Merge branch 'main' into feat-mm/238-notify-metadata-state-change

lib/workload/stateless/stacks/metadata-manager/README.md

@@ -101,6 +101,33 @@ Some important notes of the sync:
 
 Please refer to the [tracking-sheet-service](proc/service/tracking_sheet_srv.py) implementation.
 
+### Custom CSV File Loader
+
+The application also supports loading data from a custom CSV file. The CSV file should have the following columns:
+
+| Sheet Header         | Table        | Field Name         |
+|----------------------|--------------|--------------------|
+| Individual_id        | `Individual` | individual_id      |
+| individual_id_source | `Individual` | subject_id         |
+| subject_id           | `Subject`    | subject_id         |
+| sample_id            | `Sample`     | sample_id          |
+| external_sample_id   | `Sample`     | external_sample_id |
+| source               | `Sample`     | source             |
+| library_id           | `Library`    | library_id         |
+| phenotype            | `Library`    | phenotype          |
+| workflow             | `Library`    | workflow           |
+| quality              | `Library`    | quality            |
+| type                 | `Library`    | type               |
+| coverage             | `Library`    | coverage           |
+| assay                | `Library`    | assay              |
+| project_name         | `Project`    | project_id         |
+| project_owner        | `Contact`    | contact_id         |
+
+The CSV file should be in a presigned URL format, where the loader will read and insert to the database.
+To trigger the loader please look at `./deploy/README.md` for more info.
+
+Please refer to the [load-csv-service](proc/service/load_csv_srv.py) implementation.
+
 ### Audit Data
 
 The application is configured with [django-simple-history](https://django-simple-history.readthedocs.io/en/latest/)

lib/workload/stateless/stacks/metadata-manager/app/management/commands/load_from_csv.py

@@ -0,0 +1,22 @@
+import logging
+from django.core.management import BaseCommand
+from libumccr import libjson
+
+from handler.load_custom_metadata_csv import handler
+
+logger = logging.getLogger()
+logger.setLevel(logging.INFO)
+
+
+class Command(BaseCommand):
+    help = "Trigger lambda handler for to sync metadata from csv url"
+
+    def handle(self, *args, **options):
+        event = {
+            "url": "SOME_URL",
+        }
+
+        print(f"Trigger lambda handler for sync tracking sheet. Event {libjson.dumps(event)}")
+        result = handler(event, {})
+
+        print(f"result: {libjson.dumps(result)}")

lib/workload/stateless/stacks/metadata-manager/app/models/library.py

@@ -112,3 +112,16 @@ class Library(BaseModel):
 
     # history
     history = HistoricalRecords(m2m_fields=[project_set])
+
+
+def sanitize_library_coverage(value: str):
+    """
+    convert value that is valid in the tracking sheet to return a value that is recognizable by the Django Model
+    """
+    try:
+        # making coverage is float-able type
+        lib_coverage = float(value)
+        return f'{lib_coverage}'
+
+    except (ValueError, TypeError):
+        return None

lib/workload/stateless/stacks/metadata-manager/deploy/README.md

@@ -58,3 +58,35 @@ aws lambda invoke \
   --cli-binary-format raw-in-base64-out \
   res.json
 ```
+
+### CustomCsvLambda
+
+- Load tracking sheet data from csv presigned url
+
+To manually trigger the sync, the lambda ARN is stored in the SSM Parameter Store named
+`/orcabus/metadata-manager/load-custom-csv-lambda-arn`.
+
+To query in a local terminal
+
+```sh
+load_custom_csv_lambda_arn=$(aws ssm get-parameter --name '/orcabus/metadata-manager/load-custom-csv-lambda-arn' --with-decryption | jq -r .Parameter.Value)
+```
+
+The lambda handler will accept a json which only accepts a single key `url` which is the presigned url of the csv file.
+
+```json
+{
+  "url": "https://example.com/csv"
+}
+```
+
+Invoking lambda cmd:
+
+```sh
+aws lambda invoke \
+  --function-name $load_custom_csv_lambda_arn \
+  --invocation-type Event \
+  --payload '{ "url": "https://the.url.csv" }' \
+  --cli-binary-format raw-in-base64-out \
+  res.json
+```

lib/workload/stateless/stacks/metadata-manager/deploy/construct/lambda-load-custom-csv/index.ts

@@ -0,0 +1,54 @@
+import path from 'path';
+import { Construct } from 'constructs';
+import { Duration } from 'aws-cdk-lib';
+import { PythonFunction } from '@aws-cdk/aws-lambda-python-alpha';
+import { ISecret } from 'aws-cdk-lib/aws-secretsmanager';
+import { StringParameter } from 'aws-cdk-lib/aws-ssm';
+import {
+  DockerImageFunction,
+  DockerImageFunctionProps,
+  DockerImageCode,
+} from 'aws-cdk-lib/aws-lambda';
+
+type LambdaProps = {
+  /**
+   * The basic common lambda properties that it should inherit from
+   */
+  basicLambdaConfig: Partial<DockerImageFunctionProps>;
+  /**
+   * The secret for the db connection where the lambda will need access to
+   */
+  dbConnectionSecret: ISecret;
+};
+
+export class LambdaLoadCustomCSVConstruct extends Construct {
+  private readonly lambda: PythonFunction;
+
+  constructor(scope: Construct, id: string, lambdaProps: LambdaProps) {
+    super(scope, id);
+
+    this.lambda = new DockerImageFunction(this, 'LoadCustomCSVLambda', {
+      environment: {
+        ...lambdaProps.basicLambdaConfig.environment,
+      },
+      securityGroups: lambdaProps.basicLambdaConfig.securityGroups,
+      vpc: lambdaProps.basicLambdaConfig.vpc,
+      vpcSubnets: lambdaProps.basicLambdaConfig.vpcSubnets,
+      architecture: lambdaProps.basicLambdaConfig.architecture,
+      code: DockerImageCode.fromImageAsset(path.join(__dirname, '../../../'), {
+        file: 'deploy/construct/lambda-load-custom-csv/lambda.Dockerfile',
+      }),
+      timeout: Duration.minutes(15),
+      memorySize: 4096,
+    });
+
+    lambdaProps.dbConnectionSecret.grantRead(this.lambda);
+
+    // We need to store this lambda ARN somewhere so that we could refer when need to load this manually
+    const ssmParameter = new StringParameter(this, 'LoadCustomCSVLambdaArnParameterStore', {
+      parameterName: '/orcabus/metadata-manager/load-custom-csv-lambda-arn',
+      description: 'The ARN of the lambda that load metadata from a presigned URL CSV file',
+      stringValue: this.lambda.functionArn,
+    });
+  }
+}

lib/workload/stateless/stacks/metadata-manager/deploy/construct/lambda-load-custom-csv/lambda.Dockerfile

@@ -0,0 +1,12 @@
+FROM public.ecr.aws/lambda/python:3.12
+
+WORKDIR ${LAMBDA_TASK_ROOT}
+
+# COPY all files
+COPY . .
+
+# Install the specified packages
+RUN pip install -r deps/requirements-full.txt
+
+# Specify handler
+CMD [ "handler.load_custom_metadata_csv.handler" ]

lib/workload/stateless/stacks/metadata-manager/deploy/stack.ts

@@ -11,6 +11,7 @@ import { LambdaMigrationConstruct } from './construct/lambda-migration';
 import { LambdaAPIConstruct } from './construct/lambda-api';
 import { ApiGatewayConstructProps } from '../../../../components/api-gateway';
 import { PostgresManagerStack } from '../../../../stateful/stacks/postgres-manager/deploy/stack';
+import { LambdaLoadCustomCSVConstruct } from './construct/lambda-load-custom-csv';
 
 export type MetadataManagerStackProps = {
   /**
@@ -82,6 +83,7 @@ export class MetadataManagerStack extends Stack {
     // 1. To handle API calls
     // 2. To do migrations
     // 3. To sync db with external sources (e.g. metadata in gsheet)
+    // 4. To load-db from external csv presigned url file
 
     // (1)
     new LambdaAPIConstruct(this, 'APILambda', {
@@ -103,5 +105,11 @@ export class MetadataManagerStack extends Stack {
       dbConnectionSecret: dbSecret,
       isDailySync: props.isDailySync,
     });
+
+    // (4)
+    new LambdaLoadCustomCSVConstruct(this, 'CustomCsvLoaderLambda', {
+      basicLambdaConfig: basicLambdaConfig,
+      dbConnectionSecret: dbSecret,
+    });
   }
 }

lib/workload/stateless/stacks/metadata-manager/handler/load_custom_metadata_csv.py

@@ -0,0 +1,35 @@
+import django
+import os
+import logging
+
+from libumccr import libjson
+
+from proc.service.utils import sanitize_lab_metadata_df, warn_drop_duplicated_library
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'app.settings.base')
+django.setup()
+
+from proc.service.load_csv_srv import load_metadata_csv, download_csv_to_pandas
+
+logger = logging.getLogger()
+logger.setLevel(logging.INFO)
+
+
+def handler(event, _context):
+    logger.info(f'event: {libjson.dumps(event)}')
+
+    csv_url = event.get('url', None)
+    if csv_url is None:
+        raise ValueError("URL is required")
+
+    csv_df = download_csv_to_pandas(csv_url)
+    sanitize_df = sanitize_lab_metadata_df(csv_df)
+    duplicate_clean_df = warn_drop_duplicated_library(sanitize_df)
+    result = load_metadata_csv(duplicate_clean_df)
+
+    logger.info(f'persist report: {libjson.dumps(result)}')
+    return result
+
+
+if __name__ == '__main__':
+    handler({}, {})