Bulk Expression Atlas Solr scripts
Scripts to create and version-manage Solr collections used by bulk Expression Atlas.
Environment variables
The following environment variables are used in all scripts. Default values are indicated in parentheses.
SOLR_HOST
: host and port of the Solr server (localhost:8983
)SOLR_COLLECTION
: name of the collection to create (bulk-analytics-v1
)SOLR_BASE_CONFIG
: base configset to use for the collection (default
)SOLR_NUM_SHARDS
: number of shards (1
, recommended value2
)SOLR_REPLICATION_FACTOR
: replication factor (1
)
bulk-analytics
Collection This collection is used by Expression Atlas to store data and metadata of all experiments.
To create the collection run the following two scripts:
./bin/create-bulk-analytics-collection.sh
./bin/create-bulk-analytics-schema.sh
The scripts delete any previous version of the collection, its fields and field types, so error messages are to be expected the first time the scripts are run.
The collection is populated from the web app using these URLs:
/admin/analyticsIndex/buildIndex
: imports the data of public experiments only. Use the URL/admin/analyticsIndex/buildIndex/status
to follow the indexing progress./admin/experiments/{experiment-accession}/ANALYTICS_IMPORT
: loads into the collection a single experiment. Use/admin/experiments/{experiment-accession}/LOG
to track progress. Private experiments may be loaded using this endpoint./admin/experiments/{experiment-accession}/ANALYTICS_DELETE
: removes data of a single experiment from the collection.