- Delay reading the properties until the first call of the getProperty method.
- Added the initializeIfNeeded method: load properties and check them if the properties field is null.
- Call the initializeIfNeeded method from the getProperty method.
- Made the checkConfiguration method static, check whether the configuration file exists, and removed the call to the System.exit method.
Added the design (in json format) of a test Galaxy workflow for concatenation as a resource file.
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Added some information about the tool: written in Java, uses blend4j.
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Added links to BioMedBridges and CTMM TraIT.
Create DevelopersInformation.md

First version of developer information, derived from https://github.com/CTMM-TraIT/trait_proteomics_qc_tool/edit/master/ProteomicsQCReportViewer/devinf/DevelopersInformation.md.
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Added links to tranSMART, Galaxy and blend4j.
- Added some BioBlend and Galaxy API links.
- Renamed test workflow to "TestWorkflowConcatenate".
- Added more parameters to the runWorkflow method to make it more generic: TEST_WORKFLOW_JSON and workflowInputs.
- Made the prepareConcatenationWorkflow method more generic using the workflowInputs parameter.
- Moved the getTestFile method to where it's called.
Refactored the Maven pom.xml file
- Removed old/unused parts.
- Used properties for all dependency and build versions.
- Reordered parts: first the dependencies section and after that the build section.
Checkstyle and logging improvements
- Added Checkstyle configuration files (checkstyle.xml and checkstyle-suppressions.xml). Both are modified versions of the ones from the ConceptWiki project (see https://trac.nbic.nl/conceptwiki/browser/trunk/code/conceptwiki).
- Resolved all sorts of Checkstyle issues: added Javadocs, hidden constructors, reordering import statements, and package-info.java files for two packages.
- Used logging instead of println statements in several classes and switched to the simple logging facade for Java (SLF4J) instead of Log4j.
Checkstyle issues
- Split up the runWorkflow method by creating several new smaller methods.
- Used a logger instead of println statements and printStackTrace calls.
- Log problems with uploading input files.
- Created several constants.
- Created and expanded Javadocs.
- checkstyle.xml: added 2 as an ignored magic number and disabled the Indentation check because the throwsIndent property is not supported (requires Checkstyle 5.7; maven-checkstyle-plugin currently uses Checkstyle 5.6).
More minor Checkstyle issues
- Created Javadocs.
- Created constant.
- Replaced asserts by logger calls.
- WorkflowUtils: added hidden constructor.
- checkstyle.xml: added -2 as an ignored magic number.
Update DevelopersInformation.md

Added a section on Checkstyle.
Explicit encoding and improved Javadoc
- Specified the UTF-8 encoding explicitly for creating a file in the getTestFile method (which fixed a FindBugs issue).
- Added more details to the @return tag in the Javadoc of the getOutputLength method.
Merge remote-tracking branch 'remotes/origin/master'
Update DevelopersInformation.md

Added a section on FindBugs.
Update README.md

Added a link to the DevelopersInformation.md file.
Changed the logging configuration
- In WorkflowRunner: added logging initialization.
- In pom.xml: changed logging properties and dependencies to use SLF4J and log4j, moved comment about the maven-jxr-plugin (was causing issues).
- Added log4j.xml logging configuration file with a file appender and a console appender.
Update README.md

Added PMD and CPD in tools list.