added pre-qc-failed status filter

EBI-Metagenomics · Dec 17, 2024 · 4dea336 · 4dea336
1 parent fc4fbd3
commit 4dea336
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Showing 4 changed files with 6 additions and 3 deletions.
diff --git a/analyses/models.py b/analyses/models.py
@@ -504,7 +504,7 @@ class AnalysisStates(str, Enum):
         ANALYSIS_COMPLETED = "analysis_completed"
         ANALYSIS_BLOCKED = "analysis_blocked"
         ANALYSIS_FAILED = "analysis_failed"
-        ANALYSIS_QC_FAILED = "analysis_qc_failed"
+        ANALYSIS_PRE_QC_FAILED = "analysis_pre_qc_failed"
         ANALYSIS_POST_SANITY_CHECK_FAILED = "analysis_post_sanity_check_failed"
 
         @classmethod
@@ -514,6 +514,7 @@ def default_status(cls):
                 cls.ANALYSIS_COMPLETED: False,
                 cls.ANALYSIS_BLOCKED: False,
                 cls.ANALYSIS_FAILED: False,
+                cls.ANALYSIS_PRE_QC_FAILED: False,
             }
 
     status = models.JSONField(

diff --git a/workflows/flows/analysis_amplicon_study.py b/workflows/flows/analysis_amplicon_study.py
@@ -64,6 +64,7 @@ def get_analyses_to_attempt(
             **{
                 f"status__{analyses.models.Analysis.AnalysisStates.ANALYSIS_COMPLETED}": False,
                 f"status__{analyses.models.Analysis.AnalysisStates.ANALYSIS_BLOCKED}": False,
+                f"status__{analyses.models.Analysis.AnalysisStates.ANALYSIS_PRE_QC_FAILED}": False,
             }
         )
         .filter(experiment_type=for_experiment_type)
@@ -546,7 +547,7 @@ 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=analyses.models.Analysis.AnalysisStates.ANALYSIS_FAILED,
+                status=analyses.models.Analysis.AnalysisStates.ANALYSIS_PRE_QC_FAILED,
                 reason=qc_failed_runs[analysis.run.first_accession],
             )
         elif analysis.run.first_accession in qc_completed_runs:

diff --git a/workflows/flows/assemble_study.py b/workflows/flows/assemble_study.py
@@ -126,6 +126,7 @@ def get_assemblies_to_attempt(study: analyses.models.Study) -> List[Union[str, i
         **{
             f"status__{analyses.models.Assembly.AssemblyStates.ASSEMBLY_COMPLETED}": False,
             f"status__{analyses.models.Assembly.AssemblyStates.ASSEMBLY_BLOCKED}": False,
+            f"status__{analyses.models.Assembly.AssemblyStates.PRE_ASSEMBLY_QC_FAILED}": False,
         }
     ).values_list("id", flat=True)
     return assemblies_worth_trying

diff --git a/workflows/tests/test_analysis_amplicon_study_flow.py b/workflows/tests/test_analysis_amplicon_study_flow.py
@@ -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_pre_qc_failed=True
         ).acount()
         == 1
     )