v1 (I2B2 Demodata)
The v1 loader expects an already existing i2b2 database (in .csv format) that will be converted in a way that is compliant with the MedCo data model. This involves encrypting and deterministically tagging some of the data.
List of input (‘original’) files:
    all i2b2metadata files (e.g. i2b2.csv)
    dummy_to_patient.csv
    patient_dimension.csv
    visit_dimension.csv
    concept_dimension.csv
    modifier_dimension.csv
    observation_fact.csv
    table_access.csv

How to use

Ensure you have downloaded the data before proceeding to the loading.
The following examples show you how to load data into a running MedCo deployment. Adapt accordingly the commands your use-case.

Examples

Loading the three nodes on the dev-local-3nodes profile

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export MEDCO_SETUP_DIR=~/medco \
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MEDCO_DEPLOYMENT_PROFILE=dev-local-3nodes
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cd "${MEDCO_SETUP_DIR}/deployments/${MEDCO_DEPLOYMENT_PROFILE}"
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docker-compose -f docker-compose.tools.yml run medco-loader-srv0 v1 \
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--sen /data/i2b2/sensitive.txt \
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--files /data/i2b2/files.toml
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docker-compose -f docker-compose.tools.yml run medco-loader-srv1 v1 \
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--sen /data/i2b2/sensitive.txt \
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--files /data/i2b2/files.toml
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docker-compose -f docker-compose.tools.yml run medco-loader-srv2 v1 \
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--sen /data/i2b2/sensitive.txt \
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--files /data/i2b2/files.toml
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Loading one node on a network-test profile

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export MEDCO_SETUP_DIR=~/medco \
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MEDCO_DEPLOYMENT_PROFILE=test-network-xxx-node0
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cd "${MEDCO_SETUP_DIR}/deployments/${MEDCO_DEPLOYMENT_PROFILE}"
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docker-compose -f docker-compose.tools.yml run medco-loader v1 \
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--sen /data/i2b2/sensitive.txt \
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--files /data/i2b2/files.toml
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Explanation of the command's arguments

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NAME:
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medco-loader v1 - Convert existing i2b2 data model
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USAGE:
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medco-loader v1 [command options] [arguments...]
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OPTIONS:
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--group value, -g value UnLynx group definition file
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--entryPointIdx value, --entry value Index (relative to the group definition file) of the collective authority server to load the data
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--sensitive value, --sen value File containing a list of sensitive concepts
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--dbHost value, --dbH value Database hostname
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--dbPort value, --dbP value Database port (default: 0)
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--dbName value, --dbN value Database name
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--dbUser value, --dbU value Database user
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--dbPassword value, --dbPw value Database password
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--files value, -f value Configuration toml with the path of the all the necessary i2b2 files
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--empty, -e Empty patient and visit dimension tables (y/n)
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Test that the loading was successful

To check that it is working you can query for:
-> Diagnoses -> Neoplasm -> Benign neoplasm -> Benign neoplasm of breast
You should obtain 2 matching subjects.
Last modified 8mo ago