After you have generated the JSON data files (see Building the CellBase database), you can now load them in your Mongo database.
Before loading the data into the database, your settings.xml file must have been appropriately configured indicating the database host names, ports, user and password. Here are the expected parameters:
name | default |
---|---|
CELLBASE.DB.MONGODB.HOST | localhost:27017 |
CELLBASE.DB.USER | <empty> |
CELLBASE.DB.PASSWORD | <empty> |
CELLBASE.SERVER.REST.PORT | 9090 |
Use the CellBase CLI to load the data models. For example, to load all human (GRCh37) data models from the /tmp/data/cellbase/v4/homo_sapiens_grch37/mongodb/
created in section "Build Data Models", into the cellbase_hsapiens_grch37_v4
database:
cellbase/build/bin$ ./cellbase.sh load -d variation --database cellbase_hsapiens_grch37_v4 -i /mnt/data/downloads/cellbase/v4/homo_sapiens_grch37/mongodb/ -L debug -Dmongodb-index-folder=/home/cafetero/appl/dev/cellbase/cellbase-app/app/mongodb-scripts/ |
Please, note that the whole loading and indexing process may need ~24h to complete, depending on the available hardware.
After successful load of all data, the corresponding database shall look like:
$ mongo mongodb-dev/cellbase_hsapiens_grch37_v4 MongoDB shell version: 3.0.9 connecting to: mongodb-dev/cellbase_hsapiens_grch37_v4clinical_variants > show collections; clinical_variants conservation gene genome_info genome_sequence metadata protein protein_functional_prediction protein_protein_interaction regulatory_region repeats variation variation_functional_score
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