first commit

README.md

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+# qPortal
+Working qPortal with ProjectBrowser and ProjectWizard

projectbrowser-portlet/.gitignore

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+# Eclipse
+.classpath
+.project
+.settings/
+
+# VS Code
+.vscode
+
+# Intellij
+.idea/
+*.iml
+*.iws
+
+# Mac
+.DS_Store
+
+# Maven
+target/
+
+# Some of our applications generate logs, which should be ignored by git
+logs/
+
+# Other
+**/.factorypath
+
+# compiled Vaadin widgetsets
+src/main/webapp/VAADIN/widgetsets

projectbrowser-portlet/.travis.settings.xml

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+<settings>
+    <servers>
+        <server>
+            <id>nexus-snapshots</id>
+            <username>${env.MAVEN_REPO_USERNAME}</username>
+            <password>${env.MAVEN_REPO_PASSWORD}</password>
+        </server>
+        <server>
+            <id>nexus-releases</id>
+            <username>${env.MAVEN_REPO_USERNAME}</username>
+            <password>${env.MAVEN_REPO_PASSWORD}</password>
+        </server>
+    </servers>
+</settings>

projectbrowser-portlet/.travis.yml

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+# Build script for Travis CI
+#
+
+# use fast-boot container-based hosts
+sudo: false 
+dist: trusty
+
+# no need to check for oracle's java
+language: java
+jdk: openjdk8
+
+# speed up builds by caching maven local repository
+cache:
+  directories:
+  - "$HOME/.m2/repository"
+
+# as agreed in our SOP
+branches:
+  only:
+  - master
+  - development
+
+# added to make logs look cleaner, crisper, certified fresh
+before_install: unset _JAVA_OPTIONS 
+
+# speed up builds by telling Travis that we don't need any special "installation"
+install: true
+
+# check if we need to add a license file for Vaadin charts
+before_script: if [ "$VAADIN_CHARTS_LICENSE_CODE" != "" ]; then
+                  echo "$VAADIN_CHARTS_LICENSE_CODE" > ~/.vaadin.charts.developer.license;
+               fi;
+
+# as agreed in our SOP, build everything (don't deploy, just try to 'mvn install' locally, which covers all phases)
+script: mvn --quiet --activate-profiles !development-build,!release-build --settings .travis.settings.xml clean cobertura:cobertura install
+# upload code coverage report, generate maven site (javadocs, documentation, static code analysis, etc.)
+after_success: 
+- bash <(curl -s https://codecov.io/bash)
+- mvn --quiet --activate-profiles !development-build,!release-build --settings .travis.settings.xml site
+
+# upload to maven
+deploy:
+  # as agreed in our SOP, builds on development branch will deploy to our maven repository after validating
+  # the artifact has a proper SNAPSHOT version
+  # artifact will be installed in our testing instance if it is a .war file
+- skip_cleanup: true
+  provider: script
+  script: mvn --quiet --activate-profiles development-build,!release-build --settings .travis.settings.xml deploy
+  on:
+    branch: development
+    condition: '"$TRAVIS_EVENT_TYPE" = "push"'
+  # as agreed in our SOP, tagging a commit on the master branch will upload to our maven repository
+  # after validating the artifact has a proper release version
+  # artifact will be installed in our testing instance if it is a .war file
+- skip_cleanup: true
+  provider: script
+  script: mvn --quiet --activate-profiles !development-build,release-build --settings .travis.settings.xml deploy
+  on:
+    branch: master
+    condition: '"$TRAVIS_EVENT_TYPE" = "push"'
+
+# change according to your needs, but we recommend to deactivate email notifications
+# for now, we configured Travis to send a notification to the #travis-ci channel 
+notifications:
+  email:
+    on_success: never
+    on_failure: never
+  slack: 
+    on_success: never
+    on_failure: always
+    # edit the following section if you want to get slack notifications
+    rooms:
+      - secure: "***"
+
+# credentials
+env:
+  global:
+    - secure: "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"
+    - secure: "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"

projectbrowser-portlet/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at info@qbic.uni-tuebingen.de. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

projectbrowser-portlet/LICENSE

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+MIT License
+
+Copyright (c) 2018, QBiC.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

projectbrowser-portlet/README.md

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+# ProjectBrowser Portlet
+
+[![Build Status](https://travis-ci.com/qbicsoftware/projectbrowser-portlet.svg?branch=development)](https://travis-ci.com/qbicsoftware/projectbrowser-portlet)[![Code Coverage]( https://codecov.io/gh/qbicsoftware/projectbrowser-portlet/branch/development/graph/badge.svg)](https://codecov.io/gh/qbicsoftware/projectbrowser-portlet)
+
+ProjectBrowser Portlet, version 1.6.3 - Browse and manage biomedical projects
+
+## Author
+Created by 
+* Christopher Mohr (christopher.mohr@qbic.uni-tuebingen.de) 
+* David Wojnar
+
+## Description
+
+The portlet ProjectBrowser offers functionality to view, manage and edit projects that are stored in an [openBIS](https://wiki-bsse.ethz.ch/display/bis/Home) instance. Users may download project-specific data or run analysis pipelines on the available datasets. Currently the workflow system gUSE is supported by ProjectBrowser. An interface to [Nextflow](https://www.nextflow.io/) is currently **under development**. 
+
+For further details please refer to:
+
+> Mohr, C., Friedrich, A., Wojnar, D., Kenar, E., Polatkan, A. C., Codrea, M. C., ... & Nahnsen, S. (2018). qPortal: A platform for data-driven biomedical research. PloS one, 13(1), e0191603.
+
+
+## How to Install
+
+If you want to use the ProjectBrowser portlet in your local Liferay instance do the following:
+* clone the git repository
+* run **mvn clean package** in the directory
+
+
+The generated *\*.war* file will be located in: 
+> /path/to/git/projectbrowser-portlet/target/
+
+Copy the file **projectbrowser-portlet-{version}.war** in the *deploy* folder of your Liferay instance.

projectbrowser-portlet/pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project 
+	xmlns="http://maven.apache.org/POM/4.0.0" 
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>life.qbic</groupId>
+		<artifactId>portlet-parent-pom</artifactId>
+		<version>1.3.0</version>
+	</parent>
+	<groupId>life.qbic</groupId>
+	<artifactId>projectbrowser-portlet</artifactId>
+	<version>1.7.0-SNAPSHOT</version>
+	<name>ProjectBrowser Portlet</name>
+	<url>http://github.com/qbicsoftware/projectbrowser-portlet</url>
+	<description>Browse and manage biomedical projects</description>
+	<packaging>war</packaging>
+	<!-- we only need to tell maven where to find our parent pom and other QBiC dependencies -->
+	<repositories>
+		<repository>
+			<releases>
+				<enabled>false</enabled>
+			</releases>
+			<snapshots>
+				<enabled>true</enabled>
+				<updatePolicy>always</updatePolicy>
+				<checksumPolicy>fail</checksumPolicy>
+			</snapshots>
+			<id>nexus-snapshots</id>
+			<name>QBiC Snapshots</name>
+			<url>https://qbic-repo.am10.uni-tuebingen.de/repository/maven-snapshots</url>
+		</repository>
+		<repository>
+			<releases>
+				<enabled>true</enabled>
+				<updatePolicy>always</updatePolicy>
+				<checksumPolicy>fail</checksumPolicy>
+			</releases>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+			<id>nexus-releases</id>
+			<name>QBiC Releases</name>
+			<url>https://qbic-repo.am10.uni-tuebingen.de/repository/maven-releases</url>
+		</repository>
+	</repositories>
+
+	<dependencies>
+		<dependency>
+			<groupId>life.qbic</groupId>
+			<artifactId>portal-utils-lib</artifactId>
+			<version>1.2.0-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>life.qbic</groupId>
+			<artifactId>core-utils-lib</artifactId>
+			<version>1.0.0</version>
+		</dependency>
+
+		<!-- openBIS client (version defined in parent POM) -->
+		<dependency>
+			<groupId>life.qbic</groupId>
+			<artifactId>openbis-client-lib</artifactId>
+			<version>1.1.4</version>
+		</dependency>
+
+		<!-- Access to our custom databases (portlets use direct JDBC to access data for now),
+			 but we will create a client library that portlets will use 
+			 (version  is defined in the parent POM hierarchy (/portal/pom.xml)) -->
+		<dependency>
+			<groupId>org.mariadb.jdbc</groupId>
+			<artifactId>mariadb-java-client</artifactId>
+		</dependency>
+
+		<!-- vaadin addon filteringtable -->
+		<dependency>
+			<groupId>org.vaadin.addons</groupId>
+			<artifactId>filteringtable</artifactId>
+			<version>0.9.15.v7</version>
+		</dependency>
+
+		<!-- vaadin addon expandingtextarea -->
+		<dependency>
+			<groupId>org.vaadin.addons</groupId>
+			<artifactId>expandingtextarea</artifactId>
+			<version>1.2.0</version>
+		</dependency>
+
+		<!-- apache commons-io -->
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.4</version>
+		</dependency>
+
+		<!-- apache commons-httpclient -->
+		<dependency>
+			<groupId>commons-httpclient</groupId>
+			<artifactId>commons-httpclient</artifactId>
+			<version>3.1</version>
+		</dependency>
+
+		<!-- apache commons-collections4 -->
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-collections4</artifactId>
+			<version>4.0</version>
+		</dependency>
+
+		<!-- sardine -->
+		<dependency>
+			<groupId>com.github.lookfirst</groupId>
+			<artifactId>sardine</artifactId>
+			<version>5.8</version>
+		</dependency>
+
+		<!-- XML manager lib -->
+		<dependency>
+			<groupId>life.qbic</groupId>
+			<artifactId>xml-manager-lib</artifactId>
+			<version>1.0.0</version>
+		</dependency>
+
+		<!-- workflow API based on guse -->
+		<dependency>
+			<groupId>life.qbic.guse</groupId>
+			<artifactId>guse-workflow-api</artifactId>
+			<version>20180720-1</version>
+		</dependency>
+
+        <!-- json read and write be aware that vaadin uses element.json -->
+		<dependency>
+			<groupId>org.json</groupId>
+			<artifactId>json</artifactId>
+			<version>20090211</version>
+		</dependency>
+
+        <!-- https://oss.sonatype.org/content/repositories/releases/com/github/vlsi/mxgraph/jgraphx/ -->
+		<dependency>
+			<groupId>com.github.vlsi.mxgraph</groupId>
+			<artifactId>jgraphx</artifactId>
+			<version>3.9.8.1</version>
+		</dependency>
+
+		<!-- docx4j -->
+		<dependency>
+			<groupId>org.docx4j</groupId>
+			<artifactId>docx4j</artifactId>
+			<version>3.3.2</version>
+		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/org.apache.ant/ant -->
+		<dependency>
+			<groupId>org.apache.ant</groupId>
+			<artifactId>ant</artifactId>
+			<version>1.10.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>life.qbic.knime</groupId>
+			<artifactId>knime-config-lib</artifactId>
+			<version>20180720-1</version>
+		</dependency>
+
+	</dependencies>
+</project>