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Suppression state propagation #328

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merged 15 commits into from
Jan 12, 2024
Merged

Suppression state propagation #328

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f9dfe0c
[wip] support propagation of suppression state from ancestor data typ…
SandyRogers Sep 13, 2023
f9e6b78
propagate suppression status through models using "suppression tree"
SandyRogers Sep 20, 2023
e660d9f
Merge branch 'develop' into suppression-state-propagation
SandyRogers Sep 21, 2023
6482feb
resolve migration conflicts
SandyRogers Sep 21, 2023
130e53d
typo
SandyRogers Sep 21, 2023
388c6e4
optimising analysis query relationships
SandyRogers Sep 21, 2023
b658921
Update emgapi/models.py
SandyRogers Sep 26, 2023
4cd7721
WIP, investigating cause of failing tests, after removing ANALYSIS_JO…
MGS-sails Sep 28, 2023
665a056
Deprecated AnalysisJobAnn
MGS-sails Sep 30, 2023
9580966
Bumped api version
MGS-sails Jan 9, 2024
c1a1252
commented out assertion of empty attributes
MGS-sails Jan 9, 2024
1160ee3
Merge branch 'develop' into Feature-Analysis-Job-Ann-Deprecation
MGS-sails Jan 9, 2024
26a4dd0
Merge branch 'develop' into suppression-state-propagation
SandyRogers Jan 12, 2024
58e701c
Merge remote-tracking branch 'origin/Feature-Analysis-Job-Ann-Depreca…
SandyRogers Jan 12, 2024
6f552e7
resolves migration merge conflicts
SandyRogers Jan 12, 2024
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2 changes: 1 addition & 1 deletion emgapi/management/commands/clean_empty_studies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,5 +56,5 @@ def handle(self, *args, **kwargs):
run.ena_study_accession = study.secondary_accession
run.study = None
Run.objects.bulk_update(runs, ["ena_study_accession", "study"])
study.suppress()
study.suppress(propagate=False)
logger.info(f"{study} suppressed")
44 changes: 44 additions & 0 deletions emgapi/migrations/0012_suppression_reason_ancestor_suppressed.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
# Generated by Django 3.2.18 on 2023-09-14 07:16

from django.db import migrations, models
import django.db.models.deletion


class Migration(migrations.Migration):

dependencies = [
('emgapi', '0011_analysisjob_analysis_summary_json'),
]

operations = [
migrations.AlterField(
model_name='analysisjob',
name='suppression_reason',
field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
),
migrations.AlterField(
model_name='assembly',
name='study',
field=models.ForeignKey(blank=True, db_column='STUDY_ID', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='assemblies', to='emgapi.study'),
),
migrations.AlterField(
model_name='assembly',
name='suppression_reason',
field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
),
migrations.AlterField(
model_name='run',
name='suppression_reason',
field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
),
migrations.AlterField(
model_name='sample',
name='suppression_reason',
field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
),
migrations.AlterField(
model_name='study',
name='suppression_reason',
field=models.IntegerField(blank=True, choices=[(1, 'Draft'), (3, 'Cancelled'), (5, 'Suppressed'), (6, 'Killed'), (7, 'Temporary Suppressed'), (8, 'Temporary Killed'), (100, 'Ancestor Suppressed')], db_column='SUPPRESSION_REASON', null=True),
),
]
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