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Fix database schema migration conflicts and optimize Docker startup #3558

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19 changes: 12 additions & 7 deletions augur/application/schema/alembic/versions/1_augur_new_changes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@

def upgrade():

op.execute("SET search_path TO augur_data, augur_operations, public")
change_tables_to_mimic_current_db_1()
change_natural_keys_for_bulk_upsert_2()
add_config_table_3()
Expand Down Expand Up @@ -62,31 +63,35 @@ def change_tables_to_mimic_current_db_1(upgrade=True):

if upgrade:

op.drop_constraint('fk_commits_contributors_4', 'commits', schema='augur_data', type_='foreignkey')
op.execute(text('ALTER TABLE augur_data.commits DROP CONSTRAINT IF EXISTS fk_commits_contributors_4'))
op.create_foreign_key('fk_commits_contributors_4', 'commits', 'contributors', ['cmt_author_platform_username'], ['cntrb_login'], source_schema='augur_data', referent_schema='augur_data', onupdate='CASCADE', ondelete='CASCADE', initially='DEFERRED', deferrable=True)

op.drop_constraint('fk_commits_contributors_3', 'commits', schema='augur_data', type_='foreignkey')
op.execute(text('ALTER TABLE augur_data.commits DROP CONSTRAINT IF EXISTS fk_commits_contributors_3'))
op.create_foreign_key('fk_commits_contributors_3', 'commits', 'contributors', ['cmt_author_platform_username'], ['cntrb_login'], source_schema='augur_data', referent_schema='augur_data', onupdate='CASCADE', ondelete='CASCADE', initially='DEFERRED', deferrable=True)

op.drop_index('therepo', table_name='repo', schema='augur_data')
op.execute(text('DROP INDEX IF EXISTS augur_data.therepo'))
op.create_index('therepo', 'repo', ['repo_id'], unique=True, schema='augur_data')

# add unique to pull_request assignees
op.execute(text('ALTER TABLE augur_data.pull_request_assignees DROP CONSTRAINT IF EXISTS "assigniees-unique"'))
op.create_unique_constraint('assigniees-unique', 'pull_request_assignees', ['pull_request_id', 'pr_assignee_src_id'], schema='augur_data')

# modify unique-pr-event-id
op.drop_constraint('unique-pr-event-id', 'pull_request_events', schema='augur_data', type_='unique')
op.execute(text('ALTER TABLE augur_data.pull_request_events DROP CONSTRAINT IF EXISTS "unique-pr-event-id"'))
op.create_unique_constraint('unique-pr-event-id', 'pull_request_events', ['platform_id', 'node_id'], schema='augur_data')

# add pr-unqiue-event
op.execute(text('ALTER TABLE augur_data.pull_request_events DROP CONSTRAINT IF EXISTS "pr-unqiue-event"'))
op.create_unique_constraint('pr-unqiue-event', 'pull_request_events', ['node_id'], schema='augur_data')

# modify pr reviewers unique
op.drop_constraint('unique_pr_src_reviewer_key', 'pull_request_reviewers', schema='augur_data', type_='unique')
op.execute(text('ALTER TABLE augur_data.pull_request_reviewers DROP CONSTRAINT IF EXISTS unique_pr_src_reviewer_key'))
op.create_unique_constraint('unique_pr_src_reviewer_key', 'pull_request_reviewers', ['pull_request_id', 'pr_reviewer_src_id'], schema='augur_data')

op.execute(text('ALTER TABLE augur_data.pull_requests DROP CONSTRAINT IF EXISTS "unique-pr"'))
op.create_unique_constraint('unique-pr', 'pull_requests', ['repo_id', 'pr_src_id'], schema='augur_data')

op.execute(text('ALTER TABLE augur_data.repo DROP CONSTRAINT IF EXISTS "repo_git-unique"'))
op.create_unique_constraint('repo_git-unique', 'repo', ['repo_git'], schema='augur_data')

else:
Expand Down Expand Up @@ -547,8 +552,8 @@ def add_user_repo_table_12(upgrade=True):
cli_user_id = 1
conn.execute(text(f"""INSERT INTO "augur_operations"."users" ("user_id", "login_name", "login_hashword", "email", "text_phone", "first_name", "last_name", "tool_source", "tool_version", "data_source", "data_collection_date", "admin") VALUES({cli_user_id}, 'cli_user', 'pbkdf2:sha256:260000$oDmAfipU8Ef8TAau$835fce1fc3290b57b5e02ec83aef4613cc06664e6e7535bb6d267dc44563d5d5', 'cli_user', NULL, 'cli_user', 'cli_user', 'Schema Generaation', NULL, 'Schema Generation', '2022-10-02 21:49:13', 'f');

ALTER SEQUENCE users_user_id_seq RESTART WITH 2;
ALTER SEQUENCE repo_repo_id_seq RESTART WITH 25480;
ALTER SEQUENCE augur_operations.users_user_id_seq RESTART WITH 2;
ALTER SEQUENCE augur_data.repo_repo_id_seq RESTART WITH 25480;
"""))


Expand Down
18 changes: 14 additions & 4 deletions docker-compose.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,11 @@ services:
- augurpostgres:/var/lib/postgresql/data
networks:
- augur
healthcheck:
test: ["CMD-SHELL", "pg_isready -U $${AUGUR_DB_USER:-augur} -d augur"]
interval: 5s
timeout: 5s
retries: 5

redis:
image: "redis:alpine"
Expand Down Expand Up @@ -77,11 +82,16 @@ services:
- CACHE_DATADIR=/cache
- CACHE_LOCKDIR=/cache
- CELERYBEAT_SCHEDULE_DB=/tmp/celerybeat-schedule.db
- HOME=/tmp
depends_on:
- augur-db
- redis
- augur-keyman
- rabbitmq
augur-db:
condition: service_healthy
redis:
condition: service_started
augur-keyman:
condition: service_started
rabbitmq:
condition: service_started
networks:
- augur
user: 2345:2345 # Run as an arbitrary non-root user
Expand Down
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