Add Nallo workflow metrics-deliver

[peterpru]

Description

This PR aims to add the cg workflow metrics-deliver command for nallo, and adds nallo to more config-case pytests.

For sysdev: this is identical to how it is implemented for tomte and the first PR of raredisease.

Added

• cg workflow nallo metrics-deliver
• nallo to config-case pytests

Changed

Fixed

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b add-nallo-metrics-deliver

How to test

• cg workflow nallo metrics-deliver trustingchipmunk
• nano /home/proj/stage/analysis/cases/trustingchipmunk/multiqc/multiqc_data/multiqc_data.json
• change median coverage in the json file to 14
• cg workflow nallo metrics-deliver trustingchipmunk

Expected test outcome

• Check that command succeeds and metrics yaml file is generated.
• Take a screenshot and attach or copy/paste the output.

• Check that the command show an error with the low coverage set to 14.
• Check that Trailblazer status is set to failed and shows the failed metric as comment.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[fevac]

To avoid those obscure errors due to cases missing in trailblazer I wonder if you could replace the validate_qc_metrics cg/meta/workflow/nf_analysis.py by the following code. It would need to be tested though:

    def _validate_metrics(self, case_id: str) -> None:
        """Perform the actual QC metrics validation."""
        metrics_deliverables_path: Path = self.get_metrics_deliverables_path(case_id=case_id)
        qc_metrics_raw: dict = ReadFile.get_content_from_file(
            file_format=FileFormat.YAML, file_path=metrics_deliverables_path
        )
        MetricsDeliverablesCondition(**qc_metrics_raw)

    def _set_analysis_status(self, case_id: str, status: AnalysisStatus) -> None:
        """Safely set the analysis status in Trailblazer, with error logging."""
        try:
            self.trailblazer_api.set_analysis_status(case_id=case_id, status=str(status))
        except Exception as error:
            LOG.error(f"Failed to set analysis status to '{status}' for {case_id}: {error}")

    def _generate_trailblazer_comment(self, case_id: str, error: MetricsQCError) -> str:
        """Safely generate a formatted Trailblazer comment based on the error."""
        try:
            samples = self.status_db.get_samples_by_case_id(case_id=case_id)
            trailblazer_comment = str(error)
            for sample in samples:
                trailblazer_comment = trailblazer_comment.replace(
                    f"{sample.internal_id} - ", f"{sample.name} ({sample.internal_id}) - "
                )
            return trailblazer_comment
        except Exception as error:
            LOG.error(f"Failed to generate Trailblazer comments for {case_id}: {error}")

    def _add_trailblazer_comment(self, case_id: str, comment: str) -> None:
        """Safely add a comment in Trailblazer, with error logging."""
        try:
            self.trailblazer_api.add_comment(case_id=case_id, comment=comment)
        except Exception as error:
            LOG.error(f"Failed to add comment in Trailblazer for {case_id}: {error}")

    def validate_qc_metrics(self, case_id: str, dry_run: bool = False) -> None:
        """Validate the information from a QC metrics deliverable file."""

        if dry_run:
            LOG.info("Dry-run: QC metrics validation would be performed")
            return

        LOG.info("Validating QC metrics")
        try:
            self._validate_metrics(case_id)
        except MetricsQCError as error:
            LOG.error(f"QC metrics validation failed for {case_id}, with: {error}")
            self._set_analysis_status(case_id, AnalysisStatus.ERROR)
            trailblazer_comment = self._generate_trailblazer_comment(case_id, error)
            self._add_trailblazer_comment(case_id, trailblazer_comment)
            raise
        except CgError as error:
            LOG.error(f"Failed to create metrics deliverables file for {case_id}: {error}")
            self._set_analysis_status(case_id, AnalysisStatus.ERROR)
            raise
        else:
            self._set_analysis_status(case_id, AnalysisStatus.COMPLETED)

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[peterpru]

To avoid those obscure errors due to cases missing in trailblazer I wonder if you could replace the validate_qc_metrics cg/meta/workflow/nf_analysis.py by the following code. It would need to be tested though:

    def _validate_metrics(self, case_id: str) -> None:
        """Perform the actual QC metrics validation."""
        metrics_deliverables_path: Path = self.get_metrics_deliverables_path(case_id=case_id)
        qc_metrics_raw: dict = ReadFile.get_content_from_file(
            file_format=FileFormat.YAML, file_path=metrics_deliverables_path
        )
        MetricsDeliverablesCondition(**qc_metrics_raw)

    def _set_analysis_status(self, case_id: str, status: AnalysisStatus) -> None:
        """Safely set the analysis status in Trailblazer, with error logging."""
        try:
            self.trailblazer_api.set_analysis_status(case_id=case_id, status=str(status))
        except Exception as error:
            LOG.error(f"Failed to set analysis status to '{status}' for {case_id}: {error}")

    def _generate_trailblazer_comment(self, case_id: str, error: MetricsQCError) -> str:
        """Safely generate a formatted Trailblazer comment based on the error."""
        try:
            samples = self.status_db.get_samples_by_case_id(case_id=case_id)
            trailblazer_comment = str(error)
            for sample in samples:
                trailblazer_comment = trailblazer_comment.replace(
                    f"{sample.internal_id} - ", f"{sample.name} ({sample.internal_id}) - "
                )
            return trailblazer_comment
        except Exception as error:
            LOG.error(f"Failed to generate Trailblazer comments for {case_id}: {error}")

    def _add_trailblazer_comment(self, case_id: str, comment: str) -> None:
        """Safely add a comment in Trailblazer, with error logging."""
        try:
            self.trailblazer_api.add_comment(case_id=case_id, comment=comment)
        except Exception as error:
            LOG.error(f"Failed to add comment in Trailblazer for {case_id}: {error}")

    def validate_qc_metrics(self, case_id: str, dry_run: bool = False) -> None:
        """Validate the information from a QC metrics deliverable file."""

        if dry_run:
            LOG.info("Dry-run: QC metrics validation would be performed")
            return

        LOG.info("Validating QC metrics")
        try:
            self._validate_metrics(case_id)
        except MetricsQCError as error:
            LOG.error(f"QC metrics validation failed for {case_id}, with: {error}")
            self._set_analysis_status(case_id, AnalysisStatus.ERROR)
            trailblazer_comment = self._generate_trailblazer_comment(case_id, error)
            self._add_trailblazer_comment(case_id, trailblazer_comment)
            raise
        except CgError as error:
            LOG.error(f"Failed to create metrics deliverables file for {case_id}: {error}")
            self._set_analysis_status(case_id, AnalysisStatus.ERROR)
            raise
        else:
            self._set_analysis_status(case_id, AnalysisStatus.COMPLETED)

Thanks for this, Eva. In this case it turned out that the error was from something else, but this would be good to implement. I will add it in a separate issue and I will leave it out of this PR.