muni.ics.ga4gh.aop.LogTimes;
+import cz.muni.ics.ga4gh.config.LdapConfig;
+import lombok.Getter;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.pool2.impl.GenericObjectPoolConfig;
+import org.apache.directory.api.ldap.model.message.SearchScope;
+import org.apache.directory.api.ldap.model.name.Dn;
+import org.apache.directory.ldap.client.api.DefaultLdapConnectionFactory;
+import org.apache.directory.ldap.client.api.DefaultPoolableLdapConnectionFactory;
+import org.apache.directory.ldap.client.api.LdapConnectionConfig;
+import org.apache.directory.ldap.client.api.LdapConnectionPool;
+import org.apache.directory.ldap.client.api.NoVerificationTrustManager;
+import org.apache.directory.ldap.client.api.search.FilterBuilder;
+import org.apache.directory.ldap.client.template.EntryMapper;
+import org.apache.directory.ldap.client.template.LdapConnectionTemplate;
+import org.springframework.beans.factory.DisposableBean;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Repository;
+import org.springframework.util.StringUtils;
+
+import java.util.List;
+import java.util.Objects;
+
+@Repository
+@Slf4j
+@Getter
+public class PerunConnectorLdap implements DisposableBean {
+
+ private final String baseDN;
+ private final LdapConnectionPool pool;
+ private final LdapConnectionTemplate ldap;
+
+ @Autowired
+ public PerunConnectorLdap(LdapConfig config) {
+ if (config.getHost() == null || config.getHost().trim().isEmpty()) {
+ throw new IllegalArgumentException("Host cannot be null or empty");
+ } else if (config.getBaseDn() == null || config.getBaseDn().trim().isEmpty()) {
+ throw new IllegalArgumentException("baseDN cannot be null or empty");
+ }
+
+ boolean useTLS = Objects.requireNonNullElse(config.getUseTls(), false);
+ boolean useSSL = Objects.requireNonNullElse(config.getUseSsl(), false);
+ boolean allowUntrustedSsl = Objects.requireNonNullElse(config.getAllowUntrustedSsl(), false);
+ long timeoutSecs = Objects.requireNonNullElse(config.getTimeoutSecs(), 5L);
+
+
+ this.baseDN = config.getBaseDn();
+
+ LdapConnectionConfig ldapConnectionConfig = getLdapConnectionConfig(config.getHost(), config.getPort(), useTLS, useSSL, allowUntrustedSsl);
+ if (config.getUser() != null && !config.getUser().isEmpty()) {
+ log.debug("setting ldap user to {}", config.getUser());
+ ldapConnectionConfig.setName(config.getUser());
+ }
+ if (config.getPassword() != null && !config.getPassword().isEmpty()) {
+ log.debug("setting ldap password");
+ ldapConnectionConfig.setCredentials(config.getPassword());
+ }
+ DefaultLdapConnectionFactory factory = new DefaultLdapConnectionFactory(ldapConnectionConfig);
+ factory.setTimeOut(timeoutSecs * 1000L);
+
+ GenericObjectPoolConfig poolConfig = new GenericObjectPoolConfig();
+ poolConfig.setTestOnBorrow(true);
+
+ pool = new LdapConnectionPool(new DefaultPoolableLdapConnectionFactory(factory), poolConfig);
+ ldap = new LdapConnectionTemplate(pool);
+ log.debug("initialized LDAP connector");
+ }
+
+ public String getBaseDN() {
+ return baseDN;
+ }
+
+ private LdapConnectionConfig getLdapConnectionConfig(String host, int port, boolean useTLS, boolean useSSL,
+ boolean allowUntrustedSsl) {
+ LdapConnectionConfig config = new LdapConnectionConfig();
+ config.setLdapHost(host);
+ config.setLdapPort(port);
+ config.setUseSsl(useSSL);
+ config.setUseTls(useTLS);
+ if (allowUntrustedSsl) {
+ config.setTrustManagers(new NoVerificationTrustManager());
+ }
+
+ return config;
+ }
+
+ @Override
+ public void destroy() {
+ if (!pool.isClosed()) {
+ pool.close();
+ }
+ }
+
+ /**
+ * Search for the first entry that satisfies criteria.
+ * @param dnPrefix Prefix to be added to the base DN. (i.e. ou=People) !DO NOT END WITH A COMMA!
+ * @param filter Filter for entries
+ * @param scope Search scope
+ * @param attributes Attributes to be fetch for entry
+ * @param entryMapper Mapper of entries to the target class T
+ * @param <T> Class that the result should be mapped to.
+ * @return Found entry mapped to target class
+ */
+ @LogTimes
+ public <T> T searchFirst(String dnPrefix, FilterBuilder filter, SearchScope scope, String[] attributes,
+ EntryMapper<T> entryMapper)
+ {
+ Dn fullDn = getFullDn(dnPrefix);
+ return ldap.searchFirst(fullDn, filter, scope, attributes, entryMapper);
+ }
+
+ /**
+ * Perform lookup for the entry that satisfies criteria.
+ * @param dnPrefix Prefix to be added to the base DN. (i.e. ou=People) !DO NOT END WITH A COMMA!
+ * @param attributes Attributes to be fetch for entry
+ * @param entryMapper Mapper of entries to the target class T
+ * @param <T> Class that the result should be mapped to.
+ * @return Found entry mapped to target class
+ */
+ @LogTimes
+ public <T> T lookup(String dnPrefix, String[] attributes, EntryMapper<T> entryMapper) {
+ Dn fullDn = getFullDn(dnPrefix);
+ return ldap.lookup(fullDn, attributes, entryMapper);
+ }
+
+ /**
+ * Search for the entries satisfy criteria.
+ * @param dnPrefix Prefix to be added to the base DN. (i.e. ou=People) !DO NOT END WITH A COMMA!
+ * @param filter Filter for entries
+ * @param scope Search scope
+ * @param attributes Attributes to be fetch for entry
+ * @param entryMapper Mapper of entries to the target class T
+ * @param <T> Class that the result should be mapped to.
+ * @return List of found entries mapped to target class
+ */
+ @LogTimes
+ public <T> List<T> search(String dnPrefix, FilterBuilder filter, SearchScope scope, String[] attributes,
+ EntryMapper<T> entryMapper)
+ {
+ Dn fullDn = getFullDn(dnPrefix);
+ return ldap.search(fullDn, filter, scope, attributes, entryMapper);
+ }
+
+ private Dn getFullDn(String prefix) {
+ String dn = baseDN;
+ if (StringUtils.hasText(prefix)) {
+ dn = prefix + "," + baseDN;
+ }
+
+ return ldap.newDn(dn);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorRpc.java b/src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorRpc.java
new file mode 100644
index 0000000..ecacbf7
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/connectors/PerunConnectorRpc.java
@@ -0,0 +1,188 @@
+package cz.muni.ics.ga4gh.connectors;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import cz.muni.ics.ga4gh.aop.LogTimes;
+import cz.muni.ics.ga4gh.config.RpcConfig;
+import lombok.Getter;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.http.HeaderElement;
+import org.apache.http.HeaderElementIterator;
+import org.apache.http.client.config.RequestConfig;
+import org.apache.http.conn.ConnectionKeepAliveStrategy;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.apache.http.message.BasicHeaderElementIterator;
+import org.apache.http.protocol.HTTP;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.http.client.ClientHttpRequestInterceptor;
+import org.springframework.http.client.HttpComponentsClientHttpRequestFactory;
+import org.springframework.http.client.InterceptingClientHttpRequestFactory;
+import org.springframework.http.client.support.BasicAuthorizationInterceptor;
+import org.springframework.stereotype.Repository;
+import org.springframework.util.StringUtils;
+import org.springframework.web.client.HttpClientErrorException;
+import org.springframework.web.client.RestTemplate;
+
+import javax.annotation.PostConstruct;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+@Repository
+@Slf4j
+@Getter
+public class PerunConnectorRpc {
+
+ public static final String ATTRIBUTES_MANAGER = "attributesManager";
+ public static final String FACILITIES_MANAGER = "facilitiesManager";
+ public static final String GROUPS_MANAGER = "groupsManager";
+ public static final String MEMBERS_MANAGER = "membersManager";
+ public static final String REGISTRAR_MANAGER = "registrarManager";
+ public static final String SEARCHER = "searcher";
+ public static final String USERS_MANAGER = "usersManager";
+ public static final String VOS_MANAGER = "vosManager";
+ public static final String RESOURCES_MANAGER = "resourcesManager";
+
+ private String perunUrl;
+ private String perunUser;
+ private String perunPassword;
+ private boolean isEnabled;
+ private String serializer;
+ private RestTemplate restTemplate;
+
+ @Autowired
+ public PerunConnectorRpc(RpcConfig config) {
+ this.setPerunUrl(config.getUrl());
+ this.setPerunUser(config.getUsername());
+ this.setPerunPassword(config.getPassword());
+ this.setEnabled(config.getEnabled());
+ this.setSerializer(config.getSerializer());
+ }
+
+ public void setPerunUrl(String perunUrl) {
+ if (!StringUtils.hasText(perunUrl)) {
+ throw new IllegalArgumentException("Perun URL cannot be null or empty");
+ } else if (perunUrl.endsWith("/")) {
+ perunUrl = perunUrl.substring(0, perunUrl.length() - 1);
+ }
+
+ this.perunUrl = perunUrl;
+ }
+
+ public void setPerunUser(String perunUser) {
+ if (!StringUtils.hasText(perunUser)) {
+ throw new IllegalArgumentException("Perun USER cannot be null or empty");
+ }
+
+ this.perunUser = perunUser;
+ }
+
+ public void setPerunPassword(String perunPassword) {
+ if (!StringUtils.hasText(perunPassword)) {
+ throw new IllegalArgumentException("Perun PASSWORD cannot be null or empty");
+ }
+
+ this.perunPassword = perunPassword;
+ }
+
+ public void setEnabled(Boolean enabled) {
+ this.isEnabled = Objects.requireNonNullElse(enabled, false);
+ }
+
+ public void setSerializer(String serializer) {
+ if (!StringUtils.hasText(serializer)) {
+ this.serializer = "json";
+ }
+
+ this.serializer = serializer;
+ }
+
+ @PostConstruct
+ public void postInit() {
+ restTemplate = new RestTemplate();
+ //HTTP connection pooling, see https://howtodoinjava.com/spring-restful/resttemplate-httpclient-java-config/
+ RequestConfig requestConfig = RequestConfig.custom()
+ .setConnectionRequestTimeout(30000) // The timeout when requesting a connection from the connection manager
+ .setConnectTimeout(30000) // Determines the timeout in milliseconds until a connection is established
+ .setSocketTimeout(60000) // The timeout for waiting for data
+ .build();
+
+ PoolingHttpClientConnectionManager poolingConnectionManager = new PoolingHttpClientConnectionManager();
+ poolingConnectionManager.setMaxTotal(20); // maximum connections total
+ poolingConnectionManager.setDefaultMaxPerRoute(18);
+
+ ConnectionKeepAliveStrategy connectionKeepAliveStrategy = (response, context) -> {
+ HeaderElementIterator it = new BasicHeaderElementIterator(response.headerIterator(HTTP.CONN_KEEP_ALIVE));
+
+ while (it.hasNext()) {
+ HeaderElement he = it.nextElement();
+ String param = he.getName();
+ String value = he.getValue();
+
+ if (value != null && param.equalsIgnoreCase("timeout")) {
+ return Long.parseLong(value) * 1000;
+ }
+ }
+
+ return 20000L;
+ };
+
+ CloseableHttpClient httpClient = HttpClients.custom()
+ .setDefaultRequestConfig(requestConfig)
+ .setConnectionManager(poolingConnectionManager)
+ .setKeepAliveStrategy(connectionKeepAliveStrategy)
+ .build();
+
+ HttpComponentsClientHttpRequestFactory poolingRequestFactory = new HttpComponentsClientHttpRequestFactory();
+ poolingRequestFactory.setHttpClient(httpClient);
+ //basic authentication
+ List<ClientHttpRequestInterceptor> interceptors =
+ Collections.singletonList(new BasicAuthorizationInterceptor(perunUser, perunPassword));
+ InterceptingClientHttpRequestFactory authenticatingRequestFactory = new InterceptingClientHttpRequestFactory(poolingRequestFactory, interceptors);
+ restTemplate.setRequestFactory(authenticatingRequestFactory);
+ }
+
+ /**
+ * Make post call to Perun RPC
+ * @param manager String value representing manager to be called. Use constants from this class.
+ * @param method Method to be called (i.e. getUserById)
+ * @param map Map of parameters to be passed as request body
+ * @return Response from Perun
+ */
+ @LogTimes
+ public JsonNode post(String manager, String method, Map<String, Object> map) {
+ if (!this.isEnabled) {
+ return JsonNodeFactory.instance.nullNode();
+ }
+
+ String actionUrl = perunUrl + '/' + serializer + '/' + manager + '/' + method;
+ //make the call
+ try {
+ log.debug("calling {} with {}", actionUrl, map);
+
+ return restTemplate.postForObject(actionUrl, map, JsonNode.class);
+ } catch (HttpClientErrorException ex) {
+ MediaType contentType = ex.getResponseHeaders().getContentType();
+ String body = ex.getResponseBodyAsString();
+ log.error("HTTP ERROR " + ex.getRawStatusCode() + " URL " + actionUrl + " Content-Type: " + contentType);
+
+ if ("json".equals(contentType.getSubtype())) {
+ try {
+ log.error(new ObjectMapper().readValue(body, JsonNode.class).path("message").asText());
+ } catch (IOException e) {
+ log.error("cannot parse error message from JSON", e);
+ }
+ } else {
+ log.error(ex.getMessage());
+ }
+
+ throw new RuntimeException("cannot connect to Perun RPC", ex);
+ }
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/controllers/Ga4ghBrokerController.java b/src/main/java/cz/muni/ics/ga4gh/controllers/Ga4ghBrokerController.java
new file mode 100644
index 0000000..c37ecf1
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/controllers/Ga4ghBrokerController.java
@@ -0,0 +1,35 @@
+package cz.muni.ics.ga4gh.controllers;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import cz.muni.ics.ga4gh.facade.Ga4ghBrokerFacade;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import javax.servlet.http.HttpServletResponse;
+
+@RestController
+@RequestMapping("/ga4gh")
+public class Ga4ghBrokerController {
+
+ private final Ga4ghBrokerFacade ga4GhBrokerFacade;
+
+ @Autowired
+ public Ga4ghBrokerController(Ga4ghBrokerFacade ga4GhBrokerFacade) {
+ this.ga4GhBrokerFacade = ga4GhBrokerFacade;
+ }
+
+ @GetMapping(value = "/{eppn}", produces = MediaType.APPLICATION_JSON_VALUE)
+ public ArrayNode getGa4ghPassport(@PathVariable String eppn, HttpServletResponse response) {
+ ArrayNode result = ga4GhBrokerFacade.getGa4ghPassport(eppn);
+
+ if (result == null) {
+ response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
+ }
+
+ return result;
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/controllers/JwkSetPublishingEndpoint.java b/src/main/java/cz/muni/ics/ga4gh/controllers/JwkSetPublishingEndpoint.java
new file mode 100644
index 0000000..90bd9c7
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/controllers/JwkSetPublishingEndpoint.java
@@ -0,0 +1,40 @@
+package cz.muni.ics.ga4gh.controllers;
+
+import com.nimbusds.jose.jwk.JWK;
+import com.nimbusds.jose.jwk.JWKSet;
+import cz.muni.ics.ga4gh.service.JWTSigningAndValidationService;
+import lombok.Getter;
+import lombok.Setter;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.util.ArrayList;
+import java.util.Map;
+
+@CrossOrigin(originPatterns = "*")
+@RestController
+@RequestMapping("/public")
+@Getter
+@Setter
+public class JwkSetPublishingEndpoint {
+
+ public static final String URL = "jwk";
+
+ private JWTSigningAndValidationService jwtService;
+
+ @Autowired
+ public JwkSetPublishingEndpoint(JWTSigningAndValidationService jwtService) {
+ this.jwtService = jwtService;
+ }
+
+ @RequestMapping(value = "/" + URL, produces = MediaType.APPLICATION_JSON_VALUE)
+ public String getJwk() {
+ // map from key id to key
+ Map<String, JWK> keys = jwtService.getAllPublicKeys();
+ JWKSet jwkSet = new JWKSet(new ArrayList<>(keys.values()));
+ return jwkSet.toString();
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/enums/MemberStatus.java b/src/main/java/cz/muni/ics/ga4gh/enums/MemberStatus.java
new file mode 100644
index 0000000..9794780
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/enums/MemberStatus.java
@@ -0,0 +1,31 @@
+package cz.muni.ics.ga4gh.enums;
+
+public enum MemberStatus {
+
+ VALID,
+ EXPIRED,
+ INVALID,
+ DISABLED,
+ SUSPENDED;
+
+ public static MemberStatus fromString(String status) {
+ if (status == null) {
+ return null;
+ }
+
+ switch (status.toUpperCase().trim()) {
+ case "VALID":
+ return VALID;
+ case "INVALID":
+ return INVALID;
+ case "EXPIRED":
+ return EXPIRED;
+ case "DISABLED":
+ return DISABLED;
+ case "SUSPENDED":
+ return SUSPENDED;
+ default:
+ return null;
+ }
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/exceptions/InconvertibleValueException.java b/src/main/java/cz/muni/ics/ga4gh/exceptions/InconvertibleValueException.java
new file mode 100644
index 0000000..5816702
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/exceptions/InconvertibleValueException.java
@@ -0,0 +1,24 @@
+package cz.muni.ics.ga4gh.exceptions;
+
+public class InconvertibleValueException extends RuntimeException {
+
+ public InconvertibleValueException() {
+ super();
+ }
+
+ public InconvertibleValueException(String s) {
+ super(s);
+ }
+
+ public InconvertibleValueException(String s, Throwable throwable) {
+ super(s, throwable);
+ }
+
+ public InconvertibleValueException(Throwable throwable) {
+ super(throwable);
+ }
+
+ protected InconvertibleValueException(String s, Throwable throwable, boolean b, boolean b1) {
+ super(s, throwable, b, b1);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/exceptions/MissingFieldException.java b/src/main/java/cz/muni/ics/ga4gh/exceptions/MissingFieldException.java
new file mode 100644
index 0000000..a889a9b
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/exceptions/MissingFieldException.java
@@ -0,0 +1,24 @@
+package cz.muni.ics.ga4gh.exceptions;
+
+public class MissingFieldException extends RuntimeException {
+
+ public MissingFieldException() {
+ super();
+ }
+
+ public MissingFieldException(String s) {
+ super(s);
+ }
+
+ public MissingFieldException(String s, Throwable throwable) {
+ super(s, throwable);
+ }
+
+ public MissingFieldException(Throwable throwable) {
+ super(throwable);
+ }
+
+ protected MissingFieldException(String s, Throwable throwable, boolean b, boolean b1) {
+ super(s, throwable, b, b1);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/exceptions/UserNotUniqueException.java b/src/main/java/cz/muni/ics/ga4gh/exceptions/UserNotUniqueException.java
new file mode 100644
index 0000000..dc3eee0
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/exceptions/UserNotUniqueException.java
@@ -0,0 +1,24 @@
+package cz.muni.ics.ga4gh.exceptions;
+
+public class UserNotUniqueException extends RuntimeException {
+
+ public UserNotUniqueException() {
+ super();
+ }
+
+ public UserNotUniqueException(String s) {
+ super(s);
+ }
+
+ public UserNotUniqueException(String s, Throwable throwable) {
+ super(s, throwable);
+ }
+
+ public UserNotUniqueException(Throwable throwable) {
+ super(throwable);
+ }
+
+ protected UserNotUniqueException(String s, Throwable throwable, boolean b, boolean b1) {
+ super(s, throwable, b, b1);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/facade/Ga4ghBrokerFacade.java b/src/main/java/cz/muni/ics/ga4gh/facade/Ga4ghBrokerFacade.java
new file mode 100644
index 0000000..2c4ebf4
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/facade/Ga4ghBrokerFacade.java
@@ -0,0 +1,8 @@
+package cz.muni.ics.ga4gh.facade;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+
+public interface Ga4ghBrokerFacade {
+
+ ArrayNode getGa4ghPassport(String eppn);
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/facade/impl/Ga4GhBrokerFacadeImpl.java b/src/main/java/cz/muni/ics/ga4gh/facade/impl/Ga4GhBrokerFacadeImpl.java
new file mode 100644
index 0000000..bf3ce54
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/facade/impl/Ga4GhBrokerFacadeImpl.java
@@ -0,0 +1,23 @@
+package cz.muni.ics.ga4gh.facade.impl;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import cz.muni.ics.ga4gh.facade.Ga4ghBrokerFacade;
+import cz.muni.ics.ga4gh.service.Ga4ghBrokerService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+@Service
+public class Ga4GhBrokerFacadeImpl implements Ga4ghBrokerFacade {
+
+ Ga4ghBrokerService ga4GhBrokerService;
+
+ @Autowired
+ public Ga4GhBrokerFacadeImpl(Ga4ghBrokerService ga4GhBrokerService) {
+ this.ga4GhBrokerService = ga4GhBrokerService;
+ }
+
+ @Override
+ public ArrayNode getGa4ghPassport(String eppn) {
+ return ga4GhBrokerService.getGa4ghPassport(eppn);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/jose/keystore/JWKSetKeyStore.java b/src/main/java/cz/muni/ics/ga4gh/jose/keystore/JWKSetKeyStore.java
new file mode 100644
index 0000000..0c03f88
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/jose/keystore/JWKSetKeyStore.java
@@ -0,0 +1,79 @@
+package cz.muni.ics.ga4gh.jose.keystore;
+
+import com.nimbusds.jose.jwk.JWK;
+import com.nimbusds.jose.jwk.JWKSet;
+import lombok.Getter;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.Resource;
+import org.springframework.stereotype.Component;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
+import java.text.ParseException;
+import java.util.List;
+import java.util.stream.Collectors;
+
+@Component
+@Getter
+public class JWKSetKeyStore {
+
+ private JWKSet jwkSet;
+ private Resource location;
+
+ @Autowired
+ public JWKSetKeyStore(Resource location) {
+ setLocation(location);
+ }
+
+ public JWKSetKeyStore(JWKSet jwkSet) {
+ this.setJwkSet(jwkSet);
+ initializeJwkSet();
+ }
+
+ public void setJwkSet(JWKSet jwkSet) {
+ if (jwkSet == null) {
+ throw new IllegalArgumentException("Argument cannot be null");
+ }
+
+ this.jwkSet = jwkSet;
+ initializeJwkSet();
+ }
+
+ public void setLocation(Resource location) {
+ this.location = location;
+ initializeJwkSet();
+ }
+
+ public List<JWK> getKeys() {
+ if (jwkSet == null) {
+ initializeJwkSet();
+ }
+
+ return jwkSet.getKeys();
+ }
+
+ private void initializeJwkSet() {
+ if (jwkSet != null) {
+ return;
+ } else if (location == null) {
+ return;
+ }
+
+ if (location.exists() && location.isReadable()) {
+ try (BufferedReader br = new BufferedReader(
+ new InputStreamReader(location.getInputStream(), StandardCharsets.UTF_8))
+ ) {
+ String s = br.lines().collect(Collectors.joining());
+ jwkSet = JWKSet.parse(s);
+ } catch (IOException e) {
+ throw new IllegalArgumentException("Key Set resource could not be read: " + location);
+ } catch (ParseException e) {
+ throw new IllegalArgumentException("Key Set resource could not be parsed: " + location);
+ }
+ } else {
+ throw new IllegalArgumentException("Key Set resource could not be read: " + location);
+ }
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/mappers/RpcMapper.java b/src/main/java/cz/muni/ics/ga4gh/mappers/RpcMapper.java
new file mode 100644
index 0000000..37254d6
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/mappers/RpcMapper.java
@@ -0,0 +1,277 @@
+package cz.muni.ics.ga4gh.mappers;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import cz.muni.ics.ga4gh.enums.MemberStatus;
+import cz.muni.ics.ga4gh.exceptions.MissingFieldException;
+import cz.muni.ics.ga4gh.model.AttributeMapping;
+import cz.muni.ics.ga4gh.model.ExtSource;
+import cz.muni.ics.ga4gh.model.Group;
+import cz.muni.ics.ga4gh.model.Member;
+import cz.muni.ics.ga4gh.model.PerunAttributeValue;
+import cz.muni.ics.ga4gh.model.UserExtSource;
+
+
+/**
+ * This class is mapping JsonNodes to object models.
+ *
+ * @author Dominik Frantisek Bucik <bucik@ics.muni.cz>
+ */
+public class RpcMapper {
+
+ public static final String ID = "id";
+ public static final String UUID = "uuid";
+ public static final String PARENT_GROUP_ID = "parentGroupId";
+ public static final String NAME = "name";
+ public static final String DESCRIPTION = "description";
+ public static final String VO_ID = "voId";
+ public static final String USER_ID = "userId";
+ public static final String STATUS = "status";
+ public static final String TYPE = "type";
+ public static final String LOGIN = "login";
+ public static final String EXT_SOURCE = "extSource";
+ public static final String LOA = "loa";
+ public static final String LAST_ACCESS = "lastAccess";
+ public static final String PERSISTENT = "persistent";
+ public static final String FRIENDLY_NAME = "friendlyName";
+ public static final String NAMESPACE = "namespace";
+ public static final String VALUE = "value";
+
+ /**
+ * Maps JsonNode to Group model.
+ *
+ * @param json Group in JSON format from Perun to be mapped.
+ * @return Mapped Group object.
+ */
+ public static Group mapGroup(JsonNode json) {
+ if (json == null || json.isNull()) {
+ return null;
+ }
+
+ Long id = getRequiredFieldAsLong(json, ID);
+ Long parentGroupId = getFieldAsLong(json, PARENT_GROUP_ID);
+ String name = getFieldAsString(json, NAME);
+ String description = getFieldAsString(json, DESCRIPTION);
+ Long voId = getRequiredFieldAsLong(json, VO_ID);
+ String uuid = getRequiredFieldAsString(json, UUID);
+
+ return new Group(id, parentGroupId, name, description, null, uuid, voId);
+ }
+
+ /**
+ * Maps JsonNode to List of Groups.
+ *
+ * @param jsonArray JSON array of groups in JSON format from Perun to be mapped.
+ * @return List of groups.
+ */
+ public static List<Group> mapGroups(JsonNode jsonArray) {
+ if (jsonArray.isNull()) {
+ return new ArrayList<>();
+ }
+
+ List<Group> result = new ArrayList<>();
+ for (int i = 0; i < jsonArray.size(); i++) {
+ JsonNode groupNode = jsonArray.get(i);
+ Group mappedGroup = RpcMapper.mapGroup(groupNode);
+ result.add(mappedGroup);
+ }
+
+ return result;
+ }
+
+ /**
+ * Maps JsonNode to Member model.
+ *
+ * @param json Member in JSON format from Perun to be mapped.
+ * @return Mapped Member object.
+ */
+ public static Member mapMember(JsonNode json) {
+ if (json == null || json.isNull()) {
+ return null;
+ }
+
+ Long id = getRequiredFieldAsLong(json, ID);
+ Long userId = getRequiredFieldAsLong(json, USER_ID);
+ Long voId = getRequiredFieldAsLong(json, VO_ID);
+ MemberStatus status = MemberStatus.fromString(getRequiredFieldAsString(json, STATUS));
+
+ return new Member(id, userId, voId, status);
+ }
+
+ /**
+ * Maps JsonNode to List of Members.
+ *
+ * @param jsonArray JSON array of members in JSON format from Perun to be mapped.
+ * @return List of members.
+ */
+ public static List<Member> mapMembers(JsonNode jsonArray) {
+ if (jsonArray.isNull()) {
+ return new ArrayList<>();
+ }
+
+ List<Member> members = new ArrayList<>();
+ for (int i = 0; i < jsonArray.size(); i++) {
+ JsonNode memberNode = jsonArray.get(i);
+ Member mappedMember = RpcMapper.mapMember(memberNode);
+ members.add(mappedMember);
+ }
+
+ return members;
+ }
+
+ /**
+ * Maps JsonNode to ExtSource model.
+ *
+ * @param json ExtSource in JSON format from Perun to be mapped.
+ * @return Mapped ExtSource object.
+ */
+ public static ExtSource mapExtSource(JsonNode json) {
+ if (json == null || json.isNull()) {
+ return null;
+ }
+
+ Long id = getRequiredFieldAsLong(json, ID);
+ String name = getRequiredFieldAsString(json, NAME);
+ String type = getRequiredFieldAsString(json, TYPE);
+
+ return new ExtSource(id, name, type);
+ }
+
+ /**
+ * Maps JsonNode to UserExtSource model.
+ *
+ * @param json UserExtSource in JSON format from Perun to be mapped.
+ * @return Mapped UserExtSource object.
+ */
+ public static UserExtSource mapUserExtSource(JsonNode json) {
+ if (json == null || json.isNull()) {
+ return null;
+ }
+
+ Long id = getRequiredFieldAsLong(json, ID);
+ String login = getRequiredFieldAsString(json, LOGIN);
+ ExtSource extSource = RpcMapper.mapExtSource(getRequiredFieldAsJsonNode(json, EXT_SOURCE));
+ int loa = getRequiredFieldAsInt(json, LOA);
+ boolean persistent = getRequiredFieldAsBoolean(json, PERSISTENT);
+ Timestamp lastAccess = Timestamp.valueOf(getRequiredFieldAsString(json, LAST_ACCESS));
+
+ return new UserExtSource(id, extSource, login, loa, persistent, lastAccess);
+ }
+
+ /**
+ * Maps JsonNode to List of UserExtSources.
+ *
+ * @param jsonArray JSON array of userExtSources in JSON format from Perun to be mapped.
+ * @return List of userExtSources.
+ */
+ public static List<UserExtSource> mapUserExtSources(JsonNode jsonArray) {
+ if (jsonArray.isNull()) {
+ return new ArrayList<>();
+ }
+
+ List<UserExtSource> userExtSources = new ArrayList<>();
+
+ for (int i = 0; i < jsonArray.size(); i++) {
+ JsonNode userExtSource = jsonArray.get(i);
+ UserExtSource mappedUes = RpcMapper.mapUserExtSource(userExtSource);
+ userExtSources.add(mappedUes);
+ }
+
+ return userExtSources;
+ }
+
+ public static PerunAttributeValue mapAttributeValue(JsonNode json) {
+ if (json == null || json.isNull()) {
+ return null;
+ }
+
+ String friendlyName = getRequiredFieldAsString(json, FRIENDLY_NAME);
+ String namespace = getRequiredFieldAsString(json, NAMESPACE);
+ String type = getRequiredFieldAsString(json, TYPE);
+ JsonNode value = getFieldAsJsonNode(json, VALUE);
+
+ return new PerunAttributeValue(namespace + ':' + friendlyName, type, value);
+ }
+
+ public static Map<String, PerunAttributeValue> mapAttributes(JsonNode jsonNode, Map<String, AttributeMapping> attrMappings) {
+ Map<String, PerunAttributeValue> attributesAsMap = new HashMap<>();
+
+ for (int i = 0; i < jsonNode.size(); i++) {
+ JsonNode attribute = jsonNode.get(i);
+ PerunAttributeValue mappedAttributeValue = mapAttributeValue(attribute);
+
+ for (Map.Entry<String, AttributeMapping> entry : attrMappings.entrySet()) {
+ if (entry.getValue().getRpcName().equals(mappedAttributeValue.getAttrName())) {
+ attributesAsMap.put(entry.getKey(), mappedAttributeValue);
+ }
+ }
+ }
+
+ return attributesAsMap;
+ }
+
+ private static Long getRequiredFieldAsLong(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ throw new MissingFieldException();
+ }
+ return json.get(name).asLong();
+ }
+
+ private static Long getFieldAsLong(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ return 0L;
+ }
+ return json.get(name).asLong();
+ }
+
+ private static int getRequiredFieldAsInt(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ throw new MissingFieldException();
+ }
+ return json.get(name).asInt();
+ }
+
+ private static int getFieldAsInt(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ return 0;
+ }
+ return json.get(name).asInt();
+ }
+
+ private static boolean getRequiredFieldAsBoolean(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ throw new MissingFieldException();
+ }
+ return json.get(name).asBoolean();
+ }
+
+ private static String getRequiredFieldAsString(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ throw new MissingFieldException();
+ }
+ return json.get(name).asText();
+ }
+
+ private static String getFieldAsString(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ return "";
+ }
+ return json.get(name).asText();
+ }
+
+ private static JsonNode getRequiredFieldAsJsonNode(JsonNode json, String name) {
+ if (!json.hasNonNull(name)) {
+ throw new MissingFieldException();
+ }
+ return json.get(name);
+ }
+
+ private static JsonNode getFieldAsJsonNode(JsonNode json, String name) {
+ return json.get(name);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/Affiliation.java b/src/main/java/cz/muni/ics/ga4gh/model/Affiliation.java
new file mode 100644
index 0000000..767a472
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/Affiliation.java
@@ -0,0 +1,19 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.ToString;
+
+@Getter
+@ToString
+@EqualsAndHashCode
+@AllArgsConstructor
+public class Affiliation {
+
+ private final String source;
+
+ private final String value;
+
+ private final long asserted;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/AttributeMapping.java b/src/main/java/cz/muni/ics/ga4gh/model/AttributeMapping.java
new file mode 100644
index 0000000..c90f81f
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/AttributeMapping.java
@@ -0,0 +1,23 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+@ToString
+@EqualsAndHashCode
+public class AttributeMapping {
+
+ private String internalName;
+
+ private String rpcName;
+
+ private String ldapName;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/ExtSource.java b/src/main/java/cz/muni/ics/ga4gh/model/ExtSource.java
new file mode 100644
index 0000000..eeb1cd9
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/ExtSource.java
@@ -0,0 +1,40 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+import org.springframework.util.StringUtils;
+
+@Getter
+@NoArgsConstructor
+@AllArgsConstructor
+@EqualsAndHashCode
+@ToString
+public class ExtSource {
+
+ @Setter
+ private Long id;
+
+ private String name;
+
+ private String type;
+
+ public void setName(String name) {
+ if (StringUtils.hasText(name)) {
+ throw new IllegalArgumentException("name cannot be null nor empty");
+ }
+
+ this.name = name;
+ }
+
+ public void setType(String type) {
+ if (!StringUtils.hasText(type)) {
+ throw new IllegalArgumentException("type cannot be null nor empty");
+ }
+
+ this.type = type;
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/Ga4ghClaimRepository.java b/src/main/java/cz/muni/ics/ga4gh/model/Ga4ghClaimRepository.java
new file mode 100644
index 0000000..f9c7bd9
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/Ga4ghClaimRepository.java
@@ -0,0 +1,20 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.ToString;
+import org.springframework.web.client.RestTemplate;
+
+@Getter
+@ToString
+@EqualsAndHashCode
+@AllArgsConstructor
+public class Ga4ghClaimRepository {
+
+ private final String name;
+
+ private final String actionURL;
+
+ private final RestTemplate restTemplate;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/Ga4ghPassportVisa.java b/src/main/java/cz/muni/ics/ga4gh/model/Ga4ghPassportVisa.java
new file mode 100644
index 0000000..6917574
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/Ga4ghPassportVisa.java
@@ -0,0 +1,59 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.Setter;
+import lombok.ToString;
+
+@Getter
+@Setter
+@ToString
+@EqualsAndHashCode
+public class Ga4ghPassportVisa {
+
+ public static final String GA4GH_VISA_V1 = "ga4gh_visa_v1";
+
+ public static final String TYPE_AFFILIATION_AND_ROLE = "AffiliationAndRole";
+ public static final String TYPE_ACCEPTED_TERMS_AND_POLICIES = "AcceptedTermsAndPolicies";
+ public static final String TYPE_RESEARCHER_STATUS = "ResearcherStatus";
+ public static final String TYPE_LINKED_IDENTITIES = "LinkedIdentities";
+
+ public static final String BY_SYSTEM = "system";
+ public static final String BY_SO = "so";
+ public static final String BY_PEER = "peer";
+ public static final String BY_SELF = "self";
+
+ public static final String SUB = "sub";
+ public static final String EXP = "exp";
+ public static final String ISS = "iss";
+ public static final String TYPE = "type";
+ public static final String ASSERTED = "asserted";
+ public static final String VALUE = "value";
+ public static final String SOURCE = "source";
+ public static final String BY = "by";
+ public static final String CONDITION = "condition";
+
+ private boolean verified = false;
+ private String linkedIdentity;
+ private String sub;
+ private String iss;
+ private String type;
+ private String value;
+
+ @ToString.Exclude
+ private String signer;
+
+ @ToString.Exclude
+ private String jwt;
+
+ @ToString.Exclude
+ private String prettyPayload;
+
+ public Ga4ghPassportVisa(String jwt) {
+ this.jwt = jwt;
+ }
+
+ public String getPrettyString() {
+ return prettyPayload + ", signed by " + signer;
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/Group.java b/src/main/java/cz/muni/ics/ga4gh/model/Group.java
new file mode 100644
index 0000000..49aea56
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/Group.java
@@ -0,0 +1,45 @@
+package cz.muni.ics.ga4gh.model;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+@Getter
+@Setter
+@ToString
+@EqualsAndHashCode
+@NoArgsConstructor
+public class Group {
+
+ private Long id;
+
+ private Long parentGroupId;
+
+ private String name;
+
+ private String description;
+
+ private String uniqueGroupName;
+
+ private String uuid;
+
+ private Long voId;
+
+ private Map<String, JsonNode> attributes = new LinkedHashMap<>();
+
+ public Group(Long id, Long parentGroupId, String name, String description, String uniqueGroupName, String uuid, Long voId) {
+ this.id = id;
+ this.parentGroupId = parentGroupId;
+ this.name = name;
+ this.description = description;
+ this.uniqueGroupName = uniqueGroupName;
+ this.uuid = uuid;
+ this.voId = voId;
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/Member.java b/src/main/java/cz/muni/ics/ga4gh/model/Member.java
new file mode 100644
index 0000000..ca73483
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/Member.java
@@ -0,0 +1,26 @@
+package cz.muni.ics.ga4gh.model;
+
+import cz.muni.ics.ga4gh.enums.MemberStatus;
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+
+@Getter
+@Setter
+@ToString
+@EqualsAndHashCode
+@NoArgsConstructor
+@AllArgsConstructor
+public class Member {
+
+ private Long id;
+
+ private Long userId;
+
+ private Long voId;
+
+ private MemberStatus status;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/PerunAttributeValue.java b/src/main/java/cz/muni/ics/ga4gh/model/PerunAttributeValue.java
new file mode 100644
index 0000000..541b63a
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/PerunAttributeValue.java
@@ -0,0 +1,173 @@
+package cz.muni.ics.ga4gh.model;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.BooleanNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.NullNode;
+import com.fasterxml.jackson.databind.node.NumericNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.fasterxml.jackson.databind.node.TextNode;
+import cz.muni.ics.ga4gh.exceptions.InconvertibleValueException;
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.ToString;
+import org.springframework.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+@Getter
+@NoArgsConstructor
+@AllArgsConstructor
+@EqualsAndHashCode
+@ToString
+public class PerunAttributeValue {
+
+ public final static String STRING_TYPE = "java.lang.String";
+ public final static String INTEGER_TYPE = "java.lang.Integer";
+ public final static String BOOLEAN_TYPE = "java.lang.Boolean";
+ public final static String ARRAY_TYPE = "java.util.ArrayList";
+ public final static String MAP_TYPE = "java.util.LinkedHashMap";
+ public final static String LARGE_STRING_TYPE = "java.lang.LargeString";
+ public final static String LARGE_ARRAY_LIST_TYPE = "java.util.LargeArrayList";
+
+ private String attrName;
+ private String type;
+ private JsonNode value;
+
+ public void setAttrName(String attrName) {
+ if (!StringUtils.hasText(attrName)) {
+ throw new IllegalArgumentException("type can't be null or empty");
+ }
+
+ this.attrName = attrName;
+ }
+
+ public void setType(String type) {
+ if (!StringUtils.hasText(type)) {
+ throw new IllegalArgumentException("type can't be null or empty");
+ }
+
+ this.type = type;
+ }
+
+ public void setValue(String type, JsonNode value) {
+ if (isNullValue(value)) {
+ if (BOOLEAN_TYPE.equals(type)) {
+ value = JsonNodeFactory.instance.booleanNode(false);
+ } else if (ARRAY_TYPE.equals(type)) {
+ value = JsonNodeFactory.instance.arrayNode();
+ } else if (MAP_TYPE.equals(type)) {
+ value = JsonNodeFactory.instance.objectNode();
+ } else {
+ value = JsonNodeFactory.instance.nullNode();
+ }
+ }
+
+ this.value = value;
+ }
+
+ public String valueAsString() {
+ if ((STRING_TYPE.equals(type) || LARGE_STRING_TYPE.equals(type))) {
+ if (isNullValue(value)) {
+ return null;
+ } else if (value instanceof TextNode) {
+ return value.textValue();
+ }
+ }
+
+ return value.asText();
+ }
+
+ public Integer valueAsInteger() {
+ if (INTEGER_TYPE.equals(type)) {
+ if (isNullValue(value)) {
+ return null;
+ } else if (value instanceof NumericNode) {
+ return value.intValue();
+ }
+ }
+
+ throw this.inconvertible(Long.class.getName());
+ }
+
+ public boolean valueAsBoolean() {
+ if (BOOLEAN_TYPE.equals(type)) {
+ if (value == null || value instanceof NullNode) {
+ return false;
+ } else if (value instanceof BooleanNode) {
+ return value.asBoolean();
+ }
+ }
+
+ throw this.inconvertible(Boolean.class.getName());
+ }
+
+ public List<String> valueAsList() {
+ List<String> arr = new ArrayList<>();
+
+ if ((ARRAY_TYPE.equals(type) || LARGE_ARRAY_LIST_TYPE.equals(type))) {
+ if (isNullValue(value)) {
+ return null;
+ } else if (value instanceof ArrayNode) {
+ ArrayNode arrJson = (ArrayNode) value;
+ arrJson.forEach(item -> arr.add(item.asText()));
+ }
+ } else {
+ arr.add(this.valueAsString());
+ }
+
+ return arr;
+ }
+
+ public Map<String, String> valueAsMap() {
+ if (MAP_TYPE.equals(type)) {
+ if (isNullValue(value)) {
+ return new HashMap<>();
+ } else if (value instanceof ObjectNode) {
+ ObjectNode objJson = (ObjectNode) value;
+
+ Map<String, String> res = new HashMap<>();
+ Iterator<String> it = objJson.fieldNames();
+
+ while (it.hasNext()) {
+ String key = it.next();
+ res.put(key, objJson.get(key).asText());
+ }
+
+ return res;
+ }
+ }
+
+ throw this.inconvertible(Map.class.getName());
+ }
+
+ public JsonNode valueAsJson() {
+ return this.value;
+ }
+
+ public boolean isNullValue() {
+ return value == null ||
+ value instanceof NullNode ||
+ value.isNull() ||
+ "null".equalsIgnoreCase(value.asText());
+ }
+
+ public static boolean isNullValue(JsonNode value) {
+ return value == null ||
+ value instanceof NullNode ||
+ value.isNull() ||
+ "null".equalsIgnoreCase(value.asText());
+ }
+
+ private InconvertibleValueException inconvertible(String clazzName) {
+ return new InconvertibleValueException("Cannot convert value of attribute to " + clazzName +
+ " for object: " + this);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/Repo.java b/src/main/java/cz/muni/ics/ga4gh/model/Repo.java
new file mode 100644
index 0000000..23016ac
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/Repo.java
@@ -0,0 +1,27 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+
+import java.util.List;
+
+@Getter
+@Setter
+@ToString
+@EqualsAndHashCode
+@NoArgsConstructor
+@AllArgsConstructor
+public class Repo {
+
+ private String name;
+
+ private String url;
+
+ private String jwks;
+
+ private List<RepoHeader> headers;
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/RepoHeader.java b/src/main/java/cz/muni/ics/ga4gh/model/RepoHeader.java
new file mode 100644
index 0000000..d8932c1
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/RepoHeader.java
@@ -0,0 +1,30 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import org.springframework.http.HttpRequest;
+import org.springframework.http.client.ClientHttpRequestExecution;
+import org.springframework.http.client.ClientHttpRequestInterceptor;
+import org.springframework.http.client.ClientHttpResponse;
+
+import java.io.IOException;
+
+@Getter
+@Setter
+@AllArgsConstructor
+@NoArgsConstructor
+public class RepoHeader implements ClientHttpRequestInterceptor {
+
+ private String header;
+
+ private String value;
+
+ @Override
+ public ClientHttpResponse intercept(HttpRequest request, byte[] body, ClientHttpRequestExecution execution) throws IOException {
+ request.getHeaders().add(header, value);
+
+ return execution.execute(request, body);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/model/UserExtSource.java b/src/main/java/cz/muni/ics/ga4gh/model/UserExtSource.java
new file mode 100644
index 0000000..19fcda5
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/model/UserExtSource.java
@@ -0,0 +1,56 @@
+package cz.muni.ics.ga4gh.model;
+
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+import org.springframework.util.StringUtils;
+
+import java.sql.Timestamp;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+@EqualsAndHashCode
+@ToString
+public class UserExtSource {
+
+ private Long id;
+
+ private ExtSource extSource;
+
+ private String login;
+
+ private int loa = 0;
+
+ private boolean persistent;
+
+ private Timestamp lastAccess;
+
+ public void setExtSource(ExtSource extSource) {
+ if (extSource == null) {
+ throw new IllegalArgumentException("extSource can't be null");
+ }
+
+ this.extSource = extSource;
+ }
+
+ public void setLogin(String login) {
+ if (!StringUtils.hasText(login)) {
+ throw new IllegalArgumentException("login can't be null or empty");
+ }
+
+ this.login = login;
+ }
+
+ public void setLoa(int loa) {
+ if (loa < 0) {
+ throw new IllegalArgumentException("loa has to be 0 or higher");
+ }
+
+ this.loa = loa;
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/security/WebSecurityConfigurer.java b/src/main/java/cz/muni/ics/ga4gh/security/WebSecurityConfigurer.java
new file mode 100644
index 0000000..20d62d1
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/security/WebSecurityConfigurer.java
@@ -0,0 +1,50 @@
+package cz.muni.ics.ga4gh.security;
+
+import cz.muni.ics.ga4gh.config.BasicAuthConfig;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
+import org.springframework.security.config.annotation.web.builders.HttpSecurity;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.security.web.SecurityFilterChain;
+
+@Configuration
+public class WebSecurityConfigurer {
+
+ private static final String ROLE_USER = "ROLE_USER";
+ private static final String PUBLIC_ENDPOINTS_PREFIX = "/public/**";
+
+ private final String username;
+ private final String password;
+
+ private final PasswordEncoder passwordEncoder;
+
+ @Autowired
+ public WebSecurityConfigurer(BasicAuthConfig config, PasswordEncoder passwordEncoder) {
+ this.username = config.getUsername();
+ this.password = config.getPassword();
+ this.passwordEncoder = passwordEncoder;
+ }
+
+ @Autowired
+ public void configureGlobal(AuthenticationManagerBuilder auth) throws Exception {
+ auth.inMemoryAuthentication()
+ .withUser(username).password(passwordEncoder.encode(password))
+ .authorities(ROLE_USER);
+ }
+
+ @Bean
+ public SecurityFilterChain filterChain(HttpSecurity http) throws Exception {
+
+ http.authorizeRequests()
+ .antMatchers(PUBLIC_ENDPOINTS_PREFIX).permitAll()
+ .anyRequest().authenticated()
+ .and()
+ .httpBasic();
+
+ http.headers().frameOptions().sameOrigin();
+
+ return http.build();
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/service/Ga4ghBrokerService.java b/src/main/java/cz/muni/ics/ga4gh/service/Ga4ghBrokerService.java
new file mode 100644
index 0000000..824d9fa
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/service/Ga4ghBrokerService.java
@@ -0,0 +1,8 @@
+package cz.muni.ics.ga4gh.service;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+
+public interface Ga4ghBrokerService {
+
+ ArrayNode getGa4ghPassport(String eppn);
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/service/JWTSigningAndValidationService.java b/src/main/java/cz/muni/ics/ga4gh/service/JWTSigningAndValidationService.java
new file mode 100644
index 0000000..9748662
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/service/JWTSigningAndValidationService.java
@@ -0,0 +1,37 @@
+package cz.muni.ics.ga4gh.service;
+
+import com.nimbusds.jose.JWSAlgorithm;
+import com.nimbusds.jose.jwk.JWK;
+import com.nimbusds.jwt.SignedJWT;
+
+import java.util.Collection;
+import java.util.Map;
+
+public interface JWTSigningAndValidationService {
+
+ Map<String, JWK> getAllPublicKeys();
+
+ JWSAlgorithm getDefaultSigningAlgorithm();
+
+ Collection<JWSAlgorithm> getAllSigningAlgsSupported();
+
+ /**
+ * Called to sign a jwt in place for a client that hasn't registered a preferred signing algorithm.
+ * Use the default algorithm to sign.
+ *
+ * @param jwt the jwt to sign
+ * @throws IllegalStateException when calling default signing with no default signer ID set
+ */
+ void signJwt(SignedJWT jwt);
+
+ /**
+ * Sign a jwt using the selected algorithm. The algorithm is selected using the String parameter values specified
+ * in the JWT spec, section 6. I.E., "HS256" means HMAC with SHA-256 and corresponds to our HmacSigner class.
+ *
+ * @param jwt the jwt to sign
+ * @param alg the name of the algorithm to use, as specified in JWS s.6
+ */
+ void signJwt(SignedJWT jwt, JWSAlgorithm alg);
+
+ String getDefaultSignerKeyId();
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/service/impl/Ga4GhBrokerBrokerServiceImpl.java b/src/main/java/cz/muni/ics/ga4gh/service/impl/Ga4GhBrokerBrokerServiceImpl.java
new file mode 100644
index 0000000..9999334
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/service/impl/Ga4GhBrokerBrokerServiceImpl.java
@@ -0,0 +1,61 @@
+package cz.muni.ics.ga4gh.service.impl;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import cz.muni.ics.ga4gh.adapters.PerunAdapter;
+import cz.muni.ics.ga4gh.config.AttributesConfig;
+import cz.muni.ics.ga4gh.config.BrokerConfig;
+import cz.muni.ics.ga4gh.exceptions.UserNotUniqueException;
+import cz.muni.ics.ga4gh.model.AttributeMapping;
+import cz.muni.ics.ga4gh.service.impl.brokers.Ga4ghBroker;
+import cz.muni.ics.ga4gh.service.Ga4ghBrokerService;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+@Service
+@Slf4j
+public class Ga4GhBrokerBrokerServiceImpl implements Ga4ghBrokerService {
+
+ private final Ga4ghBroker broker;
+
+ private final PerunAdapter adapter;
+
+ private final List<String> attributesToSearch;
+
+ private final Map<String, AttributeMapping> attributes;
+
+ @Autowired
+ public Ga4GhBrokerBrokerServiceImpl(Ga4ghBroker broker, PerunAdapter adapter, BrokerConfig brokerConfig, AttributesConfig attributesConfig) {
+ this.broker = broker;
+ this.adapter = adapter;
+ this.attributesToSearch = brokerConfig.getAttributesToSearch();
+ this.attributes = attributesConfig.getAttributeMappings();
+ }
+
+ @Override
+ public ArrayNode getGa4ghPassport(String eppn) {
+ Set<Long> userIds = new HashSet<>();
+
+ for (String attrName : attributesToSearch) {
+ if (attributes.get(attrName) != null) {
+ userIds.addAll(adapter.getAdapterPrimary().getUserIdsByAttributeValue(attributes.get(attrName), eppn));
+ }
+ }
+
+ if (userIds.isEmpty()) {
+ log.debug("User {} not found", eppn);
+ return null;
+ }
+
+ if (userIds.size() > 1) {
+ throw new UserNotUniqueException("There are more users found by " + eppn + " - " + String.join(", ", userIds.toString()));
+ }
+
+ return broker.constructGa4ghPassportVisa(userIds.iterator().next(), eppn);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/service/impl/JWTSigningAndValidationServiceImpl.java b/src/main/java/cz/muni/ics/ga4gh/service/impl/JWTSigningAndValidationServiceImpl.java
new file mode 100644
index 0000000..0fc7b3b
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/service/impl/JWTSigningAndValidationServiceImpl.java
@@ -0,0 +1,227 @@
+package cz.muni.ics.ga4gh.service.impl;
+
+import com.nimbusds.jose.JOSEException;
+import com.nimbusds.jose.JWSAlgorithm;
+import com.nimbusds.jose.JWSProvider;
+import com.nimbusds.jose.JWSSigner;
+import com.nimbusds.jose.JWSVerifier;
+import com.nimbusds.jose.crypto.ECDSASigner;
+import com.nimbusds.jose.crypto.ECDSAVerifier;
+import com.nimbusds.jose.crypto.MACSigner;
+import com.nimbusds.jose.crypto.MACVerifier;
+import com.nimbusds.jose.crypto.RSASSASigner;
+import com.nimbusds.jose.crypto.RSASSAVerifier;
+import com.nimbusds.jose.jwk.ECKey;
+import com.nimbusds.jose.jwk.JWK;
+import com.nimbusds.jose.jwk.OctetSequenceKey;
+import com.nimbusds.jose.jwk.RSAKey;
+import com.nimbusds.jwt.SignedJWT;
+import cz.muni.ics.ga4gh.jose.keystore.JWKSetKeyStore;
+import cz.muni.ics.ga4gh.service.JWTSigningAndValidationService;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.util.StringUtils;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+
+@Slf4j
+@Service
+public class JWTSigningAndValidationServiceImpl implements JWTSigningAndValidationService {
+
+ private final Map<String, JWSSigner> signers = new HashMap<>();
+ private final Map<String, JWSVerifier> verifiers = new HashMap<>();
+
+ private String defaultSignerKeyId;
+ private JWSAlgorithm defaultAlgorithm;
+ private Map<String, JWK> keys = new HashMap<>();
+
+ /**
+ * Build this service based on the keys given. All public keys will be used
+ * to make verifiers, all private keys will be used to make signers.
+ *
+ * @param keys A map of key identifier to key.
+ */
+ public JWTSigningAndValidationServiceImpl(Map<String, JWK> keys) {
+ this.keys = keys;
+ buildSignersAndVerifiers();
+ }
+
+ /**
+ * Build this service based on the given keystore. All keys must have a key
+ * id ({@code kid}) field in order to be used.
+ *
+ * @param keyStore The keystore to load all keys from.
+ */
+ @Autowired
+ public JWTSigningAndValidationServiceImpl(JWKSetKeyStore keyStore) {
+ if (keyStore!= null && keyStore.getJwkSet() != null) {
+ for (JWK key : keyStore.getKeys()) {
+ if (!StringUtils.isEmpty(key.getKeyID())) {
+ this.keys.put(key.getKeyID(), key);
+ } else {
+ String fakeKid = UUID.randomUUID().toString();
+ this.keys.put(fakeKid, key);
+ }
+ }
+ }
+
+ buildSignersAndVerifiers();
+
+ this.defaultSignerKeyId = keyStore.getKeys().get(0).getKeyID();
+ setDefaultSigningAlgorithmName(keyStore.getKeys().get(0).getAlgorithm().getName());
+ }
+
+ @Override
+ public String getDefaultSignerKeyId() {
+ return defaultSignerKeyId;
+ }
+
+ public void setDefaultSignerKeyId(String defaultSignerId) {
+ this.defaultSignerKeyId = defaultSignerId;
+ }
+
+ @Override
+ public JWSAlgorithm getDefaultSigningAlgorithm() {
+ return defaultAlgorithm;
+ }
+
+ public void setDefaultSigningAlgorithmName(String algName) {
+ defaultAlgorithm = JWSAlgorithm.parse(algName);
+ }
+
+ public String getDefaultSigningAlgorithmName() {
+ if (defaultAlgorithm != null) {
+ return defaultAlgorithm.getName();
+ } else {
+ return null;
+ }
+ }
+
+ @Override
+ public void signJwt(SignedJWT jwt) {
+ if (getDefaultSignerKeyId() == null) {
+ throw new IllegalStateException("Tried to call default signing with no default signer ID set");
+ }
+
+ JWSSigner signer = signers.get(getDefaultSignerKeyId());
+
+ try {
+ jwt.sign(signer);
+ } catch (JOSEException e) {
+ log.error("Failed to sign JWT, error was: ", e);
+ }
+ }
+
+ @Override
+ public void signJwt(SignedJWT jwt, JWSAlgorithm alg) {
+ JWSSigner signer = null;
+
+ for (JWSSigner s : signers.values()) {
+ if (s.supportedJWSAlgorithms().contains(alg)) {
+ signer = s;
+ break;
+ }
+ }
+
+ if (signer == null) {
+ log.error("No matching algorithm found for alg={}", alg);
+ } else {
+ try {
+ jwt.sign(signer);
+ } catch (JOSEException e) {
+ log.error("Failed to sign JWT, error was: ", e);
+ }
+ }
+ }
+
+ @Override
+ public Map<String, JWK> getAllPublicKeys() {
+ Map<String, JWK> pubKeys = new HashMap<>();
+
+ keys.keySet().forEach(keyId -> {
+ JWK key = keys.get(keyId);
+ JWK pub = key.toPublicJWK();
+ if (pub != null) {
+ pubKeys.put(keyId, pub);
+ }
+ });
+
+ return pubKeys;
+ }
+
+ @Override
+ public Collection<JWSAlgorithm> getAllSigningAlgsSupported() {
+ Set<JWSAlgorithm> algs = new HashSet<>();
+ signers.values().stream().map(JWSProvider::supportedJWSAlgorithms).forEach(algs::addAll);
+ verifiers.values().stream().map(JWSProvider::supportedJWSAlgorithms).forEach(algs::addAll);
+
+ return algs;
+ }
+
+ private void buildSignersAndVerifiers() {
+ for (Map.Entry<String, JWK> jwkEntry : keys.entrySet()) {
+ String id = jwkEntry.getKey();
+ JWK jwk = jwkEntry.getValue();
+
+ try {
+ if (jwk instanceof RSAKey) {
+ processRSAKey(signers, verifiers, jwk, id);
+ } else if (jwk instanceof ECKey) {
+ processECKey(signers, verifiers, jwk, id);
+ } else if (jwk instanceof OctetSequenceKey) {
+ processOctetKey(signers, verifiers, jwk, id);
+ } else {
+ log.warn("Unknown key type: {}", jwk);
+ }
+ } catch (JOSEException e) {
+ log.warn("Exception loading signer/verifier", e);
+ }
+ }
+
+ if (defaultSignerKeyId == null && keys.size() == 1) {
+ setDefaultSignerKeyId(keys.keySet().iterator().next());
+ }
+ }
+
+ private void processOctetKey(Map<String, JWSSigner> signers, Map<String, JWSVerifier> verifiers, JWK jwk, String id)
+ throws JOSEException
+ {
+ if (jwk.isPrivate()) {
+ MACSigner signer = new MACSigner((OctetSequenceKey) jwk);
+ signers.put(id, signer);
+ }
+
+ MACVerifier verifier = new MACVerifier((OctetSequenceKey) jwk);
+ verifiers.put(id, verifier);
+ }
+
+ private void processECKey(Map<String, JWSSigner> signers, Map<String, JWSVerifier> verifiers, JWK jwk, String id)
+ throws JOSEException
+ {
+ if (jwk.isPrivate()) {
+ ECDSASigner signer = new ECDSASigner((ECKey) jwk);
+ signers.put(id, signer);
+ }
+
+ ECDSAVerifier verifier = new ECDSAVerifier((ECKey) jwk);
+ verifiers.put(id, verifier);
+ }
+
+ private void processRSAKey(Map<String, JWSSigner> signers, Map<String, JWSVerifier> verifiers, JWK jwk, String id)
+ throws JOSEException
+ {
+ if (jwk.isPrivate()) {
+ RSASSASigner signer = new RSASSASigner((RSAKey) jwk);
+ signers.put(id, signer);
+ }
+
+ RSASSAVerifier verifier = new RSASSAVerifier((RSAKey) jwk);
+ verifiers.put(id, verifier);
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/BbmriGa4ghBroker.java b/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/BbmriGa4ghBroker.java
new file mode 100644
index 0000000..f9a89b7
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/BbmriGa4ghBroker.java
@@ -0,0 +1,204 @@
+package cz.muni.ics.ga4gh.service.impl.brokers;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import cz.muni.ics.ga4gh.adapters.PerunAdapter;
+import cz.muni.ics.ga4gh.config.BrokerConfig;
+import cz.muni.ics.ga4gh.config.Ga4ghConfig;
+import cz.muni.ics.ga4gh.model.Affiliation;
+import cz.muni.ics.ga4gh.model.Ga4ghClaimRepository;
+import cz.muni.ics.ga4gh.service.JWTSigningAndValidationService;
+import cz.muni.ics.ga4gh.utils.Utils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Service;
+import org.springframework.util.StringUtils;
+
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.sql.Timestamp;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_PEER;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_SELF;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_SO;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_SYSTEM;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_ACCEPTED_TERMS_AND_POLICIES;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_AFFILIATION_AND_ROLE;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_LINKED_IDENTITIES;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_RESEARCHER_STATUS;
+
+@Service
+@Profile("bbmri")
+public class BbmriGa4ghBroker extends Ga4ghBroker {
+
+ private static final String BONA_FIDE_URL = "https://doi.org/10.1038/s41431-018-0219-y";
+ private static final String BBMRI_ERIC_ORG_URL = "https://www.bbmri-eric.eu/";
+ private static final String BBMRI_ID = "bbmri_id";
+ private static final String FACULTY_AT = "faculty@";
+
+ private final String bonaFideStatusAttr;
+ private final String groupAffiliationsAttr;
+ private final Long termsAndPoliciesGroupId;
+
+ @Autowired
+ public BbmriGa4ghBroker(BrokerConfig brokerConfig, PerunAdapter adapter, JWTSigningAndValidationService jwtService, Ga4ghConfig ga4ghConfig) throws URISyntaxException, MalformedURLException {
+ super(adapter, jwtService, ga4ghConfig, brokerConfig);
+
+ bonaFideStatusAttr = brokerConfig.getBonaFideStatusAttr();
+ groupAffiliationsAttr = brokerConfig.getGroupAffiliationsAttr();
+ termsAndPoliciesGroupId = Objects.requireNonNullElse(brokerConfig.getTermsAndPoliciesGroupId(), 10432L);
+ }
+
+ @Override
+ protected void addAffiliationAndRoles(long now, ArrayNode passport, List<Affiliation> affiliations, String sub, Long userId)
+ {
+ //by=system for users with affiliation asserted by their IdP (set in UserExtSource attribute "affiliation")
+ if (affiliations == null) {
+ return;
+ }
+
+ for (Affiliation affiliation: affiliations) {
+ //expires 1 year after the last login from the IdP asserting the affiliation
+ long expires = Utils.getOneYearExpires(affiliation.getAsserted());
+ if (expires < now) {
+ continue;
+ }
+
+ JsonNode visa = createPassportVisa(TYPE_AFFILIATION_AND_ROLE, sub, userId, affiliation.getValue(), affiliation.getSource(), BY_SYSTEM, affiliation.getAsserted(), expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+
+ @Override
+ protected void addAcceptedTermsAndPolicies(long now, ArrayNode passport, Long userId, String sub) {
+ //by=self for members of the group 10432 "Bona Fide Researchers"
+ boolean userInGroup = adapter.isUserInGroup(userId, termsAndPoliciesGroupId);
+ if (!userInGroup) {
+ return;
+ }
+
+ long asserted = now;
+ if (bonaFideStatusAttr != null) {
+ String bonaFideStatusCreatedAt = adapter.getAdapterRpc().getUserAttributeCreatedAt(userId, bonaFideStatusAttr);
+ if (bonaFideStatusCreatedAt != null) {
+ asserted = Timestamp.valueOf(bonaFideStatusCreatedAt).getTime() / 1000L;
+ }
+ }
+
+ long expires = Utils.getExpires(asserted, 100L);
+ if (expires < now) {
+ return;
+ }
+
+ JsonNode visa = createPassportVisa(TYPE_ACCEPTED_TERMS_AND_POLICIES, sub, userId, BONA_FIDE_URL, BBMRI_ERIC_ORG_URL, BY_SELF, asserted, expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+
+ @Override
+ protected void addResearcherStatuses(long now, ArrayNode passport, List<Affiliation> affiliations, String sub, Long userId)
+ {
+ addResearcherStatusFromBonaFideAttribute(now, passport, userId, sub);
+ addResearcherStatusFromAffiliation(affiliations, now, passport, sub, userId);
+ addResearcherStatusGroupAffiliations(now, passport, sub, userId);
+ }
+
+ @Override
+ protected void addControlledAccessGrants(long now, ArrayNode passport, String sub, Long userId) {
+ if (claimRepositories.isEmpty()) {
+ return;
+ }
+
+ Set<String> linkedIdentities = new HashSet<>();
+ for (Ga4ghClaimRepository repo: claimRepositories) {
+ callPermissionsJwtAPI(repo, Collections.singletonMap(BBMRI_ID, sub), passport, linkedIdentities);
+ }
+
+ if (linkedIdentities.isEmpty()) {
+ return;
+ }
+
+ for (String linkedIdentity : linkedIdentities) {
+ long expires = Utils.getOneYearExpires(now);
+
+ JsonNode visa = createPassportVisa(TYPE_LINKED_IDENTITIES, sub, userId, linkedIdentity, BBMRI_ERIC_ORG_URL, BY_SYSTEM, now, expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+
+ private void addResearcherStatusFromBonaFideAttribute(long now, ArrayNode passport, Long userId, String sub)
+ {
+ //by=peer for users with attribute elixirBonaFideStatusREMS
+ String bbmriBonaFideStatusCreatedAt = adapter.getAdapterRpc().getUserAttributeCreatedAt(userId, bonaFideStatusAttr);
+
+ if (bbmriBonaFideStatusCreatedAt == null) {
+ return;
+ }
+
+ long asserted = Timestamp.valueOf(bbmriBonaFideStatusCreatedAt).getTime() / 1000L;
+ long expires = Utils.getOneYearExpires(asserted);
+
+ if (expires > now) {
+ JsonNode visa = createPassportVisa(TYPE_RESEARCHER_STATUS, sub, userId, BONA_FIDE_URL, BBMRI_ERIC_ORG_URL, BY_PEER, asserted, expires, null);
+
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+
+ private void addResearcherStatusFromAffiliation(List<Affiliation> affiliations, long now, ArrayNode passport, String sub, Long userId)
+ {
+ //by=system for users with faculty affiliation asserted by their IdP (set in UserExtSource attribute "affiliation")
+ if (affiliations == null) {
+ return;
+ }
+
+ for (Affiliation affiliation: affiliations) {
+ if (!StringUtils.startsWithIgnoreCase(affiliation.getValue(), FACULTY_AT)) {
+ continue;
+ }
+
+ long expires = Utils.getOneYearExpires(affiliation.getAsserted());
+ if (expires < now) {
+ continue;
+ }
+
+ JsonNode visa = createPassportVisa(TYPE_RESEARCHER_STATUS, sub, userId, BONA_FIDE_URL, affiliation.getSource(), BY_SYSTEM, affiliation.getAsserted(), expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+
+ private void addResearcherStatusGroupAffiliations(long now, ArrayNode passport, String sub, Long userId) {
+ //by=so for users with faculty affiliation asserted by membership in a group with groupAffiliations attribute
+ List<Affiliation> groupAffiliations = adapter.getGroupAffiliations(userId, groupAffiliationsAttr);
+ if (groupAffiliations == null) {
+ return;
+ }
+
+ for (Affiliation affiliation: groupAffiliations) {
+ if (!StringUtils.startsWithIgnoreCase(affiliation.getValue(), FACULTY_AT)) {
+ continue;
+ }
+
+ long expires = Utils.getOneYearExpires(now);
+
+ JsonNode visa = createPassportVisa(TYPE_RESEARCHER_STATUS, sub, userId, BONA_FIDE_URL, BBMRI_ERIC_ORG_URL, BY_SO, affiliation.getAsserted(), expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/ElixirGa4ghBroker.java b/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/ElixirGa4ghBroker.java
new file mode 100644
index 0000000..cdef905
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/ElixirGa4ghBroker.java
@@ -0,0 +1,201 @@
+package cz.muni.ics.ga4gh.service.impl.brokers;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import cz.muni.ics.ga4gh.adapters.PerunAdapter;
+import cz.muni.ics.ga4gh.config.BrokerConfig;
+import cz.muni.ics.ga4gh.config.Ga4ghConfig;
+import cz.muni.ics.ga4gh.model.Affiliation;
+import cz.muni.ics.ga4gh.model.Ga4ghClaimRepository;
+import cz.muni.ics.ga4gh.service.JWTSigningAndValidationService;
+import cz.muni.ics.ga4gh.utils.Utils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Service;
+import org.springframework.util.StringUtils;
+
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.sql.Timestamp;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_PEER;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_SELF;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_SO;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.BY_SYSTEM;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_ACCEPTED_TERMS_AND_POLICIES;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_AFFILIATION_AND_ROLE;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_LINKED_IDENTITIES;
+import static cz.muni.ics.ga4gh.model.Ga4ghPassportVisa.TYPE_RESEARCHER_STATUS;
+
+@Service
+@Profile("elixir")
+public class ElixirGa4ghBroker extends Ga4ghBroker {
+
+ private static final String BONA_FIDE_URL = "https://doi.org/10.1038/s41431-018-0219-y";
+ private static final String ELIXIR_ORG_URL = "https://elixir-europe.org/";
+ private static final String ELIXIR_ID = "elixir_id";
+ private static final String FACULTY_AT = "faculty@";
+
+ private final String bonaFideStatusAttr;
+ private final String bonaFideStatusREMSAttr;
+ private final String groupAffiliationsAttr;
+ private final Long termsAndPoliciesGroupId;
+
+ @Autowired
+ public ElixirGa4ghBroker(BrokerConfig brokerConfig, Ga4ghConfig ga4ghConfig, PerunAdapter adapter, JWTSigningAndValidationService jwtService) throws URISyntaxException, MalformedURLException {
+ super(adapter, jwtService, ga4ghConfig, brokerConfig);
+
+ bonaFideStatusAttr = brokerConfig.getBonaFideStatusAttr();
+ bonaFideStatusREMSAttr = brokerConfig.getBonaFideStatusRemsAttr();
+ groupAffiliationsAttr = brokerConfig.getGroupAffiliationsAttr();
+ termsAndPoliciesGroupId = Objects.requireNonNullElse(brokerConfig.getTermsAndPoliciesGroupId(), 10432L);
+ }
+
+ @Override
+ protected void addAffiliationAndRoles(long now, ArrayNode passport, List<Affiliation> affiliations, String sub, Long userId) {
+ if (affiliations == null) {
+ return;
+ }
+
+ for (Affiliation affiliation: affiliations) {
+ long expires = Utils.getOneYearExpires(affiliation.getAsserted());
+
+ if (expires < now) {
+ continue;
+ }
+
+ JsonNode visa = createPassportVisa(TYPE_AFFILIATION_AND_ROLE, sub, userId, affiliation.getValue(),
+ affiliation.getSource(), BY_SYSTEM, affiliation.getAsserted(), expires, null);
+
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+
+ @Override
+ protected void addAcceptedTermsAndPolicies(long now, ArrayNode passport, Long userId, String sub) {
+ boolean userInGroup = adapter.isUserInGroup(userId, termsAndPoliciesGroupId);
+ if (!userInGroup) {
+ return;
+ }
+
+ long asserted = now;
+ if (bonaFideStatusAttr != null) {
+ String bonaFideStatusCreatedAt = adapter.getAdapterRpc().getUserAttributeCreatedAt(userId, bonaFideStatusAttr);
+ if (bonaFideStatusCreatedAt != null) {
+ asserted = Timestamp.valueOf(bonaFideStatusCreatedAt).getTime() / 1000L;
+ }
+ }
+
+ long expires = Utils.getExpires(asserted, 100L);
+ if (expires < now) {
+ return;
+ }
+
+ JsonNode visa = createPassportVisa(TYPE_ACCEPTED_TERMS_AND_POLICIES, sub, userId, BONA_FIDE_URL, ELIXIR_ORG_URL, BY_SELF, asserted, expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+
+ }
+
+ @Override
+ protected void addResearcherStatuses(long now, ArrayNode passport, List<Affiliation> affiliations, String sub, Long userId)
+ {
+ addResearcherStatusFromBonaFideAttribute(now, passport, sub, userId);
+ addResearcherStatusFromAffiliation(affiliations, now, passport, sub, userId);
+ addResearcherStatusGroupAffiliations(now, passport, userId, sub);
+ }
+
+ @Override
+ protected void addControlledAccessGrants(long now, ArrayNode passport, String sub, Long userId) {
+ if (claimRepositories.isEmpty()) {
+ return;
+ }
+ Set<String> linkedIdentities = new HashSet<>();
+ for (Ga4ghClaimRepository repo: claimRepositories) {
+ callPermissionsJwtAPI(repo, Collections.singletonMap(ELIXIR_ID, sub), passport, linkedIdentities);
+ }
+ if (linkedIdentities.isEmpty()) {
+ return;
+ }
+ for (String linkedIdentity : linkedIdentities) {
+ long expires = Utils.getOneYearExpires(now);
+ JsonNode visa = createPassportVisa(TYPE_LINKED_IDENTITIES, sub, userId, linkedIdentity,
+ ELIXIR_ORG_URL, BY_SYSTEM, now, expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+
+ private void addResearcherStatusFromBonaFideAttribute(long now, ArrayNode passport, String sub, Long userId)
+ {
+ String elixirBonaFideStatusREMSCreatedAt = adapter.getAdapterRpc().getUserAttributeCreatedAt(userId, bonaFideStatusREMSAttr);
+
+ if (elixirBonaFideStatusREMSCreatedAt == null) {
+ return;
+ }
+
+ long asserted = Timestamp.valueOf(elixirBonaFideStatusREMSCreatedAt).getTime() / 1000L;
+ long expires = Utils.getOneYearExpires(asserted);
+
+ if (expires < now) {
+ return;
+ }
+
+ JsonNode visa = createPassportVisa(TYPE_RESEARCHER_STATUS, sub, userId, BONA_FIDE_URL, ELIXIR_ORG_URL, BY_PEER, asserted, expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+
+ private void addResearcherStatusFromAffiliation(List<Affiliation> affiliations, long now, ArrayNode passport, String sub, Long userId)
+ {
+ if (affiliations == null) {
+ return;
+ }
+
+ for (Affiliation affiliation: affiliations) {
+ if (!StringUtils.startsWithIgnoreCase(affiliation.getValue(), FACULTY_AT)) {
+ continue;
+ }
+
+ long expires = Utils.getOneYearExpires(affiliation.getAsserted());
+ if (expires < now) {
+ continue;
+ }
+
+ JsonNode visa = createPassportVisa(TYPE_RESEARCHER_STATUS, sub, userId, BONA_FIDE_URL, affiliation.getSource(), BY_SYSTEM, affiliation.getAsserted(), expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+
+ private void addResearcherStatusGroupAffiliations(long now, ArrayNode passport, Long userId, String sub) {
+ List<Affiliation> groupAffiliations = adapter.getGroupAffiliations(userId, groupAffiliationsAttr);
+ if (groupAffiliations == null) {
+ return;
+ }
+
+ for (Affiliation affiliation: groupAffiliations) {
+ if (!StringUtils.startsWithIgnoreCase(affiliation.getValue(), FACULTY_AT)) {
+ continue;
+ }
+
+ long expires = Utils.getOneYearExpires(now);
+
+ JsonNode visa = createPassportVisa(TYPE_RESEARCHER_STATUS, sub, userId, BONA_FIDE_URL, ELIXIR_ORG_URL, BY_SO, affiliation.getAsserted(), expires, null);
+ if (visa != null) {
+ passport.add(visa);
+ }
+ }
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/Ga4ghBroker.java b/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/Ga4ghBroker.java
new file mode 100644
index 0000000..51e8cc5
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/service/impl/brokers/Ga4ghBroker.java
@@ -0,0 +1,223 @@
+package cz.muni.ics.ga4gh.service.impl.brokers;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.nimbusds.jose.JOSEObjectType;
+import com.nimbusds.jose.JWSAlgorithm;
+import com.nimbusds.jose.JWSHeader;
+import com.nimbusds.jose.jwk.source.RemoteJWKSet;
+import com.nimbusds.jose.proc.SecurityContext;
+import com.nimbusds.jwt.JWTClaimsSet;
+import com.nimbusds.jwt.SignedJWT;
+import cz.muni.ics.ga4gh.adapters.PerunAdapter;
+import cz.muni.ics.ga4gh.config.BrokerConfig;
+import cz.muni.ics.ga4gh.config.Ga4ghConfig;
+import cz.muni.ics.ga4gh.model.Affiliation;
+import cz.muni.ics.ga4gh.model.Ga4ghClaimRepository;
+import cz.muni.ics.ga4gh.model.Ga4ghPassportVisa;
+import cz.muni.ics.ga4gh.service.JWTSigningAndValidationService;
+import cz.muni.ics.ga4gh.utils.Utils;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.http.MediaType;
+import org.springframework.web.client.HttpClientErrorException;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.time.Instant;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+
+@Slf4j
+public abstract class Ga4ghBroker {
+
+ public static final String GA4GH_CLAIM = "ga4gh_passport_v1";
+ public static final String JSON = "json";
+
+ protected final List<Ga4ghClaimRepository> claimRepositories = new ArrayList<>();
+ protected final Map<URI, RemoteJWKSet<SecurityContext>> remoteJwkSets = new HashMap<>();
+ protected final Map<URI, String> signers = new HashMap<>();
+ protected final ObjectMapper mapper = new ObjectMapper();
+
+ private final String issuer;
+ private final URI jku;
+ protected PerunAdapter adapter;
+
+ protected JWTSigningAndValidationService jwtService;
+
+ private final String affiliationsAttr;
+
+ private final String orgUrlAttr;
+
+ public Ga4ghBroker(PerunAdapter adapter, JWTSigningAndValidationService jwtService, Ga4ghConfig config, BrokerConfig brokerConfig) throws URISyntaxException, MalformedURLException {
+ this.adapter = adapter;
+ this.jwtService = jwtService;
+ this.affiliationsAttr = brokerConfig.getAffiliationsAttr();
+ this.orgUrlAttr = brokerConfig.getOrgUrlAttr();
+ this.issuer = brokerConfig.getIssuer();
+ this.jku = new URL(brokerConfig.getJku()).toURI();
+
+ Utils.parseConfigFile(config, claimRepositories, remoteJwkSets, signers);
+ }
+
+ public ArrayNode constructGa4ghPassportVisa(Long userId, String sub) {
+ List<Affiliation> affiliations = adapter.getAdapterRpc().getUserExtSourcesAffiliations(userId, affiliationsAttr, orgUrlAttr);
+
+ ArrayNode ga4gh_passport_v1 = JsonNodeFactory.instance.arrayNode();
+ long now = Instant.now().getEpochSecond();
+
+ addAffiliationAndRoles(now, ga4gh_passport_v1, affiliations, sub, userId);
+ addAcceptedTermsAndPolicies(now, ga4gh_passport_v1, userId, sub);
+ addResearcherStatuses(now, ga4gh_passport_v1, affiliations, sub, userId);
+ addControlledAccessGrants(now, ga4gh_passport_v1, sub, userId);
+
+ return ga4gh_passport_v1;
+ }
+
+
+ protected abstract void addAffiliationAndRoles(long now, ArrayNode passport, List<Affiliation> affiliations, String sub, Long userId);
+
+ protected abstract void addAcceptedTermsAndPolicies(long now, ArrayNode passport, Long userId, String sub);
+
+ protected abstract void addResearcherStatuses(long now, ArrayNode passport, List<Affiliation> affiliations, String sub, Long userId);
+
+ protected abstract void addControlledAccessGrants(long now, ArrayNode passport, String sub, Long userId);
+
+ protected JsonNode createPassportVisa(String type, String sub, Long userId, String value, String source,
+ String by, long asserted, long expires, JsonNode condition)
+ {
+ long now = System.currentTimeMillis() / 1000L;
+
+ if (asserted > now) {
+ log.warn("Visa asserted in future, it will be ignored!");
+ log.debug("Visa information: perunUserId={}, sub={}, type={}, value={}, source={}, by={}, asserted={}",
+ userId, sub, type, value, source, by, Instant.ofEpochSecond(asserted));
+
+ return null;
+ }
+
+ if (expires <= now) {
+ log.warn("Visa is expired, it will be ignored!");
+ log.debug("Visa information: perunUserId={}, sub={}, type={}, value={}, source={}, by={}, expired={}",
+ userId, sub, type, value, source, by, Instant.ofEpochSecond(expires));
+
+ return null;
+ }
+
+ Map<String, Object> passportVisaObject = new HashMap<>();
+ passportVisaObject.put(Ga4ghPassportVisa.TYPE, type);
+ passportVisaObject.put(Ga4ghPassportVisa.ASSERTED, asserted);
+ passportVisaObject.put(Ga4ghPassportVisa.VALUE, value);
+ passportVisaObject.put(Ga4ghPassportVisa.SOURCE, source);
+ passportVisaObject.put(Ga4ghPassportVisa.BY, by);
+
+ if (condition != null && !condition.isNull() && !condition.isMissingNode()) {
+ passportVisaObject.put(Ga4ghPassportVisa.CONDITION, condition);
+ }
+
+ JWSHeader jwsHeader = new JWSHeader.Builder(JWSAlgorithm.parse(jwtService.getDefaultSigningAlgorithm().getName()))
+ .keyID(jwtService.getDefaultSignerKeyId())
+ .type(JOSEObjectType.JWT)
+ .jwkURL(jku)
+ .build();
+
+ JWTClaimsSet jwtClaimsSet = new JWTClaimsSet.Builder()
+ .issuer(issuer)
+ .issueTime(new Date())
+ .expirationTime(new Date(expires * 1000L))
+ .subject(sub)
+ .jwtID(UUID.randomUUID().toString())
+ .claim(Ga4ghPassportVisa.GA4GH_VISA_V1, passportVisaObject)
+ .build();
+
+ SignedJWT myToken = new SignedJWT(jwsHeader, jwtClaimsSet);
+ jwtService.signJwt(myToken);
+
+ return JsonNodeFactory.instance.textNode(myToken.serialize());
+ }
+
+ protected void callPermissionsJwtAPI(Ga4ghClaimRepository repo,
+ Map<String, String> uriVariables,
+ ArrayNode passport,
+ Set<String> linkedIdentities)
+ {
+ log.debug("GA4GH: {}", uriVariables);
+ JsonNode response = callHttpJsonAPI(repo, uriVariables);
+ if (response != null) {
+ JsonNode visas = response.path(GA4GH_CLAIM);
+ if (visas.isArray()) {
+ for (JsonNode visaNode : visas) {
+ if (visaNode.isTextual()) {
+ Ga4ghPassportVisa visa = Utils.parseAndVerifyVisa(visaNode.asText(), signers, remoteJwkSets, mapper);
+ if (visa.isVerified()) {
+ log.debug("Adding a visa to passport: {}", visa);
+ passport.add(passport.textNode(visa.getJwt()));
+ linkedIdentities.add(visa.getLinkedIdentity());
+ } else {
+ log.warn("Skipping visa: {}", visa);
+ }
+ } else {
+ log.warn("Element of {} is not a String: {}", GA4GH_CLAIM, visaNode);
+ }
+ }
+ } else {
+ log.warn("{} is not an array in {}", GA4GH_CLAIM, response);
+ }
+ }
+ }
+
+ @SuppressWarnings("Duplicates")
+ private static JsonNode callHttpJsonAPI(Ga4ghClaimRepository repo, Map<String, String> uriVariables) {
+ //get permissions data
+ try {
+ JsonNode result;
+ try {
+ if (log.isDebugEnabled()) {
+ log.debug("Calling Permissions API at {}", repo.getRestTemplate().getUriTemplateHandler().expand(repo.getActionURL(), uriVariables));
+ }
+
+ result = repo.getRestTemplate().getForObject(repo.getActionURL(), JsonNode.class, uriVariables);
+ } catch (HttpClientErrorException ex) {
+ MediaType contentType = ex.getResponseHeaders().getContentType();
+ String body = ex.getResponseBodyAsString();
+
+ log.error("HTTP ERROR: {}, URL: {}, Content-Type: {}", ex.getRawStatusCode(), repo.getActionURL(), contentType);
+
+ if (ex.getRawStatusCode() == 404) {
+ log.warn("Got status 404 from Permissions endpoint {}, ELIXIR AAI user is not linked to user at Permissions API",
+ repo.getActionURL());
+
+ return null;
+ }
+
+ if (JSON.equals(contentType.getSubtype())) {
+ try {
+ log.error(new ObjectMapper().readValue(body, JsonNode.class).path("message").asText());
+ } catch (IOException e) {
+ log.error("cannot parse error message from JSON", e);
+ }
+ } else {
+ log.error("cannot make REST call, exception: {} message: {}", ex.getClass().getName(), ex.getMessage());
+ }
+
+ return null;
+ }
+ log.debug("Permissions API response: {}", result);
+
+ return result;
+ } catch (Exception ex) {
+ log.error("Cannot get dataset permissions", ex);
+ }
+
+ return null;
+ }
+}
diff --git a/src/main/java/cz/muni/ics/ga4gh/utils/Utils.java b/src/main/java/cz/muni/ics/ga4gh/utils/Utils.java
new file mode 100644
index 0000000..7037cb9
--- /dev/null
+++ b/src/main/java/cz/muni/ics/ga4gh/utils/Utils.java
@@ -0,0 +1,218 @@
+package cz.muni.ics.ga4gh.utils;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.nimbusds.jose.Payload;
+import com.nimbusds.jose.crypto.RSASSAVerifier;
+import com.nimbusds.jose.jwk.JWK;
+import com.nimbusds.jose.jwk.JWKMatcher;
+import com.nimbusds.jose.jwk.JWKSelector;
+import com.nimbusds.jose.jwk.RSAKey;
+import com.nimbusds.jose.jwk.source.RemoteJWKSet;
+import com.nimbusds.jose.proc.SecurityContext;
+import com.nimbusds.jwt.JWTParser;
+import com.nimbusds.jwt.SignedJWT;
+import cz.muni.ics.ga4gh.config.Ga4ghConfig;
+import cz.muni.ics.ga4gh.model.Ga4ghClaimRepository;
+import cz.muni.ics.ga4gh.model.Ga4ghPassportVisa;
+import cz.muni.ics.ga4gh.model.Repo;
+import cz.muni.ics.ga4gh.model.RepoHeader;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.http.client.ClientHttpRequestInterceptor;
+import org.springframework.http.client.InterceptingClientHttpRequestFactory;
+import org.springframework.web.client.RestTemplate;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
+import java.time.Instant;
+import java.time.ZoneId;
+import java.time.ZonedDateTime;
+import java.time.format.DateTimeFormatter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+@Slf4j
+public class Utils {
+
+ public static void parseConfigFile(Ga4ghConfig config,
+ List<Ga4ghClaimRepository> claimRepositories,
+ Map<URI, RemoteJWKSet<SecurityContext>> remoteJwkSets,
+ Map<URI, String> signers)
+ {
+ for (Repo repo : config.getRepos()) {
+ initializeRepo(repo, claimRepositories);
+ initializeSigner(signers, remoteJwkSets, repo.getName(), repo.getJwks());
+ }
+ }
+
+ public static Ga4ghPassportVisa parseAndVerifyVisa(String jwtString,
+ Map<URI, String> signers,
+ Map<URI, RemoteJWKSet<SecurityContext>> remoteJwkSets,
+ ObjectMapper mapper)
+ {
+ Ga4ghPassportVisa visa = new Ga4ghPassportVisa(jwtString);
+
+ try {
+ SignedJWT signedJWT = (SignedJWT) JWTParser.parse(jwtString);
+ URI jku = signedJWT.getHeader().getJWKURL();
+
+ if (jku == null) {
+ log.error("JKU is missing in JWT header");
+ return visa;
+ }
+
+ visa.setSigner(signers.get(jku));
+ RemoteJWKSet<SecurityContext> remoteJWKSet = remoteJwkSets.get(jku);
+
+ if (remoteJWKSet == null) {
+ log.error("JKU '{}' is not among trusted key sets", jku);
+ return visa;
+ }
+
+ List<JWK> keys = remoteJWKSet.get(new JWKSelector(
+ new JWKMatcher.Builder().keyID(signedJWT.getHeader().getKeyID()).build()), null);
+
+ RSASSAVerifier verifier = new RSASSAVerifier(((RSAKey) keys.get(0)).toRSAPublicKey());
+ visa.setVerified(signedJWT.verify(verifier));
+
+ if (visa.isVerified()) {
+ Utils.processPayload(mapper, visa, signedJWT.getPayload());
+ }
+ } catch (Exception ex) {
+ log.error("Visa '{}' cannot be parsed and verified", jwtString, ex);
+ }
+ return visa;
+ }
+
+ public static void processPayload(ObjectMapper mapper, Ga4ghPassportVisa visa, Payload payload)
+ throws IOException
+ {
+ JsonNode doc = mapper.readValue(payload.toString(), JsonNode.class);
+ checkVisaKey(visa, doc, Ga4ghPassportVisa.SUB);
+ checkVisaKey(visa, doc, Ga4ghPassportVisa.EXP);
+ checkVisaKey(visa, doc, Ga4ghPassportVisa.ISS);
+
+ JsonNode visa_v1 = doc.path(Ga4ghPassportVisa.GA4GH_VISA_V1);
+ if (visa_v1.isMissingNode() || visa_v1.isNull() || visa_v1.isEmpty()) {
+ log.warn("Nothing available in '{}', considering visa as not verified", Ga4ghPassportVisa.GA4GH_VISA_V1);
+ visa.setVerified(false);
+ return;
+ }
+
+ checkVisaKey(visa, visa_v1, Ga4ghPassportVisa.TYPE);
+ checkVisaKey(visa, visa_v1, Ga4ghPassportVisa.ASSERTED);
+ checkVisaKey(visa, visa_v1, Ga4ghPassportVisa.VALUE);
+ checkVisaKey(visa, visa_v1, Ga4ghPassportVisa.SOURCE);
+ checkVisaKey(visa, visa_v1, Ga4ghPassportVisa.BY);
+
+ if (!visa.isVerified()) {
+ return;
+ }
+
+ long exp = doc.get(Ga4ghPassportVisa.EXP).asLong();
+ if (exp < Instant.now().getEpochSecond()) {
+ log.warn("visa expired on {}", isoDateTime(exp));
+ visa.setVerified(false);
+ return;
+ }
+
+ visa.setLinkedIdentity(URLEncoder.encode(doc.get(Ga4ghPassportVisa.SUB).asText(), StandardCharsets.UTF_8) +
+ ',' + URLEncoder.encode(doc.get(Ga4ghPassportVisa.ISS).asText(), StandardCharsets.UTF_8));
+
+ visa.setPrettyPayload(
+ visa_v1.get(Ga4ghPassportVisa.TYPE).asText() + ": '"
+ + visa_v1.get(Ga4ghPassportVisa.VALUE).asText() + "' asserted at '"
+ + isoDate(visa_v1.get(Ga4ghPassportVisa.ASSERTED).asLong()) + '\''
+ );
+ }
+
+ public static long getOneYearExpires(long asserted) {
+ return getExpires(asserted, 1L);
+ }
+
+ public static long getExpires(long asserted, long addYears) {
+ return Instant.ofEpochSecond(asserted).atZone(ZoneId.systemDefault()).plusYears(addYears).toEpochSecond();
+ }
+
+ private static void initializeSigner(Map<URI, String> signers,
+ Map<URI, RemoteJWKSet<SecurityContext>> remoteJwkSets,
+ String name,
+ String jwks)
+ {
+ try {
+ URL jku = new URL(jwks);
+ remoteJwkSets.put(jku.toURI(), new RemoteJWKSet<>(jku));
+ signers.put(jku.toURI(), name);
+
+ log.info("JWKS Signer '{}' added with keys '{}'", name, jwks);
+ } catch (MalformedURLException | URISyntaxException e) {
+ log.error("cannot add to RemoteJWKSet map: '{}' -> '{}'", name, jwks, e);
+ }
+ }
+
+ private static void initializeRepo(Repo repo, List<Ga4ghClaimRepository> claimRepositories) {
+ String name = repo.getName();
+ String actionURL = repo.getUrl();
+ List<RepoHeader> headers = repo.getHeaders();
+
+ if (actionURL == null || headers.isEmpty()) {
+ log.error("claim repository '{}' not defined with url|auth_header|auth_value", repo);
+ return;
+ }
+
+ RestTemplate restTemplate = new RestTemplate();
+ restTemplate.setRequestFactory(
+ new InterceptingClientHttpRequestFactory(restTemplate.getRequestFactory(), getClientHttpRequestInterceptors(headers))
+ );
+
+ claimRepositories.add(new Ga4ghClaimRepository(name, actionURL, restTemplate));
+ log.info("GA4GH Claims Repository '{}' configured at '{}'", name, actionURL);
+ }
+
+ private static void checkVisaKey(Ga4ghPassportVisa visa, JsonNode jsonNode, String key) {
+ if (jsonNode.path(key).isMissingNode()) {
+ log.warn("Key '{}' is missing in the Visa, therefore cannot be verified", key);
+ visa.setVerified(false);
+ } else {
+ switch (key) {
+ case Ga4ghPassportVisa.SUB:
+ visa.setSub(jsonNode.path(key).asText());
+ break;
+ case Ga4ghPassportVisa.ISS:
+ visa.setIss(jsonNode.path(key).asText());
+ break;
+ case Ga4ghPassportVisa.TYPE:
+ visa.setType(jsonNode.path(key).asText());
+ break;
+ case Ga4ghPassportVisa.VALUE:
+ visa.setValue(jsonNode.path(key).asText());
+ break;
+ default:
+ log.warn("Unknown visa key: {}", key);
+ }
+ }
+ }
+
+ private static String isoDate(long linuxTime) {
+ return isoFormat(linuxTime, DateTimeFormatter.ISO_LOCAL_DATE);
+ }
+
+ private static String isoDateTime(long linuxTime) {
+ return isoFormat(linuxTime, DateTimeFormatter.ISO_DATE_TIME);
+ }
+
+ private static String isoFormat(long linuxTime, DateTimeFormatter formatter) {
+ ZonedDateTime zdt = ZonedDateTime.ofInstant(Instant.ofEpochSecond(linuxTime), ZoneId.systemDefault());
+ return formatter.format(zdt);
+ }
+
+ private static List<ClientHttpRequestInterceptor> getClientHttpRequestInterceptors(List<RepoHeader> headers) {
+ return new ArrayList<>(headers);
+ }
+}
diff --git a/src/main/resources/application-bbmri.yml b/src/main/resources/application-bbmri.yml
new file mode 100644
index 0000000..39cd3d1
--- /dev/null
+++ b/src/main/resources/application-bbmri.yml
@@ -0,0 +1,77 @@
+---
+
+spring:
+ profiles: bbmri
+
+broker:
+ bona-fide-status-attr: bona_fide_status
+ bona-fide-status-rems-attr: bona_fide_status_rems
+ group-affiliations-attr: groupAffiliations
+ terms-and-policies-group-id: 1
+ affiliations-attr: affiliations
+ org-url-attr: orgUrl
+ ext-source-name: ext-source-name
+ issuer: issuer
+ path-to-jwk-file: path
+adapter:
+ adapter-primary: rpc
+ call-fallback: false
+ldap:
+ host: host
+ user: user
+ password: password
+ base-dn: dn
+ use-tls: false
+ use-ssl: true
+ allow-untrusted-ssl: false
+ timeout-secs: 10
+ port: 636
+rpc:
+ enabled: true
+ url: url
+ username: username
+ password: password
+ serializer: json
+attributes:
+ attributeMappings:
+ bona_fide_status:
+ internal-name: bona_fide_status
+ rpc-name: urn:perun:user:attribute-def:def:bonaFideStatus
+ ldap-name: bonaFideStatus
+ bona_fide_status_rems:
+ internal-name: bona_fide_status_rems
+ rpc-name: urn:perun:user:attribute-def:def:elixirBonaFideStatusREMS
+ ldap-name: bonaFideStatusREMS
+ groupAffiliations:
+ internal-name: groupAffiliations
+ rpc-name: urn:perun:group:attribute-def:def:groupAffiliations
+ ldap-name: groupAffiliations
+ affiliations:
+ internal-name: affiliations
+ rpc-name: urn:perun:ues:attribute-def:def:affiliation
+ ldap-name:
+ orgUrl:
+ internal-name: orgUrl
+ rpc-name: urn:perun:ues:attribute-def:def:organizationURL
+ ldap-name:
+ga4gh:
+ repos:
+ -
+ name: repo1
+ url: url1
+ jwks: jwks1
+ headers:
+ -
+ header: header
+ value: value
+ -
+ name: repo2
+ url: url2
+ jwks: jwks2
+ headers:
+ -
+ header: header
+ value: value
+basic-auth:
+ username: Honza
+ password: Lojza
diff --git a/src/main/resources/application-elixir.yml b/src/main/resources/application-elixir.yml
new file mode 100644
index 0000000..881f452
--- /dev/null
+++ b/src/main/resources/application-elixir.yml
@@ -0,0 +1,92 @@
+---
+
+spring:
+ config:
+ activate:
+ on-profile: elixir
+ mvc:
+ pathmatch:
+ matching-strategy: ant_path_matcher
+
+broker:
+ bona-fide-status-attr: bona_fide_status
+ bona-fide-status-rems-attr: bona_fide_status_rems
+ group-affiliations-attr: groupAffiliations
+ terms-and-policies-group-id: 1
+ affiliations-attr: affiliations
+ org-url-attr: orgUrl
+ attributes-to-search:
+ - "elixir-persistent-shadow"
+ issuer: issuer
+ jku: jku-url
+ path-to-jwk-file: path
+adapter:
+ adapter-primary: ldap
+ call-fallback: false
+ldap:
+ host: host
+ user: user
+ password: password
+ base-dn: dn
+ use-tls: false
+ use-ssl: true
+ allow-untrusted-ssl: false
+ timeout-secs: 10
+ port: 636
+rpc:
+ enabled: true
+ url: url
+ username: username
+ password: password
+ serializer: json
+attributes:
+ attributeMappings:
+ bona_fide_status:
+ internal-name: bona_fide_status
+ rpc-name: name
+ ldap-name: name
+ bona_fide_status_rems:
+ internal-name: bona_fide_status_rems
+ rpc-name: name
+ ldap-name: name
+ groupAffiliations:
+ internal-name: groupAffiliations
+ rpc-name: name
+ ldap-name: name
+ affiliations:
+ internal-name: affiliations
+ rpc-name: name
+ ldap-name: name
+ orgUrl:
+ internal-name: orgUrl
+ rpc-name: name
+ ldap-name: name
+ elixir-persistent-shadow:
+ internal-name: elixir-persistent-shadow
+ rpc-name: name
+ ldap-name: name
+ preferred-mail:
+ internal-name: preferred-mail
+ rpc-name: name
+ ldap-name: name
+ga4gh:
+ repos:
+ -
+ name: repo1
+ url: url1
+ jwks: jwks1
+ headers:
+ -
+ header: header
+ value: value
+ -
+ name: repo2
+ url: url2
+ jwks: jwks2
+ headers:
+ -
+ header: header
+ value: value
+basic-auth:
+ username: username
+ password: password
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
new file mode 100644
index 0000000..63d98d7
--- /dev/null
+++ b/src/main/resources/application.yml
@@ -0,0 +1,13 @@
+---
+
+spring:
+ main:
+ allow-bean-definition-overriding: true
+ profiles:
+ active: elixir
+
+logging:
+ file:
+ path: /var/lib/tomcat9/logs/broker.log
+ level:
+ root: debug
\ No newline at end of file
diff --git a/update-versions.sh b/update-versions.sh
new file mode 100755
index 0000000..d89eb68
--- /dev/null
+++ b/update-versions.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+./mvnw versions:set -DnewVersion=$1
\ No newline at end of file
--
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