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importing-data.md

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Importing Data

In order to use Blaze for queries, you have to import your data. Although you can use the full functionality of the FHIR RESTful API available under http://localhost:8080/fhir to create resources, the easiest way is to download blazectl to upload bundles.

First you should test connectivity by counting already available resources in Blaze which should be zero:

blazectl --server http://localhost:8080/fhir count-resources

which should return:

Count all resources on http://localhost:8080/fhir ...

-------------------------------------
total                             : 0

After that, you need a FHIR bundle to upload. You can generate one by downloading bbmri-fhir-gen and run:

mkdir fhir-test-data
bbmri-fhir-gen fhir-test-data

That will generate two files under fhir-test-data:

-rw-r--r--  1 akiel  staff    31K Nov  8 10:16 biobank.json
-rw-r--r--  1 akiel  staff   757K Nov  8 10:16 transaction-0.json

After you have the test data, you can upload it with:

blazectl --server http://localhost:8080/fhir upload fhir-test-data

which will output:

Starting Upload to http://localhost:8080/fhir ...
Uploads          [total, concurrency]     2, 2
Success          [ratio]                  100.00 %
Duration         [total]                  3s
Requ. Latencies  [mean, 50, 95, 99, max]  2.414s, 3.313s, 3.313s, 3.313s 3.313s
Proc. Latencies  [mean, 50, 95, 99, max]  2.412s, 3.31s, 3.31s, 3.31s 3.31s
Bytes In         [total, mean]            123.60 KiB, 61.80 KiB
Bytes Out        [total, mean]            788.30 KiB, 394.15 KiB
Status Codes     [code:count]             200:2

counting the FHIR resources again:

blazectl --server http://localhost:8080/fhir count-resources

should return:

Count all resources on http://localhost:8080/fhir ...

Condition                         : 100
Observation                       : 431
Organization                      :  11
Patient                           : 100
Specimen                          : 100
---------------------------------------
total                             : 742