(Pipeline Integration) Add starter factory #4295
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| seqera_platform_client: SeqeraPlatformClient = self._get_seqera_platform_client() | ||
| return SeqeraPlatformSubmitter( | ||
| client=seqera_platform_client, | ||
| compute_environment_ids=self.cg_config.seqera_platform.compute_environments, |
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This reaching through the SeqeraPlatformConfig indicates that our server config is not designed properly.
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What if we have a method like this?
def _get_seqera_platform_submitter(config: SeqeraPlatformConfig):
client = SeqeraPlatformClient(config)
return SeqeraPlatformSubmitter(client=client, compute_environemnt_ids=config.compute_environments)There was a problem hiding this comment.
It is more the fact that the computeEnvIds are not needed by the client at all anymore, but they are set in the config we designed for the client. I guess we should have one config for the submitter and one for the client?
| params_file_creator: ParamsFileCreator = RarediseaseParamsFileCreator( | ||
| lims=self.cg_config.lims_api, store=self.store, params=pipeline_config.params | ||
| ) | ||
| sample_sheet_creator: RarediseaseSampleSheetCreator = RarediseaseSampleSheetCreator( |
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Clearly these should be initiated in a dynamic way and not only be Raredisease do we know if the inits are the same? What do we need to pass to fetch the correct one?
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I'm 99% sure the signatures of other NF pipelines will be the same
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You can make a function that pulls the correct one from a map for example. workflow_to_samplesheet_creator (so pass the workflow)
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Yeah, that might be the nicest approach but then we need to fix the init in the parent NextflowSampleSheetCreator class.
| pipeline_extension=self._get_pipeline_extension(workflow), | ||
| ) | ||
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| def _get_pipeline_config(self, workflow: Workflow) -> CommonAppConfig: |
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The fact that all the nextflow configs inherit only from CommonAppConfig leads to our code being riddled with warnings because of unknown attributes.
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We need to create a separate basemodel to inherit from IMO
| workflow_config_path=pipeline_config.workflow_config_path, | ||
| ) | ||
| params_file_creator: ParamsFileCreator = RarediseaseParamsFileCreator( | ||
| lims=self.cg_config.lims_api, store=self.store, params=pipeline_config.params |
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what are the params here?
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It is what the devbio have named the pipeline parameters file path that you can find in the cg.yaml
| configurator: Configurator = self._get_configurator(case_id) | ||
| input_fetcher: InputFetcher = self._get_input_fetcher(case_id) | ||
| submitter: Submitter = self._get_submitter(case_id) |
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These all take the case_id as input but they all just depend on the workflow. And some of the smaller functions take workflow as input. Do you think it makes sense to just pass the workflow here as well?
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My thinking initially was that the input fetcher depends on the delivery type, but then I remembered that most delivery types are not only fastq or bam, so at this point, yeah - we should probably pass the workflow.
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Unless there is more information required than just the workflow it makes sense, if it turns out later you need more information than case_id will allow to fetch more information of course. I'd wait with changing it until it is more final.
| params_file_creator: ParamsFileCreator = RarediseaseParamsFileCreator( | ||
| lims=self.cg_config.lims_api, store=self.store, params=pipeline_config.params | ||
| ) | ||
| sample_sheet_creator: RarediseaseSampleSheetCreator = RarediseaseSampleSheetCreator( |
There was a problem hiding this comment.
I'm 99% sure the signatures of other NF pipelines will be the same
| pipeline_extension=self._get_pipeline_extension(workflow), | ||
| ) | ||
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| def _get_pipeline_config(self, workflow: Workflow) -> CommonAppConfig: |
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We need to create a separate basemodel to inherit from IMO
| seqera_platform_client: SeqeraPlatformClient = self._get_seqera_platform_client() | ||
| return SeqeraPlatformSubmitter( | ||
| client=seqera_platform_client, | ||
| compute_environment_ids=self.cg_config.seqera_platform.compute_environments, |
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What if we have a method like this?
def _get_seqera_platform_submitter(config: SeqeraPlatformConfig):
client = SeqeraPlatformClient(config)
return SeqeraPlatformSubmitter(client=client, compute_environemnt_ids=config.compute_environments)
| store=self.store, | ||
| workflow_config_path=pipeline_config.workflow_config_path, | ||
| ) | ||
| params_file_creator: ParamsFileCreator = RarediseaseParamsFileCreator( |
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These likely needs it own function as soon as there are more than the "RareDiseaseParamsFileCreator"
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