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Fix run device cascading #5304

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Fix run device cascading #5304

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59a7542
Created alembic revision
islean Aug 28, 2026
5cad699
Initial commit
islean Aug 31, 2026
11f6f7f
Fix removal of run device for Admin view deletions of Pacbio data
islean Sep 8, 2026
09fb500
Fix removal of run device for Admin view deletions of Pacbio data
islean Sep 8, 2026
e6b7ba8
Merge branch 'master' into fix-run-device-cascading
islean Sep 8, 2026
5076434
Whitelist
islean Sep 8, 2026
7f8e86d
Merge branch 'master' into fix-run-device-cascading
islean Sep 10, 2026
68e6589
Fix merge conflict
islean Sep 10, 2026
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11 changes: 11 additions & 0 deletions cg/server/admin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1051,6 +1051,17 @@ class PacbioSmrtCellMetricsView(BaseView):
"completed_at",
]

def delete_model(self, model):
try:
# Pacbio SMRT cells are only run once, so cascading to the run_device table is okay.
self.session.delete(model.device)
self.session.commit()
return True
except Exception as ex:
if not self.handle_view_exception(ex):
raise
return False

@staticmethod
def view_smrt_cell_link(unused1, unused2, model, unused3):
"""column formatter to open this view"""
Expand Down
17 changes: 7 additions & 10 deletions vulture_whitelist.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -755,11 +755,11 @@ column_labels # unused variable (cg/server/admin.py:1040)
column_default_sort # unused variable (cg/server/admin.py:1041)
column_searchable_list # unused variable (cg/server/admin.py:1042)
column_sortable_list # unused variable (cg/server/admin.py:1048)
column_filters # unused variable (cg/server/admin.py:1075)
column_formatters # unused variable (cg/server/admin.py:1079)
column_labels # unused variable (cg/server/admin.py:1083)
column_list # unused variable (cg/server/admin.py:1087)
column_searchable_list # unused variable (cg/server/admin.py:1097)
column_filters # unused variable (cg/server/admin.py:1086)
column_formatters # unused variable (cg/server/admin.py:1090)
column_labels # unused variable (cg/server/admin.py:1094)
column_list # unused variable (cg/server/admin.py:1098)
column_searchable_list # unused variable (cg/server/admin.py:1108)
_.secret_key # unused attribute (cg/server/app.py:69)
_.json_provider_class # unused attribute (cg/server/app.py:83)
blueprint # unused variable (cg/server/app.py:98)
Expand All @@ -770,10 +770,6 @@ gunicorn_timeout # unused variable (cg/server/app_config.py:14)
invoice_max_price # unused variable (cg/server/app_config.py:21)
support_system_email # unused variable (cg/server/app_config.py:29)
email_uri # unused variable (cg/server/app_config.py:30)
nats_ca_cert_path # unused variable (cg/server/app_config.py:48)
nats_client_cert_path # unused variable (cg/server/app_config.py:49)
nats_client_key_path # unused variable (cg/server/app_config.py:50)
nats_token_path # unused variable (cg/server/app_config.py:51)
CUSTOMER_ID # unused variable (cg/server/dto/orders/orders_request.py:8)
ASCENDING # unused variable (cg/server/dto/samples/requests.py:13)
require_qc_ok # unused variable (cg/server/dto/samples/samples_response.py:74)
Expand Down Expand Up @@ -817,6 +813,7 @@ sessionId # unused variable (cg/services/analysis_starter/submitters/seqera_pla
workDir # unused variable (cg/services/analysis_starter/submitters/seqera_platform/dtos.py:16)
launch # unused variable (cg/services/analysis_starter/submitters/seqera_platform/dtos.py:22)
_.minimum_version # unused attribute (cg/services/events/event_listener.py:67)
_.minimum_version # unused attribute (cg/services/events/event_publisher.py:57)
model_config # unused variable (cg/services/illumina/data_transfer/models.py:20)
model_config # unused variable (cg/services/illumina/data_transfer/models.py:60)
model_config # unused variable (cg/services/illumina/data_transfer/models.py:82)
Expand Down Expand Up @@ -968,14 +965,14 @@ _.initialise_db # unused method (cg/apps/housekeeper/hk.py:360)
_.destroy_db # unused method (cg/apps/housekeeper/hk.py:364)
_.is_accessible # unused method (cg/server/admin.py:26)
_.inaccessible_callback # unused method (cg/server/admin.py:30)
_.get_analysis_starter_for_case # unused method (cg/services/analysis_starter/factories/starter_factory.py:40)
_.add_collaboration # unused method (cg/store/crud/create.py:100)
_.get_sample_coverage_metrics # unused method (cg/clients/chanjo2/models.py:48)
get_tables # unused function (cg/store/database.py:53)
_.get_sequencing_run_unaligned_dir # unused method (cg/apps/demultiplex/demultiplex_api.py:133)
_.link_case_to_order # unused method (cg/store/crud/create.py:412)
_.get_applications # unused method (cg/store/crud/read.py:911)
_.get_bed_by_name # unused method (cg/store/crud/read.py:1007)
_.delete_model # unused method (cg/server/admin.py:1054)
_.get_coverage # unused method (cg/clients/chanjo2/client.py:22)
_.add_panel # unused method (cg/store/crud/create.py:306)
_.add_application_version # unused method (cg/store/crud/create.py:147)
Expand Down
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