Skip to content

Stacky clean up #1046

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Oct 10, 2025
Merged

Stacky clean up #1046

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
94 changes: 47 additions & 47 deletions lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/index.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -101,33 +101,33 @@ export class GlueConstruct extends Construct {
/*
Part D: Plumber-up the oncoanalyser services
*/
const handyPal = new OncoanalyserGlueHandlerConstruct(this, 'handyPal', {
/* Event Objects */
eventBusObj: props.eventBusObj,
/* Tables */
oncoanalyserGlueTableObj: props.oncoanalyserGlueTableObj,
/* SSM Parameter Objects */
analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
});
// const handyPal = new OncoanalyserGlueHandlerConstruct(this, 'handyPal', {
// /* Event Objects */
// eventBusObj: props.eventBusObj,
// /* Tables */
// oncoanalyserGlueTableObj: props.oncoanalyserGlueTableObj,
// /* SSM Parameter Objects */
// analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
// analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
// analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
// });
Comment on lines +104 to +113
Copy link

Copilot AI Oct 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This commented-out glue handler construct should be removed entirely rather than left as commented code. Leaving deprecated code commented out can lead to confusion and maintenance overhead.

Copilot uses AI. Check for mistakes.

/*
Part D: Plumber-up the cttso v2 to the shower services
*/
const jb_weld = new Cttsov2GlueHandlerConstruct(this, 'jb_weld', {
/* Event Bus */
eventBusObj: props.eventBusObj,
/* Tables */
cttsov2GlueTableObj: props.cttsov2GlueTableObj,
/* SSM Parameters */
icav2ProjectIdSsmParameterObj: props.icav2ProjectIdSsmParameterObj,
analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
/* Secrets */
icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
});
// const jb_weld = new Cttsov2GlueHandlerConstruct(this, 'jb_weld', {
// /* Event Bus */
// eventBusObj: props.eventBusObj,
// /* Tables */
// cttsov2GlueTableObj: props.cttsov2GlueTableObj,
// /* SSM Parameters */
// icav2ProjectIdSsmParameterObj: props.icav2ProjectIdSsmParameterObj,
// analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
// analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
// analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
// /* Secrets */
// icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
// });
Comment on lines +118 to +130
Copy link

Copilot AI Oct 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This commented-out glue handler construct should be removed entirely rather than left as commented code. Leaving deprecated code commented out can lead to confusion and maintenance overhead.

Suggested change
// const jb_weld = new Cttsov2GlueHandlerConstruct(this, 'jb_weld', {
// /* Event Bus */
// eventBusObj: props.eventBusObj,
// /* Tables */
// cttsov2GlueTableObj: props.cttsov2GlueTableObj,
// /* SSM Parameters */
// icav2ProjectIdSsmParameterObj: props.icav2ProjectIdSsmParameterObj,
// analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
// analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
// analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
// /* Secrets */
// icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
// });

Copilot uses AI. Check for mistakes.

/*
Part E: Plumber-up the WGTS QC Execution Service to the shower services
Expand Down Expand Up @@ -183,20 +183,20 @@ export class GlueConstruct extends Construct {
/*
Part H: Plumber-up the cttsov2 to pieriandx services
*/
const nails = new PieriandxGlueHandlerConstruct(this, 'nails', {
/* Event Bus */
eventBusObj: props.eventBusObj,

/* Tables */
pieriandxGlueTableObj: props.pieriandxGlueTableObj,

/* Secrets */
icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,

/* Extras */
pieriandxProjectInfoSsmParameterObj: props.pieriandxProjectInfoSsmParameterObj,
redcapLambdaObj: props.redcapLambdaObj,
});
// const nails = new PieriandxGlueHandlerConstruct(this, 'nails', {
// /* Event Bus */
// eventBusObj: props.eventBusObj,
//
// /* Tables */
// pieriandxGlueTableObj: props.pieriandxGlueTableObj,
//
// /* Secrets */
// icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
//
// /* Extras */
// pieriandxProjectInfoSsmParameterObj: props.pieriandxProjectInfoSsmParameterObj,
// redcapLambdaObj: props.redcapLambdaObj,
// });

Comment on lines +186 to 200
Copy link

Copilot AI Oct 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This commented-out glue handler construct should be removed entirely rather than left as commented code. Leaving deprecated code commented out can lead to confusion and maintenance overhead.

Suggested change
// const nails = new PieriandxGlueHandlerConstruct(this, 'nails', {
// /* Event Bus */
// eventBusObj: props.eventBusObj,
//
// /* Tables */
// pieriandxGlueTableObj: props.pieriandxGlueTableObj,
//
// /* Secrets */
// icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
//
// /* Extras */
// pieriandxProjectInfoSsmParameterObj: props.pieriandxProjectInfoSsmParameterObj,
// redcapLambdaObj: props.redcapLambdaObj,
// });

Copilot uses AI. Check for mistakes.
/*
Part I: Plumber-up the UMCCRise Execution Service to the shower services
Expand Down Expand Up @@ -236,16 +236,16 @@ export class GlueConstruct extends Construct {
Part K: Plumber up the oncoanalyser-wgts-dna-rna and sash service - both
have the same entry point so we can use the same construct
*/
const tRex = new OncoanalyserBothSashGlueHandlerConstruct(this, 'trex', {
/* Event Objects */
eventBusObj: props.eventBusObj,
/* Tables */
oncoanalyserBothSashGlueTableObj: props.oncoanalyserBothSashGlueTableObj,
/* SSM Parameter Objects */
analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
});
// const tRex = new OncoanalyserBothSashGlueHandlerConstruct(this, 'trex', {
// /* Event Objects */
// eventBusObj: props.eventBusObj,
// /* Tables */
// oncoanalyserBothSashGlueTableObj: props.oncoanalyserBothSashGlueTableObj,
// /* SSM Parameter Objects */
// analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
// analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
// analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
// });
Comment on lines +239 to +248
Copy link

Copilot AI Oct 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This commented-out glue handler construct should be removed entirely rather than left as commented code. Leaving deprecated code commented out can lead to confusion and maintenance overhead.

Suggested change
// const tRex = new OncoanalyserBothSashGlueHandlerConstruct(this, 'trex', {
// /* Event Objects */
// eventBusObj: props.eventBusObj,
// /* Tables */
// oncoanalyserBothSashGlueTableObj: props.oncoanalyserBothSashGlueTableObj,
// /* SSM Parameter Objects */
// analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
// analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
// analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
// });

Copilot uses AI. Check for mistakes.
}
}

Expand Down
138 changes: 60 additions & 78 deletions lib/workload/stateless/statelessStackCollectionClass.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,7 @@ import { Stack, Environment, StackProps } from 'aws-cdk-lib';
import { FilemanagerProps } from './stacks/filemanager/deploy/stack';
import { BsshIcav2FastqCopyManagerStackProps } from './stacks/bssh-icav2-fastq-copy-manager/deploy/stack';
import { BclconvertInteropQcIcav2PipelineManagerStackProps } from './stacks/bclconvert-interop-qc-pipeline-manager/deploy/stack';
import {
Cttsov2Icav2PipelineManagerStackProps,
Cttsov2Icav2PipelineManagerStack,
} from './stacks/cttso-v2-pipeline-manager/deploy/stack';
import { Cttsov2Icav2PipelineManagerStackProps } from './stacks/cttso-v2-pipeline-manager/deploy/stack';
import { SchemaStack, SchemaStackProps } from './stacks/schema/stack';
import {
BclConvertManagerStack,
Expand All @@ -33,28 +30,13 @@ import {
RnasumIcav2PipelineManagerStack,
RnasumIcav2PipelineManagerStackProps,
} from './stacks/rnasum-pipeline-manager/deploy';
import {
OraCompressionIcav2PipelineManagerStack,
OraCompressionIcav2PipelineManagerStackProps,
} from './stacks/ora-compression-manager/deploy';
import { OraCompressionIcav2PipelineManagerStackProps } from './stacks/ora-compression-manager/deploy';

import { FMAnnotatorProps } from './stacks/fmannotator/deploy/stack';
import {
PieriandxPipelineManagerStack,
PierianDxPipelineManagerStackProps,
} from './stacks/pieriandx-pipeline-manager/deploy';
import {
OncoanalyserNfPipelineManagerStack,
OncoanalyserNfPipelineManagerStackProps,
} from './stacks/oncoanalyser-pipeline-manager/deploy';
import {
SashNfPipelineManagerStack,
SashNfPipelineManagerStackProps,
} from './stacks/sash-pipeline-manager/deploy';
import {
OraDecompressionManagerStack,
OraDecompressionManagerStackProps,
} from './stacks/ora-decompression-manager/deploy';
import { PierianDxPipelineManagerStackProps } from './stacks/pieriandx-pipeline-manager/deploy';
import { OncoanalyserNfPipelineManagerStackProps } from './stacks/oncoanalyser-pipeline-manager/deploy';
import { SashNfPipelineManagerStackProps } from './stacks/sash-pipeline-manager/deploy';
import { OraDecompressionManagerStackProps } from './stacks/ora-decompression-manager/deploy';
import { PgDDStackProps } from './stacks/pg-dd/deploy/stack';
import { DataMigrateStack, DataMigrateStackProps } from './stacks/data-migrate/deploy/stack';
import { HtsgetStackProps } from './stacks/htsget/stack';
Expand Down Expand Up @@ -234,6 +216,60 @@ export class StatelessStackCollection {
// ...statelessConfiguration.dataSharingStackProps,
// });

// this.pieriandxPipelineManagerStack = new PieriandxPipelineManagerStack(
// scope,
// 'PieriandxPipelineManagerStack',
// {
// ...this.createTemplateProps(env, 'PieriandxPipelineManagerStack'),
// ...statelessConfiguration.pieriandxPipelineManagerStackProps,
// }
// );
//
// this.oncoanalyserPipelineManagerStack = new OncoanalyserNfPipelineManagerStack(
// scope,
// 'OncoanalyserNfPipelineManagerStack',
// {
// ...this.createTemplateProps(env, 'OncoanalyserNfPipelineManagerStack'),
// ...statelessConfiguration.oncoanalyserPipelineManagerStackProps,
// }
// );
//
// this.sashPipelineManagerStack = new SashNfPipelineManagerStack(
// scope,
// 'SashNfPipelineManagerStack',
// {
// ...this.createTemplateProps(env, 'SashNfPipelineManagerStack'),
// ...statelessConfiguration.sashPipelineManagerStackProps,
// }
// );
//
// this.oraCompressionIcav2PipelineManagerStack = new OraCompressionIcav2PipelineManagerStack(
// scope,
// 'OraCompressionIcav2PipelineManagerStack',
// {
// ...this.createTemplateProps(env, 'OraCompressionIcav2PipelineManagerStack'),
// ...statelessConfiguration.oraCompressionIcav2PipelineManagerStackProps,
// }
// );
//
// this.oraDecompressionManagerStack = new OraDecompressionManagerStack(
// scope,
// 'OraDecompressionManagerStack',
// {
// ...this.createTemplateProps(env, 'OraDecompressionManagerStack'),
// ...statelessConfiguration.oraDecompressionManagerStackProps,
// }
// );
//
// this.cttsov2Icav2PipelineManagerStack = new Cttsov2Icav2PipelineManagerStack(
// scope,
// 'Cttsov2Icav2PipelineManagerStack',
// {
// ...this.createTemplateProps(env, 'Cttsov2Icav2PipelineManagerStack'),
// ...statelessConfiguration.cttsov2Icav2PipelineManagerStackProps,
// }
// );

Comment on lines +255 to +272
Copy link

Copilot AI Oct 9, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

These commented-out stack instantiations should be removed entirely rather than left as commented code. Commented code can cause confusion and should be cleaned up during deprecation.

Suggested change
// this.oraDecompressionManagerStack = new OraDecompressionManagerStack(
// scope,
// 'OraDecompressionManagerStack',
// {
// ...this.createTemplateProps(env, 'OraDecompressionManagerStack'),
// ...statelessConfiguration.oraDecompressionManagerStackProps,
// }
// );
//
// this.cttsov2Icav2PipelineManagerStack = new Cttsov2Icav2PipelineManagerStack(
// scope,
// 'Cttsov2Icav2PipelineManagerStack',
// {
// ...this.createTemplateProps(env, 'Cttsov2Icav2PipelineManagerStack'),
// ...statelessConfiguration.cttsov2Icav2PipelineManagerStackProps,
// }
// );

Copilot uses AI. Check for mistakes.
this.eventSchemaStack = new SchemaStack(scope, 'EventSchemaStack', {
...this.createTemplateProps(env, 'EventSchemaStack'),
...statelessConfiguration.eventSchemaStackProps,
Expand All @@ -244,15 +280,6 @@ export class StatelessStackCollection {
...statelessConfiguration.dataSchemaStackProps,
});

this.cttsov2Icav2PipelineManagerStack = new Cttsov2Icav2PipelineManagerStack(
scope,
'Cttsov2Icav2PipelineManagerStack',
{
...this.createTemplateProps(env, 'Cttsov2Icav2PipelineManagerStack'),
...statelessConfiguration.cttsov2Icav2PipelineManagerStackProps,
}
);

this.wgtsQcIcav2PipelineManagerStack = new WgtsQcIcav2PipelineManagerStack(
scope,
'WgtsQcIcav2PipelineManagerStack',
Expand Down Expand Up @@ -298,51 +325,6 @@ export class StatelessStackCollection {
}
);

this.pieriandxPipelineManagerStack = new PieriandxPipelineManagerStack(
scope,
'PieriandxPipelineManagerStack',
{
...this.createTemplateProps(env, 'PieriandxPipelineManagerStack'),
...statelessConfiguration.pieriandxPipelineManagerStackProps,
}
);

this.oncoanalyserPipelineManagerStack = new OncoanalyserNfPipelineManagerStack(
scope,
'OncoanalyserNfPipelineManagerStack',
{
...this.createTemplateProps(env, 'OncoanalyserNfPipelineManagerStack'),
...statelessConfiguration.oncoanalyserPipelineManagerStackProps,
}
);

this.sashPipelineManagerStack = new SashNfPipelineManagerStack(
scope,
'SashNfPipelineManagerStack',
{
...this.createTemplateProps(env, 'SashNfPipelineManagerStack'),
...statelessConfiguration.sashPipelineManagerStackProps,
}
);

this.oraCompressionIcav2PipelineManagerStack = new OraCompressionIcav2PipelineManagerStack(
scope,
'OraCompressionIcav2PipelineManagerStack',
{
...this.createTemplateProps(env, 'OraCompressionIcav2PipelineManagerStack'),
...statelessConfiguration.oraCompressionIcav2PipelineManagerStackProps,
}
);

this.oraDecompressionManagerStack = new OraDecompressionManagerStack(
scope,
'OraDecompressionManagerStack',
{
...this.createTemplateProps(env, 'OraDecompressionManagerStack'),
...statelessConfiguration.oraDecompressionManagerStackProps,
}
);

this.bclConvertManagerStack = new BclConvertManagerStack(scope, 'BclConvertManagerStack', {
...this.createTemplateProps(env, 'BclConvertManagerStack'),
...statelessConfiguration.bclConvertManagerStackProps,
Expand Down