pds:

pdspi-config:

pdspi-fhir-example:

pdspi-mapper-example:

pdspi-mapper-parallex-example:

pdspi-guidance-example:

tx-logging:

tx-router:

pds-release

Repo for facilitating coordinated release of multiple pds repos

step-by-step to add module

see developer guide

step-by-step to upgrade module

see developer guide

how to add your repo in a release

add submodule

Add your repo as a submodule under the module dir

If your repo have a Dockerfile, then a docker image will be built using that Dockerfile

Automatic tag discovery

If your repo have a tag <tag>, then the docker image will be tagged with <tag>, otherwise, the hash is going to be used as the tag.

add yml

Add a yml file under the plugin dir

how to write the yml file

see example under plugin/pds.yml

the image name should be the same as the submodule dir name

the tag should be from envrionment variable <submodule>_TAG

for all the images that your repo depends on, you can either specify an image with in a remote repo or you can add them as submodules of your repo to utilized the automatic tag discovery mechanism

for each submodule <a>, the image name should be the same as the submodule dir name and the tag should be from envrionment variable <submodule>_<a>_TAG

all the tag has - replaced by _

For example,

services:
  a:
    image: a-b:${a_b_TAG}
  b:
    image: c-d:${a_b_c_d_TAG}

stand up

Install fresh

git clone --recursive http://github.com/RENCI/pds-release

Pull all submodules

git submodule update --init --recursive

Python 3.8 is required.

pip install -r requirements.txt

./up.sh

Be sure to configure pds-release/test.system/env.pds to suit your needs, particularly the PDSPI_FHIR_EXAMPLE_FHIR_SERVER_URL_BASE variable.

tear down

./down.sh

system testing

python system.py test

enable fhir server

from remote server

set PDSPI_FHIR_EXAMPLE_FHIR_SERVER_URL_BASE in test.system/env.pds

from local data

Ingest local data:

cd module/pdspi-fhir-example
PYTHONPATH=tx-utils/src:tx-pcornet-to-fhir/ python ingest.py --base_url http://localhost:8080/v1/plugin/pdspi-fhir-example --input_dir <pcornet_data_path> --input_data_format pcori --output_dir <fhir_data_path>

The PCORNet data in <pcornet_data_path> will be ingested into a docker-managed volume so it will persist between ./down.sh and ./up.sh.

Check ingestion

Manually inspect the FHIR format in <fhir_data_path>
Retrieve some records

Find a in <fhir_data_path>/Patient/1000.json and run some queries:

curl http://localhost:8080/v1/plugin/pdspi-fhir-example/Patient/<patientid>

curl http://localhost:8080/v1/plugin/pdspi-fhir-example/MedicationRequest?patient=<patientid>

curl http://localhost:8080/v1/plugin/pdspi-fhir-example/Observation?patient=<patientid>

set subnet

set IPAM_CONFIG_SUBNET in module/tx-router/test/env.docker

We recommend keeping a separate "Qualified installation" (QI) document locally to record the value(s) of the subnets used for your development, staging, and production servers.

set config

set PDSPI_CONFIG_DEFAULT_CONFIG in test.system/env.pds

solving the dns error

try adding network_mode="host" in the call to build method call in system.py.

xu-hao / pds-release