update documentation related to JSON serialisation of events including dataflow

docs/advanced_usage/json.rst

+Serialising dataflow events with JSON
+=====================================
+
+There are some facilities to support serialisaiton of events such as dataflow as JSON files or streams.
+
+The :ref:`Runnable API <runnable_api_dataflows>` provides a method
+``dataflow_output_ids_from_json($filename, $default_branch)`` to read a set of paramaters (output IDs)
+serialised as JSON from a flat file.
+
+Additionally, eHive uses JSON serialisation to interface Runnables written in guest languages (such as Python)
+with Workers. This is handled by, and documented in, ``Bio::EnsEMBL::Hive::GuestProcess``. This could serve
+as an example for advanced users wishing to construct infrastructure to transmit events between eHive
+and other systems.

docs/creating_runnables/runnable_api.rst

@@ -137,4 +137,4 @@ to easily generate events. The method takes two arguments:
    the default branch number.
 #. The default branch number (defaults to 1).
 
-
+Use of this is demonstrated in the Runnable :doxehive:`Bio::EnsEMBL::Hive::RunnableDB::SystemCmd`

docs/index.rst

@@ -73,6 +73,7 @@ User documentation
    advanced_usage/mpi
    advanced_usage/slack
    advanced_usage/continuous_pipelines
+   advanced_usage/json
 
 .. toctree::
    :caption: External plugins

modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm

@@ -15,7 +15,19 @@
     The command line must be stored in the parameters() as the value corresponding to the 'cmd' key.
     It allows to pass in other parameters and use the parameter substitution mechanism in its full glory.
 
-=head1 CONFIGURATION EXAMPLE
+    This Runnable also allows the creation of dataflow using JSON stored in an external file.
+    Each line of this file contains an optional branch number, followed by a complete JSON serialisation of the parameters (output_id)
+    appearing on the same single line. For example, a line to direct dataflow on branch 2 might look like:
+
+          2 {"parameter_name" : "parameter_value"}
+
+    If no branch number is provided, then dataflow of those parameters will occour on the branch number
+    passed to SystemCmd in the 'dataflow_branch' parameter, if given. Otherwise, it will default to
+    branch 1 (autoflow).
+
+    A sample file is provided at ${EHIVE_ROOT_DIR}/modules/Bio/EnsEMBL/Hive/Examples/SystemCmd/PipeConfig/sample_files/Inject_JSON_Dataflow_example.json
+
+=head1 CONFIGURATION EXAMPLES
 
     # The following example shows how to configure SystemCmd in a PipeConfig module
     # to create a MySQL snapshot of the Hive database before executing a critical operation.
@@ -31,6 +43,17 @@
             },
         },
 
+    # The following example shows how to configure SystemCmd in a PipeConfig module
+    # to generate dataflow events based on parameters stored as JSON in a file named "some_parameters.json"
+
+        {  -logic_name => 'inject_parameters_from_file',
+           -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+           -parameters => {
+                'dataflow_file' => 'some_parameters.json',
+                'cmd'           => 'sleep 0', # a command must be provided in the cmd parameter
+           },
+        },
+
 =head1 LICENSE
 
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute