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Running PDCi2b2

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Jean Louis Raisaro edited this page Sep 13, 2017 · 20 revisions

Running PDCi2b2

PDCi2b2 is a client-server application that requires to be deployed on two distinct and independent cloud providers. The first cloud provider (also storage cloud provider - SCP) is responsible for storing encrypted aggregate-level i2b2 data. The second cloud provider (also proxy cloud provider - PCP) is responsible for helping SCP during the re-encryption phase so that the query result is only .

Cloud Servers Setup

  1. Depending on the architecture and OS of the servers being used (default is amd64) execute:

./compileLinux.sh or ./compileMac.sh or ./compileWindows.sh

  1. Copy the executable to each cloud server (both SCP and PCP)

scp $GOPATH/src/github.com/JLRgithub/PDCi2b2/app/PDCi2b2 .

  1. For each server run a "server setup" and follow the installation guide

./PDCi2b2 server setup

  1. Create in your client machine (the one that will act as your client) a group.toml and append the content of all the public.toml files created during each setup.

Extraction Transformation and Loading (ETL) Phase

  1. Extract a CSV file from an i2b2 instance or generate a new one with the following columns (e.g., testdata.csv):
  • location_cd: this column stores the code of the location at which aggregate-level data has been collected
  • time: this column stores the time unit of the data collection, which can be set at any interval (i.e., month, quarter, year) as long as the unit is consistent across the dataset;
  • concept_cd:
  1. Copy the executable and example data files to each server

scp $GOPATH/github.com/lca1/unlynx/app/default/unlynx .

scp $GOPATH/github.com/lca1/unlynx/app/default/unlynx_test_data.txt .

github.com/lca1/unlynx/services/data/handle_data_test.go

  1. For each server run a "server setup" and follow the installation guide

./unlynx server setup

  1. Create in your client machine (the one that will act as your client) a group.toml and append the content of all the public.toml files created during each setup.

  2. Start each UnLynx conode

./unlynx server -c private.toml

  1. Run a query, for example:

./unlynx -d 1 -f group.toml -s "{s0, s1}" -w "{w0, 1, w1, 1}" -p "(v0 == v1 && v2 == v3)" -g "{g0, g1, g2}"

What each flag stands for:

-d = debug level; -f = group definition file; -s = select attributes; -w = where attributes + values; -p = query predicate; -g = group by attributes

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