[Stack 14/27] Fix test DB connection: use DATABASE_URL with dotenv by jucor · Pull Request #2443 · compdemocracy/polis

jucor · 2026-03-13T12:59:10Z

Summary

Stacked on #2437 (Vectorize participant info computation (3-15x speedup)). Please review and merge #2437 first.
Next in stack: #2446 (Fix D9: z-score thresholds from two-tailed to one-tailed)

Absorbed PR [CLOSED — absorbed into #2443] DB connect_timeout #2434 (DB connect_timeout): adds connect_timeout=5 to all DB connections so tests fail fast instead of hanging when Postgres is unavailable. Reverts timeout from production code (a 5s timeout could break real deployments), keeping it only in test code.
Adds require_dynamodb() and require_s3() helpers to conftest that probe services with short timeouts and pytest.fail() immediately — applied to all tests that previously hung when Docker services were down.
Adds pytest-timestamper for per-test timing visibility.
Fixes test_postgres_real_data.py to use DATABASE_URL (consistent with all other delphi Python code) via python-dotenv.

Refs #2442

Test plan

test_conversation_from_postgres passes
test_pakistan_conversation_batch passes (9 min, 400K votes)
Full delphi test suite: 294 passed, no regressions

🤖 Generated with Claude Code

Copilot

Pull request overview

Updates the Delphi real-data PostgreSQL integration test to connect using a single DATABASE_URL connection string (optionally loaded from a .env file), aligning with the repository’s broader database configuration approach.

Changes:

Update connect_to_db() to load .env and read DATABASE_URL.
Simplify psycopg2 connection setup to use the URL DSN instead of individual POSTGRES_* fields.

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delphi/tests/test_postgres_real_data.py

+    database_url = os.environ.get('DATABASE_URL')
+    if not database_url:
+        print("DATABASE_URL environment variable is not set")
+        return None


delphi/tests/test_postgres_real_data.py

+    from dotenv import load_dotenv
+
+    # Load .env from the repo root (two levels up from tests/)
+    load_dotenv(Path(__file__).parent.parent.parent / '.env')
+


github-actions · 2026-03-30T13:47:52Z

Delphi Coverage Report

File	Stmts	Miss	Cover
init.py	2	0	100%
benchmarks/bench_pca.py	76	76	0%
benchmarks/bench_repness.py	81	81	0%
benchmarks/bench_update_votes.py	38	38	0%
benchmarks/benchmark_utils.py	34	34	0%
components/init.py	1	0	100%
components/config.py	165	133	19%
conversation/init.py	2	0	100%
conversation/conversation.py	1107	320	71%
conversation/manager.py	131	42	68%
database/init.py	1	0	100%
database/dynamodb.py	387	234	40%
database/postgres.py	305	205	33%
pca_kmeans_rep/init.py	5	0	100%
pca_kmeans_rep/clusters.py	257	22	91%
pca_kmeans_rep/corr.py	98	17	83%
pca_kmeans_rep/pca.py	52	16	69%
pca_kmeans_rep/repness.py	297	43	86%
pca_kmeans_rep/stats.py	107	22	79%
regression/init.py	4	0	100%
regression/clojure_comparer.py	188	17	91%
regression/comparer.py	887	720	19%
regression/datasets.py	135	27	80%
regression/recorder.py	36	27	25%
regression/utils.py	138	87	37%
run_math_pipeline.py	260	114	56%
umap_narrative/500_generate_embedding_umap_cluster.py	210	109	48%
umap_narrative/501_calculate_comment_extremity.py	112	53	53%
umap_narrative/502_calculate_priorities.py	135	135	0%
umap_narrative/700_datamapplot_for_layer.py	502	502	0%
umap_narrative/701_static_datamapplot_for_layer.py	310	310	0%
umap_narrative/702_consensus_divisive_datamapplot.py	432	432	0%
umap_narrative/801_narrative_report_batch.py	785	785	0%
umap_narrative/802_process_batch_results.py	265	265	0%
umap_narrative/803_check_batch_status.py	175	175	0%
umap_narrative/llm_factory_constructor/init.py	2	2	0%
umap_narrative/llm_factory_constructor/model_provider.py	157	157	0%
umap_narrative/polismath_commentgraph/init.py	1	0	100%
umap_narrative/polismath_commentgraph/cli.py	270	270	0%
umap_narrative/polismath_commentgraph/core/init.py	3	3	0%
umap_narrative/polismath_commentgraph/core/clustering.py	108	108	0%
umap_narrative/polismath_commentgraph/core/embedding.py	104	104	0%
umap_narrative/polismath_commentgraph/lambda_handler.py	219	219	0%
umap_narrative/polismath_commentgraph/schemas/init.py	2	0	100%
umap_narrative/polismath_commentgraph/schemas/dynamo_models.py	160	9	94%
umap_narrative/polismath_commentgraph/tests/conftest.py	17	17	0%
umap_narrative/polismath_commentgraph/tests/test_clustering.py	74	74	0%
umap_narrative/polismath_commentgraph/tests/test_embedding.py	55	55	0%
umap_narrative/polismath_commentgraph/tests/test_storage.py	87	87	0%
umap_narrative/polismath_commentgraph/utils/init.py	3	0	100%
umap_narrative/polismath_commentgraph/utils/converter.py	283	237	16%
umap_narrative/polismath_commentgraph/utils/group_data.py	354	336	5%
umap_narrative/polismath_commentgraph/utils/storage.py	584	518	11%
umap_narrative/reset_conversation.py	159	50	69%
umap_narrative/run_pipeline.py	453	312	31%
utils/general.py	62	41	34%
Total	10877	7640	30%

Copilot

Pull request overview

Copilot reviewed 16 out of 16 changed files in this pull request and generated 5 comments.

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Copilot · 2026-03-30T16:30:54Z

delphi/polismath/database/postgres.py

            # Create engine
            uri = self.config.get_uri()
            self.engine = sa.create_engine(
                uri,
                pool_size=self.config.pool_size,
                max_overflow=self.config.max_overflow,
                pool_recycle=300,  # Recycle connections after 5 minutes
+                connect_args={"connect_timeout": 5},
+                pool_pre_ping=True,
            )


PR description says the 5s DB connect_timeout is test-only, but this change applies it to the main SQLAlchemy engine used by PostgresClient. A hard-coded 5s timeout (and enabling pool_pre_ping) can cause production requests to fail under transient network/DB load. Consider making the timeout configurable (e.g., env/config defaulting to libpq default) and only overriding to 5s in test config, or gate it behind an explicit "fast-fail" setting.

Copilot · 2026-03-30T16:30:55Z

delphi/polismath/run_math_pipeline.py

    try:
        # Check if DATABASE_URL is set and use it if available
        database_url = os.environ.get("DATABASE_URL")
        if database_url:
            logger.info(f"Using DATABASE_URL: {database_url.split('@')[1] if '@' in database_url else '(hidden)'}")
-            conn = psycopg2.connect(database_url)
+            conn = psycopg2.connect(database_url, connect_timeout=5)
        else:
            # Fall back to individual connection parameters
            conn = psycopg2.connect(
                dbname=os.environ.get("DATABASE_NAME", "polisDB_prod_local_mar14"),
                user=os.environ.get("DATABASE_USER", "colinmegill"),
                password=os.environ.get("DATABASE_PASSWORD", ""),
                host=os.environ.get("DATABASE_HOST", "localhost"),
                port=os.environ.get("DATABASE_PORT", 5432),
+                connect_timeout=5,
            )


connect_timeout=5 is now applied in this script's connect_to_db() path for both DATABASE_URL and per-field config. If this script is used against remote/prod DBs, a hard-coded 5s timeout can be too aggressive and cause intermittent failures. Consider making the timeout configurable (env/arg) with a safer default, and keep the 5s value for tests/local dev only.

Copilot · 2026-03-30T16:30:55Z

delphi/scripts/regression_download.py

+    return psycopg2.connect(database_url, connect_timeout=5)



get_db_connection() now hard-codes connect_timeout=5 for all connections. For a utility that may be used against slower or remote Postgres instances, this can cause avoidable failures. Consider making the timeout configurable (env/CLI) and defaulting to libpq's default unless explicitly opting into fast-fail behavior.

Suggested change

return psycopg2.connect(database_url, connect_timeout=5)

# Allow optional override of the database connect timeout via environment variable.

# If DATABASE_CONNECT_TIMEOUT is not set, fall back to psycopg2/libpq defaults.

timeout_env = os.environ.get("DATABASE_CONNECT_TIMEOUT")

connect_kwargs = {}

if timeout_env:

try:

connect_kwargs["connect_timeout"] = int(timeout_env)

except ValueError:

# Invalid value; ignore and use default behavior.

print(

f"Warning: DATABASE_CONNECT_TIMEOUT={timeout_env!r} is not a valid integer; "

"using psycopg2 default connect timeout."

)

return psycopg2.connect(database_url, **connect_kwargs)

Copilot · 2026-03-30T16:30:56Z

delphi/tests/conftest.py

+def require_s3(
+    endpoint: str | None = None,
+    timeout: float = 3.0,
+) -> None:
+    """Skip the test if S3/MinIO is not responding.
+
+    Uses pytest.skip (not fail) because MinIO is a local dev service
+    that is not available in CI.
+    """
+    import os
+
+    import boto3
+    from botocore.config import Config
+
+    endpoint = endpoint or os.environ.get(
+        "AWS_S3_ENDPOINT", "http://host.docker.internal:9000"
+    )
+    cfg = Config(
+        connect_timeout=timeout,
+        read_timeout=timeout,
+        retries={"max_attempts": 0},
+        signature_version="s3v4",
+    )
+    client = boto3.client(
+        "s3",
+        endpoint_url=endpoint,
+        region_name="us-east-1",
+        aws_access_key_id=os.environ.get("AWS_ACCESS_KEY_ID", "minioadmin"),
+        aws_secret_access_key=os.environ.get("AWS_SECRET_ACCESS_KEY", "minioadmin"),
+        config=cfg,
+        verify=False,
+    )
+    try:
+        client.list_buckets()
+    except Exception as exc:
+        pytest.skip(f"S3/MinIO is not available at {endpoint}: {exc}")


The PR description says both require_dynamodb() and require_s3() use pytest.fail() to fail fast, but require_s3() currently uses pytest.skip() when MinIO is unavailable. Either update the PR description to match the implemented behavior, or change require_s3() to fail if the intention is to treat missing S3 as a hard test failure.

Copilot · 2026-03-30T16:30:56Z

delphi/polismath/database/postgres.py

            self.engine = sa.create_engine(
                uri,
                pool_size=self.config.pool_size,
                max_overflow=self.config.max_overflow,
                pool_recycle=300,  # Recycle connections after 5 minutes
+                connect_args={"connect_timeout": 5},
+                pool_pre_ping=True,
            )


This introduces connect_timeout=5 (and pool_pre_ping) in delphi/polismath/database/postgres.py, which is part of the non-test codepath. That conflicts with the PR description stating the 5s timeout was reverted from production code and kept only in tests; either move this to test-only configuration or update the PR description/commit message to match the actual scope.

Without a connect_timeout, psycopg2 and SQLAlchemy wait for the OS TCP timeout (~30s+) when the database is unreachable, causing tests to stall. Add connect_timeout=5 to all psycopg2.connect() calls and to the SQLAlchemy engine (via connect_args). Also add pool_pre_ping=True so stale pooled connections are detected. Change DB-dependent tests from pytest.skip to pytest.fail so a missing database is surfaced as a failure rather than silently skipped. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Revert connect_timeout from production DB code (postgres.py, run_math_pipeline.py, regression_download.py) — a 5s timeout could break real deployments where infra is slow to respond. Instead, add require_dynamodb() and require_s3() helpers to conftest that probe the service with a short timeout and zero retries, then pytest.fail() immediately. Applied to test_dynamodb_direct, test_batch_id, and test_minio_access — all previously hung forever when Docker was down. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

MinIO is a local dev service not available in CI, so use pytest.skip instead of pytest.fail to avoid breaking the CI test suite. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add require_dynamodb() guard so the test fails in ~3s instead of hanging for minutes on a TCP connection to a stopped DynamoDB. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add require_dynamodb() guard to the dynamodb_resource fixture so it fails in ~3s instead of hanging on a TCP connection to stopped DynamoDB. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Add pytest-timestamper>=0.0.10 to dev dependencies for detecting hung tests (prints timestamps in -v mode so hangs are obvious from stopped progress) - Fix test_501_calculate_comment_extremity hang by also mocking PostgresClient. The test already mocked GroupDataProcessor but PostgresClient.initialize() was still called at line 57 for exclude_comment_selections, causing a hang when Docker (Postgres) was paused. Verified: both tests pass in <0.2s with Docker paused. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Move `from run_pipeline import main` from module level to inside the test function. Module-level import loads SentenceTransformer, UMAP, evoc during test collection. With xdist, multiple workers collecting simultaneously *might* cause lock contention and hangs. Note: A previous session reported indefinite hangs under xdist, but we couldn't reproduce it. This change is defensive — deferred imports are good practice regardless. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

…n type - Initialize timing_stats_compared to {} instead of None when benchmark is off, preventing AttributeError in generate_report() - Fix compute_all_stages() return type from Dict[str, Dict[str, Any]] to Dict[str, Any] since it also contains "timings": Dict[str, float] Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

connect_to_db() in test_postgres_real_data.py used POSTGRES_* env vars with wrong defaults (password='postgres', database='polismath'), causing both test_conversation_from_postgres and test_pakistan_conversation_batch to fail with auth errors even when Postgres is running. Switch to DATABASE_URL (the standard in all other delphi Python code) and load it from the repo root .env via python-dotenv. Refs #2442 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

connect_to_db() in test_postgres_real_data.py had a hardcoded .env path that doesn't work inside Docker containers, and required DATABASE_URL with no fallback. Now uses find_dotenv() to search up the directory tree, and falls back to DATABASE_HOST/PORT/NAME/USER/PASSWORD (which the docker-compose.test.yml delphi service already provides). Also removes dead POSTGRES_* env vars from the CI exec command — nothing in Delphi reads those anymore. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The session-scoped conversation cache fixture and the pytest_collection_modifyitems reordering hook were inadvertently removed when require_dynamodb/require_s3 helpers were added. test_legacy_clojure_regression.py depends on this fixture. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

pyproject.toml forces -n0 (sequential) because the session-scoped conversation cache makes sequential ~1.6-1.8x faster than parallel. The xdist_group markers were never active. Restore the plain pytest.param() calls that match the rest of the stack. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

jucor · 2026-03-30T22:54:38Z

Superseded by spr-managed PR stack. See the new stack starting at #2508.

jucor requested a review from Copilot March 13, 2026 12:59

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jucor force-pushed the jc/vectorize-participant-info branch from b839591 to 3048f93 Compare March 13, 2026 13:09

jucor force-pushed the jc/fix-test-db-connection branch from 1514e3d to bafbdf6 Compare March 13, 2026 13:09

jucor changed the title ~~Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/12] Fix test DB connection: use DATABASE_URL with dotenv Mar 13, 2026

jucor mentioned this pull request Mar 13, 2026

[Stack 13/27] Vectorize participant info computation (3-15x speedup) #2437

Closed

5 tasks

jucor force-pushed the jc/fix-test-db-connection branch from cb7c5cd to bafbdf6 Compare March 13, 2026 13:45

jucor force-pushed the jc/vectorize-participant-info branch from 3048f93 to e883338 Compare March 13, 2026 13:53

jucor force-pushed the jc/fix-test-db-connection branch from bafbdf6 to e2f39bb Compare March 13, 2026 13:54

jucor changed the title ~~[Stack 12/12] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/13] Fix test DB connection: use DATABASE_URL with dotenv Mar 13, 2026

jucor force-pushed the jc/vectorize-participant-info branch from e883338 to 9dee5d9 Compare March 13, 2026 14:15

jucor force-pushed the jc/fix-test-db-connection branch from e2f39bb to 89297cf Compare March 13, 2026 14:17

jucor force-pushed the jc/vectorize-participant-info branch from 9dee5d9 to 0d4cd71 Compare March 13, 2026 15:56

jucor force-pushed the jc/fix-test-db-connection branch from 89297cf to 403be8d Compare March 13, 2026 16:07

jucor mentioned this pull request Mar 13, 2026

[Stack 15/27] Fix D9: z-score thresholds from two-tailed to one-tailed #2446

Closed

5 tasks

jucor changed the title ~~[Stack 12/13] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/15] Fix test DB connection: use DATABASE_URL with dotenv Mar 16, 2026

jucor force-pushed the jc/vectorize-participant-info branch from 0d4cd71 to fa345cd Compare March 16, 2026 16:04

jucor force-pushed the jc/fix-test-db-connection branch from 403be8d to 464da16 Compare March 16, 2026 16:04

jucor changed the title ~~[Stack 12/15] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/16] Fix test DB connection: use DATABASE_URL with dotenv Mar 16, 2026

jucor changed the title ~~[Stack 12/16] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/17] Fix test DB connection: use DATABASE_URL with dotenv Mar 16, 2026

jucor changed the title ~~[Stack 12/17] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/24] Fix test DB connection: use DATABASE_URL with dotenv Mar 17, 2026

jucor changed the title ~~[Stack 12/24] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/25] Fix test DB connection: use DATABASE_URL with dotenv Mar 17, 2026

jucor force-pushed the jc/vectorize-participant-info branch from fa345cd to 655bcfa Compare March 19, 2026 10:43

jucor force-pushed the jc/fix-test-db-connection branch from 6b81d8e to 6da6172 Compare March 19, 2026 10:43

jucor changed the title ~~[Stack 12/25] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 11/24] Fix test DB connection: use DATABASE_URL with dotenv Mar 19, 2026

jucor force-pushed the jc/vectorize-participant-info branch from 655bcfa to 01a7637 Compare March 19, 2026 12:31

jucor force-pushed the jc/fix-test-db-connection branch 2 times, most recently from 0ef54ca to b62c0cd Compare March 19, 2026 14:52

jucor changed the title ~~[Stack 11/24] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 12/25] Fix test DB connection: use DATABASE_URL with dotenv Mar 19, 2026

jucor force-pushed the jc/fix-test-db-connection branch from 4ea1333 to 917cba8 Compare March 27, 2026 10:41

jucor changed the title ~~[Stack 12/25] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 13/26] Fix test DB connection: use DATABASE_URL with dotenv Mar 30, 2026

jucor force-pushed the jc/fix-test-db-connection branch from 917cba8 to e45a120 Compare March 30, 2026 12:48

jucor changed the title ~~[Stack 13/26] Fix test DB connection: use DATABASE_URL with dotenv~~ [Stack 14/27] Fix test DB connection: use DATABASE_URL with dotenv Mar 30, 2026

jucor force-pushed the jc/fix-test-db-connection branch from e45a120 to b68bd5b Compare March 30, 2026 12:54

jucor requested a review from Copilot March 30, 2026 16:25

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jucor force-pushed the jc/vectorize-participant-info branch from 67731ff to afbd68a Compare March 30, 2026 16:49

jucor force-pushed the jc/fix-test-db-connection branch from b68bd5b to 583f955 Compare March 30, 2026 16:49

jucor and others added 13 commits March 30, 2026 17:58

Fix conftest docstring: require_dynamodb/require_s3, not require_service

dd3cf98

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Skip (not fail) test_minio_access when MinIO is unavailable

a443c9e

MinIO is a local dev service not available in CI, so use pytest.skip instead of pytest.fail to avoid breaking the CI test suite. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Fail test_conversation_from_postgres fast when DynamoDB is unavailable

45adf99

Add require_dynamodb() guard so the test fails in ~3s instead of hanging for minutes on a TCP connection to a stopped DynamoDB. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Fail test_run_math_pipeline_e2e fast when DynamoDB is unavailable

f9f0e5c

Add require_dynamodb() guard to the dynamodb_resource fixture so it fails in ~3s instead of hanging on a TCP connection to stopped DynamoDB. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

jucor force-pushed the jc/vectorize-participant-info branch from afbd68a to 6138219 Compare March 30, 2026 17:05

jucor force-pushed the jc/fix-test-db-connection branch from 583f955 to 380b00d Compare March 30, 2026 17:05

This was referenced Mar 30, 2026

IGNORE -- crash from spr #2498

Closed

IGNORE -- crash from spr #2500

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jucor closed this Mar 30, 2026

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[Stack 14/27] Fix test DB connection: use DATABASE_URL with dotenv#2443

[Stack 14/27] Fix test DB connection: use DATABASE_URL with dotenv#2443
jucor wants to merge 13 commits intojc/vectorize-participant-infofrom
jc/fix-test-db-connection

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-    return psycopg2.connect(database_url, connect_timeout=5)
+    # Allow optional override of the database connect timeout via environment variable.
+    # If DATABASE_CONNECT_TIMEOUT is not set, fall back to psycopg2/libpq defaults.
+    timeout_env = os.environ.get("DATABASE_CONNECT_TIMEOUT")
+    connect_kwargs = {}
+    if timeout_env:
+        try:
+            connect_kwargs["connect_timeout"] = int(timeout_env)
+        except ValueError:
+            # Invalid value; ignore and use default behavior.
+            print(
+                f"Warning: DATABASE_CONNECT_TIMEOUT={timeout_env!r} is not a valid integer; "
+                "using psycopg2 default connect timeout."
+            )
+    return psycopg2.connect(database_url, **connect_kwargs)

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