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Initialise ICAv2 Data Copy Manager #788
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Please on hold merge this PR until |
Depends on task token that implemented in #789 |
Similarly to this PR as well. ditto related conclusion comment here. Please set PR Ready; once finalised. Thanks. |
* SDK versions from 2.177 to 2.182 * Added vpc contexts to cdk.context.json * Upgraded yarn version to 4.7.0 * Prefix prettier with yarn prettier (takes longer but prettier was breaking for me)
Updated toolkits (and typehints) for the following services: * workflow manager * metadata manager * file manager * fastq manager Also updated the dynamodb partition table to use pointInTimeRecoverySpecification since pointInTimeRecovery parameter is deprecated
5 tasks
* Comprises fastq objects and linked fastq objects through fastq sets * Interacts with filemanager to store ingest ids for fastq objects * Runs QC analysis on samples with Sequali * Runs fileCompression information allowing easy transition between ORA and GZIP * Runs NTSM services for easy comparison within a library and for comparison between libraries
Introduced 'ResponseDict' concept to separate Response Classes from Response Dictionaries, model_dump() -> Self isn't always a viable solution. This also allows us to have dynamic logic in our file objects, either with s3 details or without s3 details. * NTSM Evaluation fixes
Handle pagination for queries
TODO list * Build stateful stack for this fastapi service * Integrate API with step functions
Allows other services' step functions to 'hang' on a put event task until the said fastq set has become available.
Handle copy jobs now is one step function that then generates jobs and waits for those jobs to complete.
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Centralised service for copying data around with ICAv2 Jobs, uses taskTokens for 'synced' events (inside AWS Step Functions).
For example an event might look like
Or
One can generate the Detail from the source with the following AWS StepFunctions Code