Create example PipeConfig using SystemCmd to create dataflow from a JSON file

modules/Bio/EnsEMBL/Hive/Examples/SystemCmd/PipeConfig/InjectJSONDataflow_conf.pm

+=pod
+
+=head1 NAME
+
+    Bio::EnsEMBL::Hive::Examples::SystemCmd::PipeConfig::InjectJSONDataflow_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::SystemCmd::PipeConfig::InjectJSONDataflow_conf --pipeline_url $HIVE_URL
+
+    seed_pipeline.pl -url $HIVE_URL -logic_name perform_cmd -input_id "{'cmd' => 'sleep 0', 'dataflow_file' => './sample_files/Inject_JSON_Dataflow_example.json'}"
+
+    runWorker.pl -url $HIVE_URL
+
+=head1 DESCRIPTION
+
+    This is an example of using the SystemCmd runnable to create dataflow events using parameters read from a JSON file.
+    There is a sample file located in ${EHIVE_ROOT_DIR}/modules/Bio/EnsEMBL/Hive/Examples/SystemCmd/PipeConfig/sample_files/
+    This file is called Inject_JSON_Dataflow_example.json
+
+    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 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).
+
+    Note that a command must be provided to SystemCmd using the 'cmd' parameter, even if JSON parameter injection
+    is the only desired behaviour.
+
+
+=head1 LICENSE
+
+    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+    Copyright [2016-2021] EMBL-European Bioinformatics Institute
+
+    Licensed 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.
+
+=head1 CONTACT
+
+    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
+
+=cut
+
+
+package Bio::EnsEMBL::Hive::Examples::SystemCmd::PipeConfig::InjectJSONDataflow_conf;
+
+use strict;
+use warnings;
+use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
+
+
+sub pipeline_analyses {
+    return [
+        {   -logic_name    => 'perform_cmd',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -flow_into     => {
+                    1 => ['autoflow_test'],
+                    2 => ['branch2_test'],
+                    3 => ['branch3_test'],
+                    4 => ['branch4_test'],
+            },
+        },
+        {   -logic_name    => 'autoflow_test',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
+        },
+        {   -logic_name    => 'branch2_test',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
+        },
+        {   -logic_name    => 'branch3_test',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
+        },
+        {   -logic_name    => 'branch4_test',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
+        },
+    ];
+}
+
+1;
+

modules/Bio/EnsEMBL/Hive/Examples/SystemCmd/PipeConfig/sample_files/Inject_JSON_Dataflow_example.json

+{"addressed_to_one"  : "message for one"}
+2 {"addressed_to_two"  : "message for two"}
+4 {"addressed_to_four" : "message for four" , "also_addressed_to_four" : "second message for four"}