From 59a7542b615ffdd185c17e6599fc143e48c07514 Mon Sep 17 00:00:00 2001 From: islean Date: Fri, 28 Aug 2026 10:08:02 +0200 Subject: [PATCH 1/6] Created alembic revision --- ...a36c11ee9862_cascade_to_rundevice_table.py | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py diff --git a/alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py b/alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py new file mode 100644 index 0000000000..ee9729716f --- /dev/null +++ b/alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py @@ -0,0 +1,25 @@ +"""Cascade to RunDevice table + +Revision ID: a36c11ee9862 +Revises: 8a0dd32c2550 +Create Date: 2026-08-28 08:56:40.081418 + +""" + +import sqlalchemy as sa + +from alembic import op + +# revision identifiers, used by Alembic. +revision = "a36c11ee9862" +down_revision = "8a0dd32c2550" +branch_labels = None +depends_on = None + + +def upgrade(): + pass + + +def downgrade(): + pass From 5cad6996a0c31a495a27031d2796710643b55df0 Mon Sep 17 00:00:00 2001 From: islean Date: Mon, 31 Aug 2026 09:55:53 +0200 Subject: [PATCH 2/6] Initial commit --- cg/server/admin.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/cg/server/admin.py b/cg/server/admin.py index 8cc565fc5e..3a85658518 100644 --- a/cg/server/admin.py +++ b/cg/server/admin.py @@ -1051,6 +1051,17 @@ class PacbioSmrtCellMetricsView(BaseView): "completed_at", ] + def delete_model(self, model): + try: + # your custom logic — e.g. soft delete, cascade, logging + model.device_run = True + 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""" From 11f6f7f2d0e8cfc90fe44f6d4237bb80380d1da6 Mon Sep 17 00:00:00 2001 From: islean Date: Tue, 8 Sep 2026 16:38:21 +0200 Subject: [PATCH 3/6] Fix removal of run device for Admin view deletions of Pacbio data --- cg/server/admin.py | 4 +- vulture_whitelist.txt | 313 +++++++++++++++++++++--------------------- 2 files changed, 160 insertions(+), 157 deletions(-) diff --git a/cg/server/admin.py b/cg/server/admin.py index 3a85658518..615cee7df1 100644 --- a/cg/server/admin.py +++ b/cg/server/admin.py @@ -1053,8 +1053,8 @@ class PacbioSmrtCellMetricsView(BaseView): def delete_model(self, model): try: - # your custom logic — e.g. soft delete, cascade, logging - model.device_run = True + # 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: diff --git a/vulture_whitelist.txt b/vulture_whitelist.txt index 66c0d28c1c..fa5614c5a7 100644 --- a/vulture_whitelist.txt +++ b/vulture_whitelist.txt @@ -619,145 +619,147 @@ method_libprep # unused variable (cg/models/workflow/mutant.py:21) sequencing_qc_pass # unused variable (cg/models/workflow/mutant.py:23) selection_criteria # unused variable (cg/models/workflow/mutant.py:24) primer # unused variable (cg/models/workflow/mutant.py:25) -column_list # unused variable (cg/server/admin.py:268) -column_editable_list # unused variable (cg/server/admin.py:270) -column_exclude_list # unused variable (cg/server/admin.py:293) -column_formatters # unused variable (cg/server/admin.py:303) -column_filters # unused variable (cg/server/admin.py:311) -column_searchable_list # unused variable (cg/server/admin.py:312) -form_excluded_columns # unused variable (cg/server/admin.py:313) -form_extra_fields # unused variable (cg/server/admin.py:314) -column_default_sort # unused variable (cg/server/admin.py:358) -column_editable_list # unused variable (cg/server/admin.py:359) -column_list # unused variable (cg/server/admin.py:367) -column_exclude_list # unused variable (cg/server/admin.py:378) -column_filters # unused variable (cg/server/admin.py:379) -column_formatters # unused variable (cg/server/admin.py:380) -column_searchable_list # unused variable (cg/server/admin.py:381) -edit_modal # unused variable (cg/server/admin.py:382) -create_modal # unused variable (cg/server/admin.py:383) -form_excluded_columns # unused variable (cg/server/admin.py:384) -column_list # unused variable (cg/server/admin.py:390) -column_formatters # unused variable (cg/server/admin.py:398) +column_list # unused variable (cg/server/admin.py:281) +column_editable_list # unused variable (cg/server/admin.py:283) +column_exclude_list # unused variable (cg/server/admin.py:306) +column_formatters # unused variable (cg/server/admin.py:320) +column_filters # unused variable (cg/server/admin.py:331) +column_searchable_list # unused variable (cg/server/admin.py:332) +form_excluded_columns # unused variable (cg/server/admin.py:333) +form_extra_fields # unused variable (cg/server/admin.py:334) +column_default_sort # unused variable (cg/server/admin.py:378) +column_editable_list # unused variable (cg/server/admin.py:379) +column_list # unused variable (cg/server/admin.py:387) +column_exclude_list # unused variable (cg/server/admin.py:398) column_filters # unused variable (cg/server/admin.py:399) -column_searchable_list # unused variable (cg/server/admin.py:400) -column_editable_list # unused variable (cg/server/admin.py:401) -form_excluded_columns # unused variable (cg/server/admin.py:402) -form_extra_fields # unused variable (cg/server/admin.py:403) -create_modal # unused variable (cg/server/admin.py:404) -edit_modal # unused variable (cg/server/admin.py:405) -column_default_sort # unused variable (cg/server/admin.py:411) -column_editable_list # unused variable (cg/server/admin.py:412) -column_exclude_list # unused variable (cg/server/admin.py:413) -column_filters # unused variable (cg/server/admin.py:414) -column_searchable_list # unused variable (cg/server/admin.py:415) -form_excluded_columns # unused variable (cg/server/admin.py:416) -column_default_sort # unused variable (cg/server/admin.py:435) -column_editable_list # unused variable (cg/server/admin.py:436) -column_exclude_list # unused variable (cg/server/admin.py:437) -form_excluded_columns # unused variable (cg/server/admin.py:438) -column_filters # unused variable (cg/server/admin.py:439) -column_formatters # unused variable (cg/server/admin.py:440) -column_searchable_list # unused variable (cg/server/admin.py:441) -edit_modal # unused variable (cg/server/admin.py:442) -column_editable_list # unused variable (cg/server/admin.py:448) -column_list # unused variable (cg/server/admin.py:457) -column_filters # unused variable (cg/server/admin.py:472) -column_formatters # unused variable (cg/server/admin.py:473) -column_searchable_list # unused variable (cg/server/admin.py:478) -form_excluded_columns # unused variable (cg/server/admin.py:479) -column_editable_list # unused variable (cg/server/admin.py:485) -column_filters # unused variable (cg/server/admin.py:486) -column_hide_backrefs # unused variable (cg/server/admin.py:487) -column_list # unused variable (cg/server/admin.py:488) -column_searchable_list # unused variable (cg/server/admin.py:489) -column_default_sort # unused variable (cg/server/admin.py:495) -column_editable_list # unused variable (cg/server/admin.py:496) -column_exclude_list # unused variable (cg/server/admin.py:497) -column_filters # unused variable (cg/server/admin.py:498) -column_formatters # unused variable (cg/server/admin.py:506) -column_searchable_list # unused variable (cg/server/admin.py:512) -form_ajax_refs # unused variable (cg/server/admin.py:518) -form_excluded_columns # unused variable (cg/server/admin.py:524) -form_extra_fields # unused variable (cg/server/admin.py:530) -column_default_sort # unused variable (cg/server/admin.py:591) -column_editable_list # unused variable (cg/server/admin.py:592) -column_list # unused variable (cg/server/admin.py:593) -column_formatters # unused variable (cg/server/admin.py:603) -column_searchable_list # unused variable (cg/server/admin.py:604) -column_default_sort # unused variable (cg/server/admin.py:630) -column_editable_list # unused variable (cg/server/admin.py:631) -column_filters # unused variable (cg/server/admin.py:632) -column_formatters # unused variable (cg/server/admin.py:633) -column_searchable_list # unused variable (cg/server/admin.py:634) -form_ajax_refs # unused variable (cg/server/admin.py:638) -column_list # unused variable (cg/server/admin.py:649) -column_formatters # unused variable (cg/server/admin.py:672) -column_default_sort # unused variable (cg/server/admin.py:676) -column_filters # unused variable (cg/server/admin.py:677) -column_editable_list # unused variable (cg/server/admin.py:678) -column_searchable_list # unused variable (cg/server/admin.py:679) -column_sortable_list # unused variable (cg/server/admin.py:680) -column_default_sort # unused variable (cg/server/admin.py:716) -column_editable_list # unused variable (cg/server/admin.py:717) -column_searchable_list # unused variable (cg/server/admin.py:718) -column_default_sort # unused variable (cg/server/admin.py:724) -column_editable_list # unused variable (cg/server/admin.py:725) -column_formatters # unused variable (cg/server/admin.py:726) -column_searchable_list # unused variable (cg/server/admin.py:730) -column_display_pk # unused variable (cg/server/admin.py:731) -create_modal # unused variable (cg/server/admin.py:732) -edit_modal # unused variable (cg/server/admin.py:733) -form_ajax_refs # unused variable (cg/server/admin.py:734) +column_formatters # unused variable (cg/server/admin.py:400) +column_searchable_list # unused variable (cg/server/admin.py:401) +edit_modal # unused variable (cg/server/admin.py:402) +create_modal # unused variable (cg/server/admin.py:403) +form_excluded_columns # unused variable (cg/server/admin.py:404) +column_list # unused variable (cg/server/admin.py:410) +column_formatters # unused variable (cg/server/admin.py:418) +column_filters # unused variable (cg/server/admin.py:419) +column_searchable_list # unused variable (cg/server/admin.py:420) +column_editable_list # unused variable (cg/server/admin.py:421) +form_excluded_columns # unused variable (cg/server/admin.py:422) +form_extra_fields # unused variable (cg/server/admin.py:423) +create_modal # unused variable (cg/server/admin.py:424) +edit_modal # unused variable (cg/server/admin.py:425) +column_default_sort # unused variable (cg/server/admin.py:431) +column_editable_list # unused variable (cg/server/admin.py:432) +column_exclude_list # unused variable (cg/server/admin.py:433) +column_filters # unused variable (cg/server/admin.py:434) +column_searchable_list # unused variable (cg/server/admin.py:435) +form_excluded_columns # unused variable (cg/server/admin.py:436) +column_default_sort # unused variable (cg/server/admin.py:455) +column_editable_list # unused variable (cg/server/admin.py:456) +column_exclude_list # unused variable (cg/server/admin.py:457) +form_excluded_columns # unused variable (cg/server/admin.py:458) +column_filters # unused variable (cg/server/admin.py:459) +column_formatters # unused variable (cg/server/admin.py:460) +column_searchable_list # unused variable (cg/server/admin.py:461) +edit_modal # unused variable (cg/server/admin.py:462) +column_editable_list # unused variable (cg/server/admin.py:468) +column_list # unused variable (cg/server/admin.py:477) +column_filters # unused variable (cg/server/admin.py:492) +column_formatters # unused variable (cg/server/admin.py:493) +column_searchable_list # unused variable (cg/server/admin.py:498) +form_excluded_columns # unused variable (cg/server/admin.py:499) +column_editable_list # unused variable (cg/server/admin.py:505) +column_filters # unused variable (cg/server/admin.py:506) +column_hide_backrefs # unused variable (cg/server/admin.py:507) +column_list # unused variable (cg/server/admin.py:508) +column_searchable_list # unused variable (cg/server/admin.py:509) +column_default_sort # unused variable (cg/server/admin.py:515) +column_editable_list # unused variable (cg/server/admin.py:516) +column_exclude_list # unused variable (cg/server/admin.py:517) +column_filters # unused variable (cg/server/admin.py:518) +column_formatters # unused variable (cg/server/admin.py:526) +column_searchable_list # unused variable (cg/server/admin.py:532) +form_ajax_refs # unused variable (cg/server/admin.py:538) +form_excluded_columns # unused variable (cg/server/admin.py:544) +form_extra_fields # unused variable (cg/server/admin.py:550) +column_default_sort # unused variable (cg/server/admin.py:611) +column_editable_list # unused variable (cg/server/admin.py:612) +column_list # unused variable (cg/server/admin.py:613) +column_formatters # unused variable (cg/server/admin.py:623) +column_searchable_list # unused variable (cg/server/admin.py:624) +column_default_sort # unused variable (cg/server/admin.py:650) +column_editable_list # unused variable (cg/server/admin.py:651) +column_filters # unused variable (cg/server/admin.py:652) +column_formatters # unused variable (cg/server/admin.py:653) +column_searchable_list # unused variable (cg/server/admin.py:654) +form_ajax_refs # unused variable (cg/server/admin.py:658) +column_list # unused variable (cg/server/admin.py:669) +column_formatters # unused variable (cg/server/admin.py:692) +column_default_sort # unused variable (cg/server/admin.py:696) +column_filters # unused variable (cg/server/admin.py:697) +column_editable_list # unused variable (cg/server/admin.py:698) +column_searchable_list # unused variable (cg/server/admin.py:699) +column_sortable_list # unused variable (cg/server/admin.py:700) +column_default_sort # unused variable (cg/server/admin.py:736) +column_editable_list # unused variable (cg/server/admin.py:737) +column_searchable_list # unused variable (cg/server/admin.py:738) +column_default_sort # unused variable (cg/server/admin.py:744) column_editable_list # unused variable (cg/server/admin.py:745) -column_filters # unused variable (cg/server/admin.py:746) -column_formatters # unused variable (cg/server/admin.py:747) -column_searchable_list # unused variable (cg/server/admin.py:748) -create_modal # unused variable (cg/server/admin.py:749) -edit_modal # unused variable (cg/server/admin.py:750) -column_default_sort # unused variable (cg/server/admin.py:756) -column_filters # unused variable (cg/server/admin.py:757) -column_formatters # unused variable (cg/server/admin.py:758) -column_list # unused variable (cg/server/admin.py:764) -column_labels # unused variable (cg/server/admin.py:778) -column_searchable_list # unused variable (cg/server/admin.py:779) -column_list # unused variable (cg/server/admin.py:785) -column_default_sort # unused variable (cg/server/admin.py:817) -column_editable_list # unused variable (cg/server/admin.py:818) -column_filters # unused variable (cg/server/admin.py:826) -column_formatters # unused variable (cg/server/admin.py:834) -column_searchable_list # unused variable (cg/server/admin.py:844) -form_excluded_columns # unused variable (cg/server/admin.py:851) -column_default_sort # unused variable (cg/server/admin.py:897) -column_editable_list # unused variable (cg/server/admin.py:898) -column_filters # unused variable (cg/server/admin.py:899) -column_formatters # unused variable (cg/server/admin.py:900) -column_searchable_list # unused variable (cg/server/admin.py:904) -create_modal # unused variable (cg/server/admin.py:905) -edit_modal # unused variable (cg/server/admin.py:906) -form_ajax_refs # unused variable (cg/server/admin.py:907) -column_default_sort # unused variable (cg/server/admin.py:930) -column_editable_list # unused variable (cg/server/admin.py:931) -column_filters # unused variable (cg/server/admin.py:932) -column_hide_backrefs # unused variable (cg/server/admin.py:933) -column_list # unused variable (cg/server/admin.py:934) -column_searchable_list # unused variable (cg/server/admin.py:935) -create_modal # unused variable (cg/server/admin.py:936) -edit_modal # unused variable (cg/server/admin.py:937) -column_list # unused variable (cg/server/admin.py:941) -column_formatters # unused variable (cg/server/admin.py:952) -column_searchable_list # unused variable (cg/server/admin.py:956) -column_list # unused variable (cg/server/admin.py:962) -column_formatters # unused variable (cg/server/admin.py:985) -column_labels # unused variable (cg/server/admin.py:989) -column_default_sort # unused variable (cg/server/admin.py:990) -column_searchable_list # unused variable (cg/server/admin.py:991) -column_sortable_list # unused variable (cg/server/admin.py:997) -column_filters # unused variable (cg/server/admin.py:1024) -column_formatters # unused variable (cg/server/admin.py:1028) -column_labels # unused variable (cg/server/admin.py:1032) -column_list # unused variable (cg/server/admin.py:1036) -column_searchable_list # unused variable (cg/server/admin.py:1046) +column_formatters # unused variable (cg/server/admin.py:746) +column_searchable_list # unused variable (cg/server/admin.py:750) +column_display_pk # unused variable (cg/server/admin.py:751) +create_modal # unused variable (cg/server/admin.py:752) +edit_modal # unused variable (cg/server/admin.py:753) +form_ajax_refs # unused variable (cg/server/admin.py:754) +column_editable_list # unused variable (cg/server/admin.py:774) +column_filters # unused variable (cg/server/admin.py:775) +column_formatters # unused variable (cg/server/admin.py:776) +column_searchable_list # unused variable (cg/server/admin.py:777) +create_modal # unused variable (cg/server/admin.py:778) +edit_modal # unused variable (cg/server/admin.py:779) +column_default_sort # unused variable (cg/server/admin.py:785) +column_filters # unused variable (cg/server/admin.py:786) +column_formatters # unused variable (cg/server/admin.py:787) +column_list # unused variable (cg/server/admin.py:793) +column_labels # unused variable (cg/server/admin.py:807) +column_searchable_list # unused variable (cg/server/admin.py:808) +form_ajax_refs # unused variable (cg/server/admin.py:810) +column_list # unused variable (cg/server/admin.py:827) +column_default_sort # unused variable (cg/server/admin.py:859) +column_editable_list # unused variable (cg/server/admin.py:860) +column_filters # unused variable (cg/server/admin.py:868) +column_formatters # unused variable (cg/server/admin.py:876) +column_searchable_list # unused variable (cg/server/admin.py:886) +form_excluded_columns # unused variable (cg/server/admin.py:893) +form_ajax_refs # unused variable (cg/server/admin.py:905) +column_default_sort # unused variable (cg/server/admin.py:948) +column_editable_list # unused variable (cg/server/admin.py:949) +column_filters # unused variable (cg/server/admin.py:950) +column_formatters # unused variable (cg/server/admin.py:951) +column_searchable_list # unused variable (cg/server/admin.py:955) +create_modal # unused variable (cg/server/admin.py:956) +edit_modal # unused variable (cg/server/admin.py:957) +form_ajax_refs # unused variable (cg/server/admin.py:958) +column_default_sort # unused variable (cg/server/admin.py:981) +column_editable_list # unused variable (cg/server/admin.py:982) +column_filters # unused variable (cg/server/admin.py:983) +column_hide_backrefs # unused variable (cg/server/admin.py:984) +column_list # unused variable (cg/server/admin.py:985) +column_searchable_list # unused variable (cg/server/admin.py:986) +create_modal # unused variable (cg/server/admin.py:987) +edit_modal # unused variable (cg/server/admin.py:988) +column_list # unused variable (cg/server/admin.py:992) +column_formatters # unused variable (cg/server/admin.py:1003) +column_searchable_list # unused variable (cg/server/admin.py:1007) +column_list # unused variable (cg/server/admin.py:1013) +column_formatters # unused variable (cg/server/admin.py:1036) +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: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) @@ -942,23 +944,23 @@ BY_CUSTOMER_IDS # unused variable (cg/store/filters/status_pool_filters.py:116) type_annotation_map # unused variable (cg/store/models.py:60) customer_collaboration # unused variable (cg/store/models.py:99) pipeline_limitations # unused variable (cg/store/models.py:180) -panel_size # unused variable (cg/store/models.py:361) -designer # unused variable (cg/store/models.py:365) -agreement_date # unused variable (cg/store/models.py:390) -lab_contact # unused variable (cg/store/models.py:400) -organisation_number # unused variable (cg/store/models.py:403) -project_account_ki # unused variable (cg/store/models.py:405) -project_account_kth # unused variable (cg/store/models.py:406) -return_samples # unused variable (cg/store/models.py:407) -uppmax_account # unused variable (cg/store/models.py:409) -delivery_contact # unused variable (cg/store/models.py:418) -primary_contact # unused variable (cg/store/models.py:422) -gene_count # unused variable (cg/store/models.py:701) -age_at_sampling # unused variable (cg/store/models.py:753) -customer_uploaded_at # unused variable (cg/store/models.py:1064) -transferred_at # unused variable (cg/store/models.py:1065) -device_id # unused variable (cg/store/models.py:1210) -pacbio_sequencing_run_id # unused variable (cg/store/models.py:1287) +panel_size # unused variable (cg/store/models.py:383) +designer # unused variable (cg/store/models.py:387) +agreement_date # unused variable (cg/store/models.py:412) +lab_contact # unused variable (cg/store/models.py:422) +organisation_number # unused variable (cg/store/models.py:425) +project_account_ki # unused variable (cg/store/models.py:427) +project_account_kth # unused variable (cg/store/models.py:428) +return_samples # unused variable (cg/store/models.py:429) +uppmax_account # unused variable (cg/store/models.py:431) +delivery_contact # unused variable (cg/store/models.py:440) +primary_contact # unused variable (cg/store/models.py:444) +gene_count # unused variable (cg/store/models.py:723) +age_at_sampling # unused variable (cg/store/models.py:778) +customer_uploaded_at # unused variable (cg/store/models.py:1089) +transferred_at # unused variable (cg/store/models.py:1090) +device_id # unused variable (cg/store/models.py:1235) +pacbio_sequencing_run_id # unused variable (cg/store/models.py:1312) SIMPLE_DATE_FORMAT # unused variable (cg/utils/date.py:11) _.initialise_db # unused method (cg/apps/housekeeper/hk.py:343) _.destroy_db # unused method (cg/apps/housekeeper/hk.py:347) @@ -972,7 +974,8 @@ _.get_sequencing_run_unaligned_dir # unused method (cg/apps/demultiplex/demulti _.link_case_to_order # unused method (cg/store/crud/create.py:411) _.get_applications # unused method (cg/store/crud/read.py:894) _.get_bed_by_name # unused method (cg/store/crud/read.py:990) -ExternalSample # unused class (cg/store/models.py:1059) +ExternalSample # unused class (cg/store/models.py:1084) +_.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:305) _.add_application_version # unused method (cg/store/crud/create.py:146) From 09fb500823f603e6c8960ed939dfbff99d2d4c39 Mon Sep 17 00:00:00 2001 From: islean Date: Tue, 8 Sep 2026 16:38:44 +0200 Subject: [PATCH 4/6] Fix removal of run device for Admin view deletions of Pacbio data --- ...a36c11ee9862_cascade_to_rundevice_table.py | 25 ------------------- 1 file changed, 25 deletions(-) delete mode 100644 alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py diff --git a/alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py b/alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py deleted file mode 100644 index ee9729716f..0000000000 --- a/alembic/versions/2026_08_28_a36c11ee9862_cascade_to_rundevice_table.py +++ /dev/null @@ -1,25 +0,0 @@ -"""Cascade to RunDevice table - -Revision ID: a36c11ee9862 -Revises: 8a0dd32c2550 -Create Date: 2026-08-28 08:56:40.081418 - -""" - -import sqlalchemy as sa - -from alembic import op - -# revision identifiers, used by Alembic. -revision = "a36c11ee9862" -down_revision = "8a0dd32c2550" -branch_labels = None -depends_on = None - - -def upgrade(): - pass - - -def downgrade(): - pass From 5076434411574b0dfe49f9a7e224285d81ca468b Mon Sep 17 00:00:00 2001 From: islean Date: Tue, 8 Sep 2026 16:59:39 +0200 Subject: [PATCH 5/6] Whitelist --- vulture_whitelist.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/vulture_whitelist.txt b/vulture_whitelist.txt index eee604b7f7..6507f22f39 100644 --- a/vulture_whitelist.txt +++ b/vulture_whitelist.txt @@ -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) @@ -965,7 +965,6 @@ _.initialise_db # unused method (cg/apps/housekeeper/hk.py:343) _.destroy_db # unused method (cg/apps/housekeeper/hk.py:347) _.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) @@ -973,6 +972,7 @@ _.get_sequencing_run_unaligned_dir # unused method (cg/apps/demultiplex/demulti _.link_case_to_order # unused method (cg/store/crud/create.py:412) _.get_applications # unused method (cg/store/crud/read.py:910) _.get_bed_by_name # unused method (cg/store/crud/read.py:1006) +_.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) From 68e658963857d65ff078bfed9799e6af8eb71786 Mon Sep 17 00:00:00 2001 From: islean Date: Thu, 10 Sep 2026 15:51:21 +0200 Subject: [PATCH 6/6] Fix merge conflict --- vulture_whitelist.txt | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/vulture_whitelist.txt b/vulture_whitelist.txt index 5bb2db6876..5eb06985cd 100644 --- a/vulture_whitelist.txt +++ b/vulture_whitelist.txt @@ -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) @@ -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) @@ -973,8 +970,8 @@ _.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:910) -_.get_bed_by_name # unused method (cg/store/crud/read.py:1006) +_.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)