Argo clinical

Requirements:

• node 12+
• Mongo 4.0

Design

How to:

Make scripts are provided to run this application and the required MongoDB using docker. In order for these scripts to start the dev server, you must have a debugger application waiting to attach on port 9229. This is easily accomplished by running these commands in the VSCode terminal, and updating the Debugger Auto Attach setting in VSCode settings to yes.

• run: make this will bootstrap everything, docker compose, and the service
• make debug will only restart the clinical service, without docker compose
• tests: make verify

To run local without engaging the debugger, run npm run local. Since this will not run the docker-compose setup, this requires MongoDB to be running locally (connections configured in the .env file) See Makefile for more details and options.

How to add new clinical entity:

Add new entity in the following files:

• src/common-model/entities.ts:

  • add to enum ClinicalEntitySchemaNames
  • add to type TypeEntitySchemaNameToIndenfiterType
  • add to ClinicalUniqueIdentifier: TypeEntitySchemaNameToIndenfiterType

• src/common-model/functions.ts:

  • update function getClinicalObjectsFromDonor to return proper entity from donor, similar to primary diagnosis

• src/clinical/clinical-entities.ts:

  • add a new entity that extends ClinicalEntity:

    export interface NewEntity extends ClinicalEntity {
    entityId: number | undefined;
    }

  • update interface Donor to include the new entity

• src/clinical/donor-repo.ts:

  • define the new schema for the new entity:

    const newSchema = new mongoose.Schema(
    {
    id: { type: Number },
    clinicalInfo: {},
    },
    { _id: false },
    );

  • add newSchema to const DonorSchema
  • define an id field for the new schema:

    newSchema.plugin(AutoIncrement, {
    inc_field: 'submitter_entity_id',
    start_seq: 1,
    });

• src/submission/submission-entities.ts:

  • add to const BatchNameRegex: Record<ClinicalEntitySchemaNames, RegExp[]>

• update src/submission/validation-clinical/utils.ts - function getRelatedEntityByFK

• update test/integration/stub-schema.json if a new schema is added

• src/submission/submission-to-clinical/stat-calculator.ts

  • update getEmptyCoreStats function to include new entity
  • update schemaNameToCoreCompletenessStat to include new entity

• src/submission/submission-to-clinical/merge-submission.ts

  • add a new entity update function into function mergeRecordsMapIntoDonor, similiar to updatePrimaryDiagnosisInfo
  • update function mergeActiveSubmissionWithDonors switch-case to make sure the new entity is updated when committing submission, similar to primary_diagnosis

• update sampleFiles/sample-schema.json to include the new schema if you are using a local schema for development

• add a new sample tsv to sampleFiles/clinical

• If cross file validation is needed for the new entity, add submission validation for the new entity in the following file:

  • src/submission/validation-clinical/index.ts:

const availableValidators: { [k: string]: any } = {
  [ClinicalEntitySchemaNames.DONOR]: donor,
  [ClinicalEntitySchemaNames.SPECIMEN]: specimen,
  [ClinicalEntitySchemaNames.PRIMARY_DIAGNOSIS]: primaryDiagnosis,
  [ClinicalEntitySchemaNames.FOLLOW_UP]: follow_up,
  [ClinicalEntitySchemaNames.NEW_ENTITY]: new_entity <--------- add here to trigger validation
}

• Run schema_builder to generate a new migration-stub-schema.json when a adding a new schema.

Debugging Notes:

If file upload fails with the error TypeError: Cannot read property 'readFile' of undefined, make sure you are running Node 12+

DB migration

We use a tool called migrate-mongo: https://www.npmjs.com/package/migrate-mongo

• create script: npx migrate-mongo create <issue #>-<my-script-name>
• run migration: npx migrate-mongo up
• rollback: npx migrate-mongo down
  • With this command, migrate-mongo will revert (only) the last applied migration
• status: npx migrate-mongo status

Notes:

• make scripts idempotent in case they fail in the middle
• if a script fails it will stay in pending state
• you can't change the the contents after the script ran, it wont run again automatically
  • if you need to change the script you have to write another script that does what you want
• the scripts are sorted by date & time
• a collection in db called changelog will keep track of executed scripts.
• the docker image will excute the scripts automatically before starting the server and if fails it runs rollback script and exits
• The Recalculate Core Completion migration depends on imports from the TS ./dist folder and requires a compiled build before executing a migration

Extending stub-schema for running DB migration Tests

• extend upon the schema builder with the new schema
• run the script using argo-clinical/test/integration/submission$ npx ts-node ./migration_utils/schema_builder.ts to generate the migration-stub-schema.json
• grab the newer schema with the one you want to compare with (usually v1.0) and run it through lectern's diff calculator
• paste the diff as a new entry into stub-diffs.ts
• _{note: this process could eventually be improved by running lectern in a container so it can automatically serve the schema and compute the diffs}

importing rxnorm

you can see the compose directory for the simplified process it's recommended to use mysql 5.7, 5.6. or 5.5 mysql 8 has issues, but works nonetheless.

• download the full zip file
• mount it in the mysql container
• move all mysql scripts from scripts folder to rrf folder.

the job to import this: https://jenkins.qa.cancercollaboratory.org/job/ARGO/job/devops/job/rxnorm-import/

Lectern client

work live with overture client without publishing new versions

in clinical package json:

1. "@overturebio-stack/lectern-client": "file:/home/ballabadi/dev/repos/overture/js-lectern-client",
2. go to lectern client, update code and npm run build
3. install the updated version npm i

how to debug schema client :

1. put debug point here: manager.ts function
2. when break point hits, step into lectern client func
3. place break point in lectern client file