feat: add affected status to ClickHouse! #5065

bpblanken · 2025-10-02T22:20:30Z

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.github/workflows/unit-tests.yml

bpblanken · 2025-10-03T13:05:57Z

clickhouse_search/migrations/0016_add_affected_status.py

+AS SELECT
+    project_guid,
+    key,
+    dictGetOrDefault('seqrdb_affected_status_dict', 'affected', (family_guid, calls.sampleId), 'U') affected,


I used dictGetOrDefault here to get things working, but assume there's fixtures that we can fix when the search logic is implemented to avoid a default value.

assume there's fixtures that we can fix when the search logic is implemented"

Modifying this migration later will not be possible, so we would functionally need to totally drop and recreate the dictionary in a new migration if we want this to change which essentially negates this migration. If there is fixture data that needs to change in order to get thsi to work, now is the time to change it

drop and recreate is what we're doing here. the "materialized view" isn't a table, but a set of instructions route data from one table to another, so there's no reason to use an ALTER.

I can go investigate the fixtures.

Some more insight after looking into the fixtures. I think the issue is this line loads both the postgres and clickhouse fixtures together; we need an opportunity to refresh the dictionary after '1kg_project' is loaded into postgres but before the clickhouse models are loaded.

I think the easiest option is to manage the fixture creation manually within setUpTestData? Something like:

def setUpTestData(cls): postgres_fixtures = ['users', '1kg_project', 'variant_searches', 'reference_data'] clickhouse_fixtures = ['clickhouse_search', 'clickhouse_transcripts'] for fixture in postgres_fixtures: call_command('loaddata', fixture, verbosity=0) with connections['clickhouse_write'].cursor() as cursor: cursor.execute('SYSTEM RELOAD DICTIONARY "seqrdb_affected_status_dict"') for fixture in clickhouse_fixtures: call_command('loaddata', fixture, verbosity=0) ...

does that sound reasonable?

Why wouldn't it work to just load all the data using the default way fixture data is loading and then refresh the dictionaries and materialized views the way we do in the clickhosue search tests:
https://github.com/broadinstitute/seqr/blob/master/clickhouse_search/search_tests.py#L36-L41
I just don't see why the refresh command has to be before the clickhouse fixture data is loaded. Anything thats part of a view or dict should not be defined in the fixture

The dictGet is called as the fixture is loaded, when a row is inserted into the entries table.

bpblanken · 2025-10-03T13:07:01Z

clickhouse_search/migrations/0016_add_affected_status.py

+    ]
+
+    operations = [
+        migrations.RunSQL(


The sql created by the model change itself included mutations_sync=1 and I couldn't figure out a way to remove it. We don't want the mutation to be synchronous for this.

This approach gives column ordering control too, which is a plus.

Unless it would be a problem if this is added to all requests, you should be able to change this setting globally in the settings.py connection config. Alternatively, it should work as a keyword arg to the migration command itself, you can just modify it once its auto generated
For column ordering, the list of columns that are generated can be reordered however you want without needing to execute raw SQL, the order they are in the list is the order they will be in when the SQL is generated so you can still set it explicitly

I tried changing the setting yesterday after reading the docs and it didn't work for this column ALTER. My reading of the documentation was that that setting was applied for ORM calls (data updates and deletes, which are also async) but not for schema changes.

The default makemigrations output produces:

migrations.AddField( model_name='gtstatsgrch37snvindel', name='ac_affected', field=clickhouse_backend.models.UInt32Field(default=0), ),

which I was unable to modify to change the column ordering in the same way we were with the CreateModel in the other migrations.

my concern is I do not think django will be able to tell that all the changes you made to the models are actually in the migration, as it checks the models.py against the migrations themselves, not against the database - if you run makemigrations again does it report no changes or does it generate another migration with the add columns?
Also, if this has to repopulate anyways is there any harm in just dropping and recreating these tables instead of modifying them in place? or would that make us lose a whole bunch of data that would need to be recomputed?

makemigrations generates a new migrations as is. We need to modify the RunSQL like:

migrations.RunSQL( "ALTER TABLE `GRCh37/SNV_INDEL/gt_stats` ADD COLUMN `hom_affected` UInt32 DEFAULT 0 AFTER `hom_wgs`;", hints={'clickhouse': True}, state_operations=[ migrations.AddField( model_name='gtstatsgrch37snvindel', name='hom_affected', field=clickhouse_backend.models.UInt32Field(default=0), ), ], ),

I think there's potentially no harm in dropping the gt_stats tables - they're recomputed from scratch on every load. However, the project_gt_stats table is not and would need the expensive multi-hour rebuild that is not yet built. If data were loaded during that time the downstream rollups would all be wrong.

I have never looked into state_operations before but this looks like exactly what we need! And if we are doing these raw ALTER TABLE commands for project_gt_stats then I think theres no harm in also using them for gt_stats

just as a sanity check, if you now run makeigrations does it generate anything?

Nope! It's clean.

bpblanken · 2025-10-03T13:09:14Z

clickhouse_search/migrations/0016_add_affected_status.py

+            'DROP DICTIONARY `GRCh38/SNV_INDEL/gt_stats_dict`',
+            hints={'clickhouse': True},
+        ),
+        migrations.RunSQL(


note that this doesn't drop the table itself, just the "view" in between the two tables.

bpblanken · 2025-10-03T13:10:17Z

seqr/testrunner.py

+
+class OrderedDatabaseDeletionRunner(DiscoverRunner):
+
+    def teardown_databases(self, old_config, **kwargs):


Due to the new dictionary opening a connection from ClickHouse to Postgres, we need to drop the clickhouse database first. This custom runner helps with that.

is there a reason not to just put this into the DifferentDbTransactionSupportMixin

This method subclasses DiscoverRunner, which is different than a TestCase. It's used in a different way

Django allows you to specify the creation order for database in the settings, and I would assume it would tear them down in reverse order - have we tried setting that up instead of needing a custome test runner?
https://docs.djangoproject.com/en/4.2/topics/testing/advanced/#topics-testing-creation-dependencies

alternatively, have we tried just closing whichever connection is causing the issue in the test class teardown?

Just tried, I don't think it works. We get the:

django.db.utils.OperationalError: database "test_seqrdb" is being accessed by other users

during teardown. Reading through the docs I think there's already an implicit depends on the default db, so I'm not sure the code I wrote is even doing anything.

I'm just worried because I think that this solution is like a scorched earth approach, but it feels like theres a connection thats not being properly managed or torn down somewhere and I am worried this is an actual bug with how these databases are connected. If clickhouse has been cleaned up first, which it seems like it should always be, then this error should not be able to happen. Like in the event that clickhouse does fail in production I don't want to have postgres leaving this open connection to a dead service in perpetuity

if this is actually just a test-specific thing thats unrelated to real world connections I am less worried

yeah, I think it's mostly a test-specific thing, though potentially something to keep an eye on. Postgres does not have an open connection to Clickhouse, it's only the reverse (Clickhouse connecting to Postgres) and it's not bidirectional. The issue is with postgres itself blocking database deletion when there are open connections. It's actually a reasonable safety mechanism for a production system! But we will never delete the "seqrdb" not in the tests.

Going into the django source, the code that evaluates the DEPENDENCIES seems to be referenced when databases are setup. The docs say the return value of setup_databases is passed to teardown_databases, indicating that the db ordering is not reversed for teardown.

.github/workflows/unit-tests.yml

hanars · 2025-10-03T14:14:31Z

clickhouse_search/migrations/0015_remove_gnomadgenomessnvindel_key_and_more.py

            hints={'clickhouse': True},
        ),
        migrations.RunSQL(
-            GT_STATS_DICT.substitute(


this is not a safe pattern for migrations - if the GT_STATS_DICT model changes in the future then new migrations will get that model here, and then the next migration will have a conflict and fail. Now that we have released clickhouse broadly we pretty much can never modify existing migrations. If we really have to, like if the env vars removed here are actually removed from the env, then we need to just modify them to use dummy variables and the next migration needs to be able to handle that

So GT_STATS_DICT isn't actually a model, it's a string template. The migrations are being managed entirely manually. I moved the template into the models file because it was entirely shared by the two migrations, the new one just tweaks the columns (which are passed as strings).

Given the question though, I think it makes more sense to leave the existing migration as is and just duplicate the template in the new migration as it will be less confusing.

hanars · 2025-10-03T14:16:53Z

clickhouse_search/migrations/0016_add_affected_status.py

+AS SELECT
+    project_guid,
+    key,
+    dictGetOrDefault('seqrdb_affected_status_dict', 'affected', (family_guid, calls.sampleId), 'U') affected,


assume there's fixtures that we can fix when the search logic is implemented"

Modifying this migration later will not be possible, so we would functionally need to totally drop and recreate the dictionary in a new migration if we want this to change which essentially negates this migration. If there is fixture data that needs to change in order to get thsi to work, now is the time to change it

hanars · 2025-10-03T14:25:01Z

clickhouse_search/migrations/0016_add_affected_status.py

+    ]
+
+    operations = [
+        migrations.RunSQL(


Unless it would be a problem if this is added to all requests, you should be able to change this setting globally in the settings.py connection config. Alternatively, it should work as a keyword arg to the migration command itself, you can just modify it once its auto generated
For column ordering, the list of columns that are generated can be reordered however you want without needing to execute raw SQL, the order they are in the list is the order they will be in when the SQL is generated so you can still set it explicitly

hanars · 2025-10-03T14:27:47Z

clickhouse_search/migrations/0016_add_affected_status.py

+            hints={'clickhouse': True},
+        ),
+        migrations.RunSQL(
+            clickhouse_search.models.GT_STATS_DICT.substitute(


per my above comment ,it is never safe to reference a model directly in a migration. If you need to, like in a RunPython context, you need to use the apps.get_model function and the migration-specific db_alias: https://github.com/broadinstitute/seqr/blob/master/seqr/migrations/0081_savedvariant_gene_ids.py#L17-L19

but TBH it would be safer to just define the template directly in this file they way you did in the past and not store it in models.py at all, unless there is a reason why we need to access that template anytime thats not a miration

hanars · 2025-10-03T14:31:39Z

seqr/testrunner.py

+
+class OrderedDatabaseDeletionRunner(DiscoverRunner):
+
+    def teardown_databases(self, old_config, **kwargs):


is there a reason not to just put this into the DifferentDbTransactionSupportMixin

clickhouse_search/models.py

hanars

I am happy to take over dealing with the testing issues if you are getting frustrated, just let me know

clickhouse_search/models.py

hanars · 2025-10-06T11:56:38Z

clickhouse_search/search_tests.py


    @classmethod
    def setUpTestData(cls):
+        super().setUpClickhouseEntriesFixtures(['clickhouse_search'])


I do not think this is going to be a viable pattern in the long term - being unable to add fixtures using the normal fixture syntax and instead always needing to remember to do a separate special call is a real frustrating technical debt burden. 99% of our test that load clickhouse fixtures do not actually use or care about gt stats being accurate - in fact I think this is literally the only file where that matters. I think we should leave the fixture initialization pattern alone and inline the refresh calls here along with all the existing refresh calls we have below - if in the future there is another file that needs those calls run we can always abstract the logic accordingly
I do not understand why it should matter if the gt stats tables are empty during a test if they are not actually being used

So here's the context here:

This doesn't have to do with gt_stats accuracy, but the choice here to use dictGet, which enforces the sample existing in the ClickHouse dictionary at the moment the clickhouse_search fixture is run. Inlining the REFRESH call does not work as it is run after the fixture is loaded. The dictionary is still empty at load time and the fixture fails.

The other additional wrench here is that, even with several more manual attempts at the postgres fixtures, I was never able to get the ClickHouse dictionary to access the postgres fixtures because they're running in a different transaction context with a different connection. I felt that changing the postgres transaction flow was much worse and well out of scope. Mocking the dictionary from scratch was the only way to actually get values there.

Confirming the behavior for posterity and thoroughness:

I added a debug statement in the clickhouse search unit test.

def setUpTestData(cls): import pdb; pdb.set_trace() super().setUpClickhouseEntriesFixtures(['clickhouse_search'])

The postgres fixtures are loaded and data is visible within the tests:

(Pdb) Project.objects.all() <QuerySet [<Project: 1kg project nåme with uniçøde>, <Project: Empty Project>, <Project: Test Reprocessed Project>, <Project: Non-Analyst Project>]>

Confirmed that I cannot see the data when logging in via psql:

test_seqrdb=# select count(*) FROM seqr_project; count ------- 0 (1 row)

I can see the project query as idle in transaction:

test_seqrdb=# SELECT pid, usename, application_name, client_addr, backend_start, xact_start, state, query FROM pg_stat_activity WHERE xact_start IS NOT NULL; pid | usename | application_name | client_addr | backend_start | xact_start | state | query -------+----------+------------------+-------------+-------------------------------+-------------------------------+---------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 39590 | postgres | | ::1 | 2025-10-06 11:20:35.686583-04 | 2025-10-06 11:20:56.117842-04 | idle in transaction | SELECT "seqr_project"."id", "seqr_project"."guid", "seqr_project"."created_date", "seqr_project"."created_by_id", "seqr_project"."last_modified_date", "seqr_project"."name", "seqr_project"."description", "seqr_project"."can_edit_group_id", "seqr_project"."can_view_group_id", "seqr_project"."subscribers_id", "seqr_project"."genome_version", "seqr_project"."consent_code", "seqr_project"."is_mme_enabled", "seqr_project"."mme_primary_data_owner", "seqr_project"."mme_contact_url", "seqr_project"."mme_contact_institution", "seqr_project"."vlm_contact_email", "seqr_project"."has_case_review", "seqr_project"."enable_hgmd", "seqr_project"."all_user_demo", "seqr_project"."is_demo", "seqr_project"."last_accessed_date", "seqr_project"."workspace_namespace", "seqr_project"."workspace_name" FROM "seqr_project" LIMIT 21 39763 | postgres | | ::1 | 2025-10-06 11:20:50.081399-04 | 2025-10-06 11:20:56.653383-04 | idle in transaction | RELEASE SAVEPOINT "s8745295616_x1"

The dictionary exists with the right source in Clickhouse:

SHOW CREATE DICTIONARY seqrdb_affected_status_dict Query id: 51a59322-587a-411e-a48d-1ef24c88d252 ┌─statement───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ 1. │ CREATE DICTIONARY test_seqr.seqrdb_affected_status_dict ↴│ │↳( ↴│ │↳ `family_guid` String, ↴│ │↳ `sampleId` String, ↴│ │↳ `affected` String ↴│ │↳) ↴│ │↳PRIMARY KEY family_guid, sampleId ↴│ │↳SOURCE(POSTGRESQL(NAME 'seqr_postgres_named_collection' DATABASE test_seqrdb QUERY 'select f.guid as family_guid, i.individual_id as sample_id, i.affected FROM seqr_individual i INNER JOIN seqr_family f ON i.family_id = f.id'))↴│ │↳LIFETIME(MIN 0 MAX 0) ↴│ │↳LAYOUT(COMPLEX_KEY_HASHED()) │ └─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ 1 row in set. Elapsed: 0.001 sec.

Reloading is successful but the dict stays empty:

wmbbe-67c :) system reload dictionary seqrdb_affected_status_dict; SYSTEM RELOAD DICTIONARY seqrdb_affected_status_dict Query id: ce7ed94d-5553-4425-af99-956ffb9f4a67 Ok. 0 rows in set. Elapsed: 0.021 sec. wmbbe-67c :) \l^C wmbbe-67c :) select count(*) FROM seqrdb_affected_status_dict; SELECT count(*) FROM seqrdb_affected_status_dict Query id: 65ff90fb-0986-463e-ab86-249ec4b59f56 ┌─count()─┐ 1. │ 0 │ └─────────┘ 1 row in set. Elapsed: 0.001 sec.

this is really helpful, thanks for documenting!

hanars · 2025-10-06T11:59:07Z

seqr/views/utils/test_utils.py

+                ('F000011_11', 'NA20885', 'A'),
+                ('F000014_14', 'NA21234', 'A'),
+                ('F000014_14', 'NA21987', 'A'),
+                ('F000014_14', 'NA21654', 'N')


why can't the tests use the actual fixture data thats already been loaded to postgres? If the fixture data is inadequate because like certain families/individuals/samples are missing we should just add those models to the clickhouse_search fixture

So the fixtures were actually mostly fine, except for F000002_2_x. if we were to finalize this approach (which I think we shouldn't) it would be straightforwards to read the fixture and parse the necessary values here. I didn't do it because I felt this approach was iffy.

hanars · 2025-10-06T12:01:39Z

seqr/views/utils/test_utils.py

+            )
+            cursor.execute(
+                f'''
+                REPLACE DICTIONARY `seqrdb_affected_status_dict`


I am not comfortable with using this approach for testing, as it means we never once test the dictionary as it is defined. Using this pattern we could easily replace the dictionary with a definition that is totally different from whats actually on prod and miss a real bug. I think this is incredibly risky to have a mission critical resource thats never unit tested.

Yes, I agree with this. I don't think this is particularly good long term solution, but it was the best way to get dictGet to work rather than dictGetOrDefault, given the issue with Clickhouse not being able to see the fixture-loaded postgres data.

After this exercise I think dictGetOrDefault might be more reasonable?

yeah and maybe its not the worse thing to have the default if we somehow end up in a funky condition where postgres samples and clickhouse data are out of sync somehow that it doesn't like actually break the dictionary. Like a real world flow I could imagine is:

User triggers the "delete family" flow which inactivates the postgres sample model and queues up a delet family job in the pipeline

before the job runs, the user then goes in and deletes the family and individual models from postgres which is now allowed because theres no active search sample associated with them

a loading job completes and the dictionary/views try to refresh

seqr/testrunner.py

hanars · 2025-10-09T12:53:44Z

clickhouse_search/migrations/0016_add_affected_status.py

+    ]
+
+    operations = [
+        migrations.RunSQL(


just as a sanity check, if you now run makeigrations does it generate anything?

hanars · 2025-10-09T12:57:04Z

clickhouse_search/search_tests.py

+        # TransactionTestCase does not call setupTestData in the same way as TestCase
+        # https://github.com/django/django/blob/stable/4.2.x/django/test/testcases.py#L1466
+        # As a warning to a future reader, this method changes from an instance to a class method
+        # between versions 4.x and 6.x (alongside several other impactful method changes).  When


not sure this comment is necessary as like literally none of our test classes are resilient to a major Django version bump. Basically all our tests and test helpers will need to be rearchitected when that is happening so I do not think this file needs a special reminder

👍 I can remove it. I didn't realize how ingrained we were.

hanars · 2025-10-09T13:00:09Z

seqr/testrunner.py

+from django.test.runner import DiscoverRunner
+
+
+class OrderedDatabaseDeletionRunner(DiscoverRunner):


just sanity checking that this is still necessary with the switch to using the transaction test case

yes, it's still necessary. The transaction test case change just allows the data to be viewed by the additional Clickhouse->Postgres connection, but doesn't change that there is an additional connection that we need to maneuver around.

hanars · 2025-10-09T13:13:06Z

We will not want to merge this to dev until we also have the necessary code in place to properly handle what happens when affected status is updated. Otherwise this will go live, the migration will run, and then folks will update affected status in a way that we can not track/replicate and there will not really be a way to fix it

simple pg named collection

5c6c6c1

bpblanken changed the base branch from master to dev October 2, 2025 22:20

bpblanken added 11 commits October 2, 2025 18:22

is it the restart?

e7689a5

try reload users

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add named collection

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remove networks config

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add migration back

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port over changes from other branch

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fix typo

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reference db name

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typo

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default value

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try to delete clickhouse dbs before postgres dbs

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bpblanken changed the title ~~Benb/connect postgres~~ feat: add affected status to ClickHouse! Oct 3, 2025

bpblanken commented Oct 3, 2025

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bpblanken marked this pull request as ready for review October 3, 2025 13:10

bpblanken requested a review from hanars October 3, 2025 13:10

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bpblanken added 8 commits October 3, 2025 11:56

revert to dev

5106775

use state operations

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fix imports

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reload dictionary in tests

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attempt reload within migration

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remove reload

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remove testrunner

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put back test runner

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bpblanken added 11 commits October 5, 2025 21:06

drop table in teardown

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drop dictionary as well

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drop dictionary

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try deleting after

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create or replace

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codacy

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missing super()

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finish off

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unused

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bad import

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no clickhouse fixture

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hanars reviewed Oct 6, 2025

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hanars reviewed Oct 6, 2025

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bpblanken and others added 15 commits October 6, 2025 11:50

dict get or default

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remove the additional test data method

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add comment fix bug

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missed a few

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ws

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ws

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ws

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remove defaults

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ws

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works!

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Update search_tests.py

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Update search_tests.py

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Update search_tests.py

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Update search_tests.py

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Update search_tests.py

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hanars reviewed Oct 9, 2025

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		class OrderedDatabaseDeletionRunner(DiscoverRunner):

		def teardown_databases(self, old_config, **kwargs):

		from django.test.runner import DiscoverRunner


		class OrderedDatabaseDeletionRunner(DiscoverRunner):

feat: add affected status to ClickHouse! #5065

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feat: add affected status to ClickHouse! #5065

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