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Databases without any existing migrations will fail when updating to v7.9.7 #5306

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grantfitzsimmons opened this issue Oct 3, 2024 · 0 comments
Open

Databases without any existing migrations will fail when updating to v7.9.7 #5306

grantfitzsimmons opened this issue Oct 3, 2024 · 0 comments
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@acwhite211
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1 - Bug Incorrect behavior of the product pri:high Must be resolved before releasing regression This is behavior that once worked that has broken. Must be resolved before the next release.
Milestone
7.9.11

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@grantfitzsimmons
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Describe the bug
When attempting to run all of the migrations upon first run, all databases receive this error:

`MySQLdb.OperationalError: (1054, "Unknown column 'collection.CollectionObjectTypeID' in 'field list'")`

This is due to the 0004_intialize_defaults.py migration failing. If you remove new fields that are unexpected, it succeeds, and you can add it back and compose up.

I removed this line from the models file and it succeeded:

specify7/specifyweb/specify/models.py

Line 1370 in 2a0b516

collectionobjecttype = models.ForeignKey('CollectionObjectType', db_column='CollectionObjectTypeID', related_name='collections', null=True, on_delete=models.SET_NULL)

We need to fix incorrect assumptions made by the migration that lead to this update being non-feasible.

To Reproduce
Steps to reproduce the behavior:

  1. Create a new database using the Specify Wizard in 6
  2. Configure your .env file to point to this database
  3. Run docker compose up --build after pulling the latest version of production
  4. See failure

Expected behavior

On a brand new Specify 6 database, the migration fails every time. If you remove all migrations, it will fail as well.

MySQLdb.OperationalError: (1054, "Unknown column 'collection.CollectionObjectTypeID' in 'field list'")

WARN[0009] Found orphan containers ([specify7-mariadb-1]) for this project. If you removed or renamed this service in your compose file, you can run this command with the --remove-orphans flag to clean it up. 
[+] Running 8/8
 ✔ Container specify7-report-runner-1    Created                                                                                        0.0s 
 ✔ Container specify7-redis-1            Created                                                                                        0.0s 
 ✔ Container specify7-specify6-1         Created                                                                                        0.0s 
 ✔ Container specify7-asset-server-1     Created                                                                                        0.0s 
 ✔ Container specify7-webpack-1          Recreated                                                                                      0.1s 
 ✔ Container specify7-nginx-1            Created                                                                                        0.0s 
 ✔ Container specify7-specify7-worker-1  Recreated                                                                                      0.1s 
 ✔ Container specify7-specify7-1         Recreated                                                                                      0.1s 
Attaching to asset-server-1, nginx-1, redis-1, report-runner-1, specify6-1, specify7-1, specify7-worker-1, webpack-1
report-runner-1    | rosetta error: Rosetta is only intended to run on Apple Silicon with a macOS host using Virtualization.framework with Rosetta mode enabled
redis-1            | 1:C 03 Oct 2024 14:10:24.787 * oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
redis-1            | 1:C 03 Oct 2024 14:10:24.787 * Redis version=7.4.0, bits=64, commit=00000000, modified=0, pid=1, just started
redis-1            | 1:C 03 Oct 2024 14:10:24.787 # Warning: no config file specified, using the default config. In order to specify a config file use redis-server /path/to/redis.conf
redis-1            | 1:M 03 Oct 2024 14:10:24.787 * monotonic clock: POSIX clock_gettime
redis-1            | 1:M 03 Oct 2024 14:10:24.788 * Running mode=standalone, port=6379.
redis-1            | 1:M 03 Oct 2024 14:10:24.788 * Server initialized
redis-1            | 1:M 03 Oct 2024 14:10:24.789 * Loading RDB produced by version 7.4.0
redis-1            | 1:M 03 Oct 2024 14:10:24.789 * RDB age 2952 seconds
redis-1            | 1:M 03 Oct 2024 14:10:24.789 * RDB memory usage when created 1.40 Mb
redis-1            | 1:M 03 Oct 2024 14:10:24.789 * Done loading RDB, keys loaded: 6, keys expired: 0.
redis-1            | 1:M 03 Oct 2024 14:10:24.789 * DB loaded from disk: 0.001 seconds
redis-1            | 1:M 03 Oct 2024 14:10:24.789 * Ready to accept connections tcp
report-runner-1    |  
nginx-1            | /docker-entrypoint.sh: /docker-entrypoint.d/ is not empty, will attempt to perform configuration
nginx-1            | /docker-entrypoint.sh: Looking for shell scripts in /docker-entrypoint.d/
nginx-1            | /docker-entrypoint.sh: Launching /docker-entrypoint.d/10-listen-on-ipv6-by-default.sh
nginx-1            | 10-listen-on-ipv6-by-default.sh: info: can not modify /etc/nginx/conf.d/default.conf (read-only file system?)
nginx-1            | /docker-entrypoint.sh: Sourcing /docker-entrypoint.d/15-local-resolvers.envsh
nginx-1            | /docker-entrypoint.sh: Launching /docker-entrypoint.d/20-envsubst-on-templates.sh
nginx-1            | /docker-entrypoint.sh: Launching /docker-entrypoint.d/30-tune-worker-processes.sh
nginx-1            | /docker-entrypoint.sh: Configuration complete; ready for start up
asset-server-1     | rosetta error: Rosetta is only intended to run on Apple Silicon with a macOS host using Virtualization.framework with Rosetta mode enabled
asset-server-1     |  
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: using the "epoll" event method
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: nginx/1.27.1
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: built by gcc 13.2.1 20240309 (Alpine 13.2.1_git20240309) 
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: OS: Linux 6.6.26-linuxkit
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: getrlimit(RLIMIT_NOFILE): 1048576:1048576
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker processes
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 21
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 22
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 23
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 24
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 25
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 26
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 27
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 28
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 29
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 30
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 31
nginx-1            | 2024/10/03 14:10:24 [notice] 1#1: start worker process 32
specify6-1         | Successfully updated Specify 6 files\n
specify6-1         | This container is only needed during start up to give Specify 7 information about the data model\n
specify6-1         | It will now exit
report-runner-1 exited with code 133
asset-server-1 exited with code 133
specify6-1 exited with code 0
specify7-1         | Updating static files in /volumes/static-files/.
specify7-1         | Applying Django migrations.
webpack-1          | Browserslist: caniuse-lite is outdated. Please run:
webpack-1          |   npx update-browserslist-db@latest
webpack-1          |   Why you should do it regularly: https://github.com/browserslist/update-db#readme
nginx-1            | 2024/10/03 14:10:26 [error] 22#22: *2 asset-server could not be resolved (3: Host not found), client: 192.168.65.1, server: localhost, request: "GET /web_asset_store.xml HTTP/1.1", host: "host.docker.internal"
nginx-1            | 2024/10/03 14:10:26 [error] 21#21: *1 asset-server could not be resolved (3: Host not found), client: 192.168.65.1, server: localhost, request: "GET /web_asset_store.xml HTTP/1.1", host: "host.docker.internal"
nginx-1            | 192.168.65.1 - - [03/Oct/2024:14:10:26 +0000] "GET /web_asset_store.xml HTTP/1.1" 502 157 "-" "python-requests/2.32.2" "-"
nginx-1            | 192.168.65.1 - - [03/Oct/2024:14:10:26 +0000] "GET /web_asset_store.xml HTTP/1.1" 502 157 "-" "python-requests/2.32.2" "-"
specify7-1         | [03/Oct/2024 14:10:26] [ERROR] [specifyweb.attachment_gw.views:220] Failed fetching asset server configuration
specify7-worker-1  | [03/Oct/2024 14:10:26] [ERROR] [specifyweb.attachment_gw.views:220] Failed fetching asset server configuration
specify7-worker-1  |  
specify7-worker-1  |  -------------- celery@853599ed2a94 v5.2.7 (dawn-chorus)
specify7-worker-1  | --- ***** ----- 
specify7-worker-1  | -- ******* ---- Linux-6.6.26-linuxkit-aarch64-with-glibc2.27 2024-10-03 14:10:26
specify7-worker-1  | - *** --- * --- 
specify7-worker-1  | - ** ---------- [config]
specify7-worker-1  | - ** ---------- .> app:         specify7:0xffffb469e430
specify7-worker-1  | - ** ---------- .> transport:   redis://redis:6379/0
specify7-worker-1  | - ** ---------- .> results:     redis://redis/1
specify7-worker-1  | - *** --- * --- .> concurrency: 1 (prefork)
specify7-worker-1  | -- ******* ---- .> task events: OFF (enable -E to monitor tasks in this worker)
specify7-worker-1  | --- ***** ----- 
specify7-worker-1  |  -------------- [queues]
specify7-worker-1  |                 .> geospecify       exchange=geospecify(direct) key=geospecify
specify7-worker-1  |                 
specify7-worker-1  | 
specify7-worker-1  | [tasks]
specify7-worker-1  |   . specifyweb.celery_tasks.debug_task
specify7-worker-1  |   . specifyweb.specify.record_merging.record_merge_task
specify7-worker-1  |   . specifyweb.specify.update_locality.parse_locality_task
specify7-worker-1  |   . specifyweb.specify.update_locality.update_locality_task
specify7-worker-1  |   . specifyweb.workbench.tasks.unupload
specify7-worker-1  |   . specifyweb.workbench.tasks.upload
specify7-worker-1  | 
specify7-worker-1  | [2024-10-03 14:10:26,709: INFO/MainProcess] Connected to redis://redis:6379/0
nginx-1            | 2024/10/03 14:10:27 [error] 23#23: *5 asset-server could not be resolved (3: Host not found), client: 192.168.65.1, server: localhost, request: "GET /web_asset_store.xml HTTP/1.1", host: "host.docker.internal"
nginx-1            | 192.168.65.1 - - [03/Oct/2024:14:10:27 +0000] "GET /web_asset_store.xml HTTP/1.1" 502 157 "-" "python-requests/2.32.2" "-"
specify7-1         | [03/Oct/2024 14:10:27] [ERROR] [specifyweb.attachment_gw.views:220] Failed fetching asset server configuration
specify7-1         | Operations to perform:
specify7-1         |   Apply all migrations: accounts, attachment_gw, auth, businessrules, contenttypes, notifications, permissions, sessions, specify, workbench
specify7-1         | Running migrations:
specify7-1         |   Applying accounts.0001_initial... OK
specify7-1         |   Applying accounts.0002_auto_20211223_1206... OK
specify7-1         |   Applying accounts.0003_auto_20220621_1541... OK
specify7-1         |   Applying attachment_gw.0001_initial... OK
specify7-1         |   Applying contenttypes.0001_initial... OK
specify7-1         |   Applying contenttypes.0002_remove_content_type_name... OK
specify7-1         |   Applying auth.0001_initial... OK
specify7-1         |   Applying auth.0002_alter_permission_name_max_length... OK
specify7-1         |   Applying auth.0003_alter_user_email_max_length... OK
specify7-1         |   Applying auth.0004_alter_user_username_opts... OK
specify7-1         |   Applying auth.0005_alter_user_last_login_null... OK
specify7-1         |   Applying auth.0006_require_contenttypes_0002... OK
specify7-1         |   Applying auth.0007_alter_validators_add_error_messages... OK
specify7-1         |   Applying auth.0008_alter_user_username_max_length... OK
specify7-1         |   Applying auth.0009_alter_user_last_name_max_length... OK
specify7-1         |   Applying auth.0010_alter_group_name_max_length... OK
specify7-1         |   Applying auth.0011_update_proxy_permissions... OK
specify7-1         |   Applying auth.0012_alter_user_first_name_max_length... OK
specify7-worker-1  | [2024-10-03 14:10:31,718: INFO/MainProcess] mingle: searching for neighbors
specify7-1         |   Applying businessrules.0001_initial... OK
specify7-worker-1  | [2024-10-03 14:10:32,722: INFO/MainProcess] mingle: all alone
specify7-worker-1  | [2024-10-03 14:10:32,728: WARNING/MainProcess] /opt/specify7/ve/lib/python3.8/site-packages/celery/fixups/django.py:203: UserWarning: Using settings.DEBUG leads to a memory
specify7-worker-1  |             leak, never use this setting in production environments!
specify7-worker-1  |   warnings.warn('''Using settings.DEBUG leads to a memory
specify7-worker-1  | 
specify7-worker-1  | [2024-10-03 14:10:32,728: INFO/MainProcess] celery@853599ed2a94 ready.
specify7-1         |   Applying businessrules.0002_default_unique_rules... OK
specify7-1         |   Applying permissions.0001_initial... OK
specify7-1         |   Applying permissions.0002_role_rolepolicy_userrole... OK
specify7-1         |   Applying permissions.0003_auto_20220321_1445... OK
specify7-1         | Traceback (most recent call last):
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/utils.py", line 84, in _execute
specify7-1         |     return self.cursor.execute(sql, params)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/mysql/base.py", line 73, in execute
specify7-1         |     return self.cursor.execute(query, args)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/MySQLdb/cursors.py", line 206, in execute
specify7-1         |     res = self._query(query)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/MySQLdb/cursors.py", line 319, in _query
specify7-1         |     db.query(q)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/MySQLdb/connections.py", line 254, in query
specify7-1         |     _mysql.connection.query(self, query)
specify7-1         | MySQLdb.OperationalError: (1054, "Unknown column 'collection.CollectionObjectTypeID' in 'field list'")
specify7-1         | 
specify7-1         | The above exception was the direct cause of the following exception:
specify7-1         | 
specify7-1         | Traceback (most recent call last):
specify7-1         |   File "manage.py", line 25, in <module>
specify7-1         |     execute_from_command_line(sys.argv)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/core/management/__init__.py", line 419, in execute_from_command_line
specify7-1         |     utility.execute()
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/core/management/__init__.py", line 413, in execute
specify7-1         |     self.fetch_command(subcommand).run_from_argv(self.argv)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/core/management/base.py", line 354, in run_from_argv
specify7-1         |     self.execute(*args, **cmd_options)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/core/management/base.py", line 398, in execute
specify7-1         |     output = self.handle(*args, **options)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/core/management/base.py", line 89, in wrapped
specify7-1         |     res = handle_func(*args, **kwargs)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/core/management/commands/migrate.py", line 244, in handle
specify7-1         |     post_migrate_state = executor.migrate(
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/migrations/executor.py", line 117, in migrate
specify7-1         |     state = self._migrate_all_forwards(state, plan, full_plan, fake=fake, fake_initial=fake_initial)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/migrations/executor.py", line 147, in _migrate_all_forwards
specify7-1         |     state = self.apply_migration(state, migration, fake=fake, fake_initial=fake_initial)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/migrations/executor.py", line 227, in apply_migration
specify7-1         |     state = migration.apply(state, schema_editor)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/migrations/migration.py", line 123, in apply
specify7-1         |     operation.database_forwards(self.app_label, schema_editor, old_state, project_state)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/migrations/operations/special.py", line 190, in database_forwards
specify7-1         |     self.code(from_state.apps, schema_editor)
specify7-1         |   File "/opt/specify7/specifyweb/permissions/migrations/0004_intialize_defaults.py", line 7, in initialize
specify7-1         |     init(wipe=True)
specify7-1         |   File "/opt/specify7/specifyweb/permissions/initialize.py", line 24, in initialize
specify7-1         |     assign_users_to_roles()
specify7-1         |   File "/opt/specify7/specifyweb/permissions/initialize.py", line 46, in assign_users_to_roles
specify7-1         |     for collection in Collection.objects.all():
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/models/query.py", line 280, in __iter__
specify7-1         |     self._fetch_all()
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/models/query.py", line 1324, in _fetch_all
specify7-1         |     self._result_cache = list(self._iterable_class(self))
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/models/query.py", line 51, in __iter__
specify7-1         |     results = compiler.execute_sql(chunked_fetch=self.chunked_fetch, chunk_size=self.chunk_size)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/models/sql/compiler.py", line 1175, in execute_sql
specify7-1         |     cursor.execute(sql, params)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/utils.py", line 98, in execute
specify7-1         |     return super().execute(sql, params)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/utils.py", line 66, in execute
specify7-1         |     return self._execute_with_wrappers(sql, params, many=False, executor=self._execute)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/utils.py", line 75, in _execute_with_wrappers
specify7-1         |     return executor(sql, params, many, context)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/utils.py", line 84, in _execute
specify7-1         |     return self.cursor.execute(sql, params)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/utils.py", line 90, in __exit__
specify7-1         |     raise dj_exc_value.with_traceback(traceback) from exc_value
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/utils.py", line 84, in _execute
specify7-1         |     return self.cursor.execute(sql, params)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/django/db/backends/mysql/base.py", line 73, in execute
specify7-1         |     return self.cursor.execute(query, args)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/MySQLdb/cursors.py", line 206, in execute
specify7-1         |     res = self._query(query)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/MySQLdb/cursors.py", line 319, in _query
specify7-1         |     db.query(q)
specify7-1         |   File "/opt/specify7/ve/lib/python3.8/site-packages/MySQLdb/connections.py", line 254, in query
specify7-1         |     _mysql.connection.query(self, query)
specify7-1         | django.db.utils.OperationalError: (1054, "Unknown column 'collection.CollectionObjectTypeID' in 'field list'")
specify7-1         | Watching for file changes with StatReloader
nginx-1            | 192.168.65.1 - - [03/Oct/2024:14:10:39 +0000] "GET /web_asset_store.xml HTTP/1.1" 502 157 "-" "python-requests/2.32.2" "-"
nginx-1            | 2024/10/03 14:10:39 [error] 24#24: *7 asset-server could not be resolved (3: Host not found), client: 192.168.65.1, server: localhost, request: "GET /web_asset_store.xml HTTP/1.1", host: "host.docker.internal"
specify7-1         | [03/Oct/2024 14:10:39] [ERROR] [specifyweb.attachment_gw.views:220] Failed fetching asset server configuration
webpack-1          | assets by status 53.3 MiB [cached] 89 assets
webpack-1          | asset manifest.json 15.7 KiB [compared for emit]
webpack-1          | orphan modules 77.6 KiB [orphan] 106 modules
webpack-1          | runtime modules 17.5 KiB 23 modules
webpack-1          | modules by path ./node_modules/ 12.1 MiB 1810 modules
webpack-1          | modules by path ./lib/ 3.36 MiB 638 modules
webpack-1          | modules by path ./css/*.css 149 KiB 4 modules
webpack-1          | modules by mime type image/svg+xml 1.02 KiB
webpack-1          |   data:image/svg+xml,%3csvg xmlns=%27.. 284 bytes [built] [code generated]
webpack-1          |   + 3 modules
webpack-1          | modules by mime type image/png 1.08 KiB
webpack-1          |   data:image/png;base64,iVBORw0KGgoAAAAN.. 329 bytes [built] [code generated]
webpack-1          |   + 3 modules
webpack-1          | fs (ignored) 15 bytes [built] [code generated]
webpack-1          | crypto (ignored) 15 bytes [optional] [built] [code generated]
webpack-1          | stream (ignored) 15 bytes [built] [code generated]
webpack-1          | webpack 5.73.0 compiled successfully in 13389 ms

Crash Report

Here's a sample database that you can download and import into MariaDB:
geospecify_2024_10_03.sql.zip

It has 3 disciplines and collections, and has never been used in Specify 7.
@grantfitzsimmons grantfitzsimmons added pri:high Must be resolved before releasing 1 - Bug Incorrect behavior of the product regression This is behavior that once worked that has broken. Must be resolved before the next release. labels Oct 3, 2024
@grantfitzsimmons grantfitzsimmons added this to the 7.9.8 milestone Oct 4, 2024
@CarolineDenis CarolineDenis modified the milestones: 7.9.8, 7.9.11 Oct 17, 2024
@grantfitzsimmons grantfitzsimmons changed the title Databases without any existing migrations will fail when updating to the latest version of Specify 7 Databases without any existing migrations will fail when updating to v7.9.7 version of Specify 7 Oct 17, 2024
@grantfitzsimmons grantfitzsimmons changed the title Databases without any existing migrations will fail when updating to v7.9.7 version of Specify 7 Databases without any existing migrations will fail when updating to v7.9.7 version of Specify 7 Oct 17, 2024
@grantfitzsimmons grantfitzsimmons changed the title Databases without any existing migrations will fail when updating to v7.9.7 version of Specify 7 Databases without any existing migrations will fail when updating to v7.9.7 Oct 17, 2024
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@acwhite211 acwhite211

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1 - Bug Incorrect behavior of the product pri:high Must be resolved before releasing regression This is behavior that once worked that has broken. Must be resolved before the next release.
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7.9.11
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