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* version/2.5: update documentation related to JSON serialisation of events including dataflow Create example PipeConfig using SystemCmd to create dataflow from a JSON file
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Serialising dataflow events with JSON | ||
===================================== | ||
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There are some facilities to support serialisaiton of events such as dataflow as JSON files or streams. | ||
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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. | ||
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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. |
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modules/Bio/EnsEMBL/Hive/Examples/SystemCmd/PipeConfig/InjectJSONDataflow_conf.pm
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=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 | ||
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package Bio::EnsEMBL::Hive::Examples::SystemCmd::PipeConfig::InjectJSONDataflow_conf; | ||
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use strict; | ||
use warnings; | ||
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf'); | ||
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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', | ||
}, | ||
]; | ||
} | ||
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1; | ||
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...EnsEMBL/Hive/Examples/SystemCmd/PipeConfig/sample_files/Inject_JSON_Dataflow_example.json
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{"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"} |
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