Elasticsearch

Now that installation is complete, we must configure and supply an index mapping to Elasticsearch.

The default installation comes with a sample index that can be used to demonstrate and understand how Arranger uses the ES mapping.

However, most users will wish to configure and supply their own index mapping, which is also possible.

Using the Default Index Mapping

The default index mapping, called file_centric_1.0, is a sample mapping used for cancer genomics, which represents genomic file metadata that can be searched in the data portal. In Arranger, the sample mapping is configured in the index_config.json file. The sample mapping can be examined here.

To use the default mapping, run the ES initialization script:

shell

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make init-es

Supplying a Custom Index Mapping

Alternatively, to configure and supply your own mapping:

1. First create your custom mapping. You can use the sample default mapping described earlier as a guide, but the best resource is to follow the guidelines and best practices from Elastic here.

2. Once you have your mapping created, you must copy and paste it into the aforementioned index_config.json file in the proper format. Again, use the existing sample file as a guide. The index_config.json file can be found in the arranger/docker/elasticsearch directory.

3. To use your custom mapping, run the ES initialization script:

shell

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make init-es