A restful web service exposing calls needed for the Portal UI Next.js application. The API is documented here.
This repository relies on the ingest-validation-tools as a submodule for metadata validation. The
file .gitmodules
contains the configuration for the URL and specific branch of the submodule that is to be used. Once
you already have cloned this repository and switched to the target branch, to load the latest ingest-validation-tools
submodule:
git submodule update --init --remote
Right click the src folder and select Mark directory as > sources root You should see the src folder turn blue
After completing the steps in the Working with submodule section, right click the src/submodules/ingest_validation_tools/src folder and select Mark directory as > sources root
This application is written in Flask and it includes an app.cfg.example file in the instance
directory. Copy the file and rename it app.cfg and modify with the appropriate information.
This assumes you are developing the code with the Flask development server and you have access to the remote neo4j database.
In the project root directory:
./generate-build-version.sh
Create a new Python 3.x virtual environment:
python3 -m venv venv-hm-ingest-api
source venv-hm-ingest-api/bin/activate
Upgrade pip:
python3 -m pip install --upgrade pip
Then install the dependencies with using the main
branch code of commons:
export COMMONS_BRANCH=main
pip install -r requirements.txt
Either methods below will run the search-api web service at http://localhost:5005
. Choose one:
python3 app.py
cd src
export FLASK_APP=app.py
export FLASK_ENV=development
python3 -m flask run -p 5000
There are a few configurable environment variables to keep in mind:
COMMONS_BRANCH
: build argument only to be used during image creation when we need to use a branch of commons from github rather than the published PyPI package. Default to main branch if not set or null.HOST_UID
: the user id on the host machine to be mapped to the container. Default to 1002 if not set or null.HOST_GID
: the user's group id on the host machine to be mapped to the container. Default to 1002 if not set or null.cd docker
./docker-development.sh [check|config|build|start|stop|down]
cd docker
./docker-deployment.sh [start|stop|down]
main
branch (the default branch)main
yuanzhou
) is automatically assigned as a reviewer to each PR. When all other reviewers have approved, he will approve as well, merge to TEST infrastructure, and redeploy the TEST instance.main
have been approved after test/qa on TEST, Zhou will release to PROD using the same docker image that has been tested on TEST infrastructure.main
branchdev-integrate
main
for deployment and testing on the TEST infrastructure as above.The documentation for the API calls is hosted on SmartAPI. Modifying the ingest-api-spec.yaml
file and commititng the changes to github should update the API shown on SmartAPI. SmartAPI allows users to register API documents. The documentation is associated with this github account: api-developers@sennetconsortium.org.