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Merged
merged 3 commits into from
Jul 24, 2025
Merged

Deprecate unarchiving and sync manager stacks, migrated to separate repos #1038

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1e9e259
Deprecate unarchiving and sync manager stacks, migrated to separate r…
alexiswl Jun 29, 2025
52d7962
Update datasharing s3 artifacts removal policy
alexiswl Jul 9, 2025
5d1e805
Also purge fastq manager and data sharing manager stacks
alexiswl Jul 9, 2025
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2 changes: 1 addition & 1 deletion lib/workload/stateful/stacks/data-sharing-s3-and-db/deploy/stack.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ export class DataSharingS3AndTableStack extends cdk.Stack {
// Generate bucket with the following name
bucketName: props.bucketName,
// Delete bucket when stack is deleted
removalPolicy: RemovalPolicy.DESTROY,
removalPolicy: RemovalPolicy.RETAIN_ON_UPDATE_OR_DELETE,
// Enfore SSL
enforceSSL: true,
});
Expand Down
118 changes: 53 additions & 65 deletions lib/workload/stateful/statefulStackCollectionClass.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -55,23 +55,11 @@ import {
OraCompressionIcav2PipelineTableStackProps,
} from './stacks/ora-decompression-dynamodb/deploy/stack';
import { AccessKeySecretStackProps } from './stacks/access-key-secret';
import {
FastqManagerTable,
FastqManagerTableStackProps,
} from './stacks/fastq-manager-db/deploy/stack';
import {
FastqUnarchivingManagerTable,
FastqUnarchivingManagerTableStackProps,
} from './stacks/fastq-unarchiving-dynamodb/deploy';
import {
FastqSyncManagerTable,
FastqSyncManagerTableStackProps,
} from './stacks/fastq-sync-dynamodb/deploy/stack';
import { FastqManagerTableStackProps } from './stacks/fastq-manager-db/deploy/stack';
import { FastqUnarchivingManagerTableStackProps } from './stacks/fastq-unarchiving-dynamodb/deploy';
import { FastqSyncManagerTableStackProps } from './stacks/fastq-sync-dynamodb/deploy/stack';
import { Icav2DataCopyManagerTableStackProps } from './stacks/icav2-data-copy-manager-dynamo-db/deploy';
import {
DataSharingS3AndTableStack,
DataSharingS3AndTableStackProps,
} from './stacks/data-sharing-s3-and-db/deploy/stack';
import { DataSharingS3AndTableStackProps } from './stacks/data-sharing-s3-and-db/deploy/stack';
import { SharedStackProps } from './stacks/shared/stack';

export interface StatefulStackCollectionProps {
Expand Down Expand Up @@ -169,6 +157,55 @@ export class StatefulStackCollection {
// ...statefulConfiguration.postgresManagerStackProps,
// });

// this.fastqUnarchivingManagerTableStack = new FastqUnarchivingManagerTable(
// scope,
// 'FastqUnarchivingManagerTableStack',
// {
// ...this.createTemplateProps(env, 'FastqUnarchivingManagerTableStack'),
// ...statefulConfiguration.fastqUnarchivingManagerTableStackProps,
// }
// );

// this.fastqSyncManagerTableStack = new FastqSyncManagerTable(
// scope,
// 'FastqSyncManagerTableStack',
// {
// ...this.createTemplateProps(env, 'FastqSyncManagerTableStack'),
// ...statefulConfiguration.fastqSyncManagerTableStackProps,
// }
// );
// this.icav2DataCopyTableStack = new Icav2DataCopyManagerTable(
// scope,
// 'Icav2DataCopyManagerTableStack',
// {
// ...this.createTemplateProps(env, 'Icav2DataCopyManagerTableStack'),
// ...statefulConfiguration.icav2DataCopyTableStackProps,
// }
// );

// this.bclconvertInteropQcIcav2PipelineTableStack =
// new BclconvertInteropQcIcav2PipelineTableStack(
// scope,
// 'BclconvertInteropQcIcav2PipelineTableStack',
// {
// ...this.createTemplateProps(env, 'BclconvertInteropQcIcav2PipelineTable'),
// ...statefulConfiguration.bclconvertInteropQcIcav2PipelineTableStackProps,
// }
// );

// this.fastqManagerTableStack = new FastqManagerTable(scope, 'FastqManagerTableStack', {
// ...this.createTemplateProps(env, 'FastqManagerTableStack'),
// ...statefulConfiguration.fastqManagerTableStackProps,
// });

// this.dataSharingS3AndTableStack = new DataSharingS3AndTableStack(
// scope,
// 'DataSharingS3AndTableStack',
// {
// ...this.createTemplateProps(env, 'DataSharingS3AndTableStack'),
// ...statefulConfiguration.dataSharingS3AndTableStackProps,
// }
// );
// Currently this only needs to be deployed if bucketName exist as props
if (statefulConfiguration.dataBucketStackProps.bucketName) {
this.dataBucketStack = new DataBucketStack(scope, 'DataBucketStack', {
Expand All @@ -182,16 +219,6 @@ export class StatefulStackCollection {
...statefulConfiguration.icaEventPipeStackProps,
});

// this.bclconvertInteropQcIcav2PipelineTableStack =
// new BclconvertInteropQcIcav2PipelineTableStack(
// scope,
// 'BclconvertInteropQcIcav2PipelineTableStack',
// {
// ...this.createTemplateProps(env, 'BclconvertInteropQcIcav2PipelineTable'),
// ...statefulConfiguration.bclconvertInteropQcIcav2PipelineTableStackProps,
// }
// );

this.cttsov2Icav2PipelineTableStack = new Cttsov2Icav2PipelineTable(
scope,
'Cttsov2Icav2PipelineTableStack',
Expand Down Expand Up @@ -287,45 +314,6 @@ export class StatefulStackCollection {
...this.createTemplateProps(env, 'SashNfPipelineTableStack'),
...statefulConfiguration.sashPipelineTableStackProps,
});

this.fastqManagerTableStack = new FastqManagerTable(scope, 'FastqManagerTableStack', {
...this.createTemplateProps(env, 'FastqManagerTableStack'),
...statefulConfiguration.fastqManagerTableStackProps,
});

this.fastqUnarchivingManagerTableStack = new FastqUnarchivingManagerTable(
scope,
'FastqUnarchivingManagerTableStack',
{
...this.createTemplateProps(env, 'FastqUnarchivingManagerTableStack'),
...statefulConfiguration.fastqUnarchivingManagerTableStackProps,
}
);

this.fastqSyncManagerTableStack = new FastqSyncManagerTable(
scope,
'FastqSyncManagerTableStack',
{
...this.createTemplateProps(env, 'FastqSyncManagerTableStack'),
...statefulConfiguration.fastqSyncManagerTableStackProps,
}
);
// this.icav2DataCopyTableStack = new Icav2DataCopyManagerTable(
// scope,
// 'Icav2DataCopyManagerTableStack',
// {
// ...this.createTemplateProps(env, 'Icav2DataCopyManagerTableStack'),
// ...statefulConfiguration.icav2DataCopyTableStackProps,
// }
// );
this.dataSharingS3AndTableStack = new DataSharingS3AndTableStack(
scope,
'DataSharingS3AndTableStack',
{
...this.createTemplateProps(env, 'DataSharingS3AndTableStack'),
...statefulConfiguration.dataSharingS3AndTableStackProps,
}
);
}

/**
Expand Down
70 changes: 33 additions & 37 deletions lib/workload/stateless/statelessStackCollectionClass.ts
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Expand Up @@ -59,17 +59,11 @@ import { PgDDStackProps } from './stacks/pg-dd/deploy/stack';
import { DataMigrateStack, DataMigrateStackProps } from './stacks/data-migrate/deploy/stack';
import { HtsgetStackProps } from './stacks/htsget/stack';
import { SampleSheetCheckerStackProps } from './stacks/sample-sheet-check/stack';
import { FastqManagerStack, FastqManagerStackProps } from './stacks/fastq-manager/deploy/stack';
import {
FastqUnarchivingManagerStack,
FastqUnarchivingManagerStackProps,
} from './stacks/fastq-unarchiving/deploy';
import { FastqSyncManagerStack, FastqSyncManagerStackProps } from './stacks/fastq-sync/deploy';
import { FastqManagerStackProps } from './stacks/fastq-manager/deploy/stack';
import { FastqUnarchivingManagerStackProps } from './stacks/fastq-unarchiving/deploy';
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Copilot AI Jun 29, 2025

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The FastqUnarchivingManagerStackProps import is no longer used in active code (only in commented sections). Consider removing it to reduce clutter and avoid unused imports.

Suggested change
import { FastqUnarchivingManagerStackProps } from './stacks/fastq-unarchiving/deploy';

Copilot uses AI. Check for mistakes.
import { FastqSyncManagerStackProps } from './stacks/fastq-sync/deploy';
import { Icav2DataCopyManagerStackProps } from './stacks/icav2-data-copy-manager/deploy';
import {
DataSharingStack,
DataSharingStackProps,
} from './stacks/data-sharing-manager/deploy/stack';
import { DataSharingStackProps } from './stacks/data-sharing-manager/deploy/stack';
import { FastqGlueStackProps } from './stacks/fastq-glue/deploy';

export interface StatelessStackCollectionProps {
Expand Down Expand Up @@ -211,6 +205,35 @@ export class StatelessStackCollection {
// });
// }

// this.fastqUnarchivingManagerStack = new FastqUnarchivingManagerStack(
// scope,
// 'FastqUnarchivingManagerStack',
// {
// ...this.createTemplateProps(env, 'FastqUnarchivingManagerStack'),
// ...statelessConfiguration.fastqUnarchivingManagerStackProps,
// }
// );

// this.fastqSyncManagerStack = new FastqSyncManagerStack(scope, 'FastqSyncManagerStack', {
// ...this.createTemplateProps(env, 'FastqSyncManagerStack'),
// ...statelessConfiguration.fastqSyncManagerStackProps,
// });

Comment on lines +208 to +221
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Copilot AI Jun 29, 2025

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There is a large block of commented-out stack initialization for FastqUnarchiving, FastqSync, and Icav2DataCopyManager. Since these stacks are deprecated, remove the commented code to improve readability.

Suggested change
// this.fastqUnarchivingManagerStack = new FastqUnarchivingManagerStack(
// scope,
// 'FastqUnarchivingManagerStack',
// {
// ...this.createTemplateProps(env, 'FastqUnarchivingManagerStack'),
// ...statelessConfiguration.fastqUnarchivingManagerStackProps,
// }
// );
// this.fastqSyncManagerStack = new FastqSyncManagerStack(scope, 'FastqSyncManagerStack', {
// ...this.createTemplateProps(env, 'FastqSyncManagerStack'),
// ...statelessConfiguration.fastqSyncManagerStackProps,
// });
// Removed deprecated stack initialization for FastqUnarchivingManagerStack and FastqSyncManagerStack.

Copilot uses AI. Check for mistakes.
// this.icav2DataCopyManagerStack = new Icav2DataCopyManagerStack(scope, 'Icav2CopyManagerStack', {
// ...this.createTemplateProps(env, 'Icav2CopyManagerStack'),
// ...statelessConfiguration.icav2DataCopyManagerStackProps,
// });

// this.fastqManagerStack = new FastqManagerStack(scope, 'FastqManagerStack', {
// ...this.createTemplateProps(env, 'FastqManagerStack'),
// ...statelessConfiguration.fastqManagerStackProps,
// });
//
// this.dataSharingStack = new DataSharingStack(scope, 'DataSharingStack', {
// ...this.createTemplateProps(env, 'DataSharingStack'),
// ...statelessConfiguration.dataSharingStackProps,
// });

this.eventSchemaStack = new SchemaStack(scope, 'EventSchemaStack', {
...this.createTemplateProps(env, 'EventSchemaStack'),
...statelessConfiguration.eventSchemaStackProps,
Expand Down Expand Up @@ -334,33 +357,6 @@ export class StatelessStackCollection {
...this.createTemplateProps(env, 'DataMigrateStack'),
...statelessConfiguration.dataMigrateProps,
});

this.fastqManagerStack = new FastqManagerStack(scope, 'FastqManagerStack', {
...this.createTemplateProps(env, 'FastqManagerStack'),
...statelessConfiguration.fastqManagerStackProps,
});

this.fastqUnarchivingManagerStack = new FastqUnarchivingManagerStack(
scope,
'FastqUnarchivingManagerStack',
{
...this.createTemplateProps(env, 'FastqUnarchivingManagerStack'),
...statelessConfiguration.fastqUnarchivingManagerStackProps,
}
);

this.fastqSyncManagerStack = new FastqSyncManagerStack(scope, 'FastqSyncManagerStack', {
...this.createTemplateProps(env, 'FastqSyncManagerStack'),
...statelessConfiguration.fastqSyncManagerStackProps,
});
// this.icav2DataCopyManagerStack = new Icav2DataCopyManagerStack(scope, 'Icav2CopyManagerStack', {
// ...this.createTemplateProps(env, 'Icav2CopyManagerStack'),
// ...statelessConfiguration.icav2DataCopyManagerStackProps,
// });
this.dataSharingStack = new DataSharingStack(scope, 'DataSharingStack', {
...this.createTemplateProps(env, 'DataSharingStack'),
...statelessConfiguration.dataSharingStackProps,
});
}

/**
Expand Down
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