Remove force-run-all from decider launching routine
- starting with Seqware 1.0.17, force-run-all has been renamed to "ignore-previous-runs"
- deciders install a new workflow instance and schedule with this workflow instance, so for the first run, ignore-previous-runs is not required
- if "ignore-previous-runs" is required, provided it via the extraArgs paramter (or "parameters" section of decider run test definition)
Update common-utilities to use Seqware 1.0.17
Increment common-utilities version to 1.1
Merge pull request #5 from pipedev/PDE-728

PDE-728
Updated workflow test definition parsing to use jackson json doc to pojo (TestDefinition class)
- Added parameters json option too to allow overriding key-value pairs from ini file
Merge pull request #6 from pipedev/PDE-502

Updated workflow test definition parsing to use jackson json doc to pojo...
Support for running a workflow test without an ini file
- For example, if an ini file and parameters are not specified in the test json, the workflow test will be run with the workflow's default parameters
- In the case where the ini file is not specified, an "id" should be set, and the metrics file should be name <id>.metrics.  Override this be specifying "metrics_file" (either full path, or the file name in "output_metrics_dir").
Merge pull request #7 from pipedev/PDE-502

Support for running a workflow test without an ini file
Support for multiple ini files; Parameters temporary workaround
- "parameters" specified via the json workflow test definition may not be interpreted correctly from the seqware command line
- as a workaround, parameters are saved to an ini file which is passed to the seqware command line
- this also required that multiple ini files be supported by the testing framework
- improved logging in Helpers isFileAccessible
Merge pull request #8 from pipedev/PDE-502

Support for multiple ini files; Parameters temporary workaround
Update file provenance report parsing and PDE representation from seqware 1.0.14 to 1.0.17+
- new attributes: 
Root Sample Name
Root Sample SWID
Parent Sample Organism IDs
Sample Organism ID
Sample Organism Code
Sequencer Run Platform ID
Sequencer Run Platform Name
- parent samples are now represented as objects (rather than lists or maps encoded as strings)
Merge branch 'develop' into PDE-743

Conflicts:
	common-utilities/pom.xml
Merge branch 'PDE-743' into develop
Reorganization of JSON validation code and tests
Merge pull request #10 from pipedev/PDE-502

Reorganization of JSON validation code and tests
More useful README
Fixed formatting for readme
Yet more formatting errors with the readme
We're doing one step workflows differently now, so I removed workflow-one-step. In the next few months, we will add more workflows to this repository
Improved performance and logging of FileProvenanceReport parsing
- Two validation modes are supported during parsing: string or skip.  Strict mode will throw an exception and exit if there is an error, skip will log an error and continue.
- For every 10000 records, a message will be printed to give the user an update of the process.
- Moved to log4j2 logging framework.
- Parent samples are now transformed to an object (rather than storing its seqware string representation).