Development AssayClasses RESTful service

Dev Service

This simple, standalone service is designed for quick changes to the assay class/rule chain information during development to allow for quick testing. The service two endpoints:

• /assayclasses?application_context=HUBMAP
• /assayclasses/<assay-code>?application_context=HUBMAP

JSON backing file and releasing to UBKG

The assayclasses.json file file is read directly by this service to form the responses. This file can be changed directly in GitHub (in the development branch only) to test changes to the associated rule chain/assay class information that normally is sourced from UBKG. To develop using this service and eventually release to UBKG follow this procedure:

• For each release cycle create a new release branch from main.
• On the new release branch, update the assayclasses.json file.
• From that release branch, create a PR to development and merge the changes into the development branch. Test locally or using the HuBMAP DEV infrastructure where this dev service is available at http://gateway.dev.hubmapconsortium.org:8181/assayclasses.
• If there are new changes necessary, make those changes to release and create a new PR into development. Repeat testing.
• After a week of accumulating features on the release branch, create a PR into main from the release.
• Add Alan Simmons as a reviewer on the PR.
• Alan will add the changes to UBKG Neo4j. Zhou will release to the UBKG DEV instance and can be accessed at https://ontology-api.dev.hubmapconsortium.org/.
• Test the changes on the HuBMAP TEST infrastructure (TEST infrastructure is connected to UBKG DEV instance).
• After successful testing on TEST the changes to UBKG Neo4j will be released to PROD.

Running the service locally

To run this service, in this directory:

• copy instance/app.cfg.example to instance/app.cfg
• create a python virtual environment with the contents of requirements.txt imported into the environment
• source/activate the virtual environment
• execute python app.py The service will be available on port 8181. See below for instructions to run with Docker

Both endpoints require the application_context=HUBMAP parameter. (A future version will allow SENNET context as well, which will read results from a different file).

Endpoints

The /assayclasses endpoint simply returns the contents of the assayclasses.json file as a json response.

The /assayclasses/<assay-code> endpoint searches the same assayclasses.json file for an assayclass item matching rule_description.code and returns the full matching assayclass item as a json response. If the code is not found a 404 is returned. For example if /assayclasses/C200001?application_context=HUBMAP is called the return value is:

{
  "rule_description": {
    "application_context": "HUBMAP",
    "code": "C200150",
    "name": "non-DCWG primary IMC2D"
  },
  "value": {
    "active_status": "active",
    "assaytype": "IMC2D",
    "dataset_type": {
      "PDR_category": "MxNF",
      "dataset_type": "2D Imaging Mass Cytometry",
      "fig2": {
        "aggregated_assaytype": "LC-MS",
        "category": "bulk",
        "modality": "Proteomics"
      }
    },
    "description": "2D Imaging Mass Cytometry",
    "dir_schema": "imc-v0",
    "is_multiassay": false,
    "measurement_assay": {
      "codes": [
        {
          "code": "SENNET:C006901",
          "term": "Imaging Mass Cytometry Measurement Assay"
        },
        {
          "code": "HUBMAP:C006901",
          "term": "Imaging Mass Cytometry Measurement Assay"
        },
        {
          "code": "OBI:0003096",
          "term": "imaging mass cytometry assay"
        }
      ],
      "contains_full_genetic_sequences": false
    },
    "must_contain": [],
    "pipeline_shorthand": null,
    "process_state": "primary",
    "provider": "IEC",
    "tbl_schema": "imc-v",
    "vitessce_hints": []
  }
}

Docker Deployment on DEV VM

First build a new docker image

docker-compose build

Then spin up the container

docker-compose up -d

Once the container is up running correctly, you can access at http://gateway.dev.hubmapconsortium.org:8181/assayclasses