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added pre-qc-failed status filter #24

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merged 4 commits into from
Jan 15, 2025
Merged

added pre-qc-failed status filter #24

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2b0b493
added pre-qc-failed status filter
KateSakharova Dec 17, 2024
562ba4f
added default for PRE_QC status
KateSakharova Dec 17, 2024
4a53f7a
fixes
KateSakharova Jan 15, 2025
34869e7
fixes
KateSakharova Jan 15, 2025
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4 changes: 3 additions & 1 deletion analyses/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -207,7 +207,7 @@ def __str__(self):
return f"{self.name} {self.version}" if self.version is not None else self.name


class AssemblyManager(ENADerivedManager):
class AssemblyManager(SelectByStatusManagerMixin, ENADerivedManager):
def get_queryset(self):
return super().get_queryset().select_related("run")

Expand Down Expand Up @@ -267,6 +267,7 @@ class AssemblyStates(str, Enum):
def default_status(cls):
return {
cls.ASSEMBLY_STARTED: False,
cls.PRE_ASSEMBLY_QC_FAILED: False,
cls.ASSEMBLY_FAILED: False,
cls.ASSEMBLY_COMPLETED: False,
cls.ASSEMBLY_BLOCKED: False,
Expand Down Expand Up @@ -512,6 +513,7 @@ class AnalysisStates(str, Enum):
def default_status(cls):
return {
cls.ANALYSIS_STARTED: False,
cls.ANALYSIS_QC_FAILED: False,
cls.ANALYSIS_COMPLETED: False,
cls.ANALYSIS_BLOCKED: False,
cls.ANALYSIS_FAILED: False,
Expand Down
8 changes: 6 additions & 2 deletions workflows/flows/analysis_amplicon_study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,11 @@ def get_analyses_to_attempt(
study.refresh_from_db()
analyses_worth_trying = (
study.analyses.exclude_by_statuses(
[AnalysisStates.ANALYSIS_COMPLETED, AnalysisStates.ANALYSIS_BLOCKED]
[
analyses.models.Analysis.AnalysisStates.ANALYSIS_QC_FAILED,
analyses.models.Analysis.AnalysisStates.ANALYSIS_COMPLETED,
analyses.models.Analysis.AnalysisStates.ANALYSIS_BLOCKED,
]
)
.filter(experiment_type=for_experiment_type.value)
.order_by("id")
Expand Down Expand Up @@ -545,7 +549,7 @@ def set_post_analysis_states(amplicon_current_outdir: Path, amplicon_analyses: L
if analysis.run.first_accession in qc_failed_runs:
task_mark_analysis_status(
analysis,
status=AnalysisStates.ANALYSIS_FAILED,
status=AnalysisStates.ANALYSIS_QC_FAILED,
reason=qc_failed_runs[analysis.run.first_accession],
)
elif analysis.run.first_accession in qc_completed_runs:
Expand Down
11 changes: 6 additions & 5 deletions workflows/flows/assemble_study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,11 +122,12 @@ def get_assemblies_to_attempt(study: analyses.models.Study) -> List[Union[str, i
:return:
"""
study.refresh_from_db()
assemblies_worth_trying = study.assemblies_reads.filter(
**{
f"status__{analyses.models.Assembly.AssemblyStates.ASSEMBLY_COMPLETED}": False,
f"status__{analyses.models.Assembly.AssemblyStates.ASSEMBLY_BLOCKED}": False,
}
assemblies_worth_trying = study.assemblies_reads.exclude_by_statuses(
[
analyses.models.Assembly.AssemblyStates.PRE_ASSEMBLY_QC_FAILED,
analyses.models.Assembly.AssemblyStates.ASSEMBLY_COMPLETED,
analyses.models.Assembly.AssemblyStates.ASSEMBLY_BLOCKED,
]
).values_list("id", flat=True)
return assemblies_worth_trying

Expand Down
2 changes: 1 addition & 1 deletion workflows/tests/test_analysis_amplicon_study_flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -505,7 +505,7 @@ async def test_prefect_analyse_amplicon_flow(
# check failed runs
assert (
await analyses.models.Analysis.objects.filter(
status__analysis_failed=True
status__analysis_qc_failed=True
).acount()
== 1
)
Expand Down
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