diff --git a/diagrams/erdiagram_targetdb_latest.pdf b/diagrams/erdiagram_targetdb_latest.pdf
index b3a2300..0091ba3 100644
Binary files a/diagrams/erdiagram_targetdb_latest.pdf and b/diagrams/erdiagram_targetdb_latest.pdf differ
diff --git a/docs/getting_started.md b/docs/getting_started.md
index fff26cf..6e408c8 100644
--- a/docs/getting_started.md
+++ b/docs/getting_started.md
@@ -145,6 +145,46 @@ print(df.head())
 db.close()
 ```
 
+## Running Tests Locally
+
+The unit tests (`tests/test_*.py`, excluding `tests/integration/`) do not require a database
+and can be run at any time:
+
+```bash
+uv run pytest tests -m "not integration"
+```
+
+The integration tests (`tests/integration/`) exercise the same sequence of `pfs-targetdb-cli`
+commands as the `Test Database` GitHub Actions workflow
+(`.github/workflows/test_database.yml`): creating the database, installing the Q3C extension,
+creating the schema, and inserting the example data in `examples/data/`, this time also
+verifying the inserted rows with SQL queries. They require Docker (for a disposable
+PostgreSQL + Q3C container) and are skipped automatically, with a reason, if Docker is not
+available.
+
+```bash
+# Docker must be running (e.g. Docker Desktop or OrbStack on macOS)
+uv run pytest tests/integration -v
+```
+
+A dedicated PostgreSQL container is built from `tests/docker/Dockerfile` and started/stopped
+automatically for the test session by `docker compose` (`tests/docker/docker-compose.test.yml`).
+It listens on `localhost:15433` by default; set `TARGETDB_TEST_PG_PORT` to use a different port.
+Its data directory is a tmpfs mount, so nothing is left on disk once the tests finish, and all
+generated files (converted flux standard catalogs, transferred target lists) are written under a
+pytest-managed temporary directory rather than into `examples/data/`.
+
+If a test fails and you want to inspect the database afterwards, pass `--keep-db` to leave the
+container running:
+
+```bash
+uv run pytest tests/integration -v --keep-db
+psql -h localhost -p 15433 -U postgres -d test_targetdb
+
+# once done, stop the container manually
+docker compose -f tests/docker/docker-compose.test.yml down -v
+```
+
 ## Build the Documentation
 
 The documentation can be built by the following command:
diff --git a/docs/tbls/public.fluxstd.md b/docs/tbls/public.fluxstd.md
index 7e61766..3ca7a85 100644
--- a/docs/tbls/public.fluxstd.md
+++ b/docs/tbls/public.fluxstd.md
@@ -102,9 +102,9 @@
 | fluxstd_pkey | CREATE UNIQUE INDEX fluxstd_pkey ON public.fluxstd USING btree (fluxstd_id) |
 | uq_obj_id_input_catalog_id_version | CREATE UNIQUE INDEX uq_obj_id_input_catalog_id_version ON public.fluxstd USING btree (obj_id, input_catalog_id, version) |
 | fluxstd_q3c_ang2ipix_idx | CREATE INDEX fluxstd_q3c_ang2ipix_idx ON public.fluxstd USING btree (q3c_ang2ipix(ra, "dec")) |
+| ix_fluxstd_version | CREATE INDEX ix_fluxstd_version ON public.fluxstd USING btree (version) |
 | ix_fluxstd_input_catalog_fluxstdid | CREATE INDEX ix_fluxstd_input_catalog_fluxstdid ON public.fluxstd USING btree (input_catalog_id, fluxstd_id) |
 | ix_fluxstd_version_fluxstdid | CREATE INDEX ix_fluxstd_version_fluxstdid ON public.fluxstd USING btree (version, fluxstd_id) |
-| ix_fluxstd_version | CREATE INDEX ix_fluxstd_version ON public.fluxstd USING btree (version) |
 
 ## Relations
 
diff --git a/docs/tbls/public.sky.md b/docs/tbls/public.sky.md
index 6b4f98d..f4d93bf 100644
--- a/docs/tbls/public.sky.md
+++ b/docs/tbls/public.sky.md
@@ -34,9 +34,9 @@
 | ---- | ---------- |
 | sky_pkey | CREATE UNIQUE INDEX sky_pkey ON public.sky USING btree (sky_id) |
 | sky_obj_id_input_catalog_id_version_key | CREATE UNIQUE INDEX sky_obj_id_input_catalog_id_version_key ON public.sky USING btree (obj_id, input_catalog_id, version) |
-| ix_sky_input_catalog_id | CREATE INDEX ix_sky_input_catalog_id ON public.sky USING btree (input_catalog_id) |
 | sky_q3c_ang2ipix_idx | CREATE INDEX sky_q3c_ang2ipix_idx ON public.sky USING btree (q3c_ang2ipix(ra, "dec")) |
 | ix_sky_version | CREATE INDEX ix_sky_version ON public.sky USING btree (version) |
+| ix_sky_input_catalog_id | CREATE INDEX ix_sky_input_catalog_id ON public.sky USING btree (input_catalog_id) |
 
 ## Relations
 
diff --git a/docs/tbls/public.target.md b/docs/tbls/public.target.md
index 12ceb5a..1728dae 100644
--- a/docs/tbls/public.target.md
+++ b/docs/tbls/public.target.md
@@ -121,11 +121,11 @@
 | target_pkey | CREATE UNIQUE INDEX target_pkey ON public.target USING btree (target_id) |
 | target_propid_obcode_catid_objid_resolution_key | CREATE UNIQUE INDEX target_propid_obcode_catid_objid_resolution_key ON public.target USING btree (proposal_id, ob_code, input_catalog_id, obj_id, is_medium_resolution) |
 | target_propid_obcode_key | CREATE UNIQUE INDEX target_propid_obcode_key ON public.target USING btree (proposal_id, ob_code) |
-| target_proposal_id_idx | CREATE INDEX target_proposal_id_idx ON public.target USING btree (proposal_id) |
-| target_obj_id_input_catalog_id_idx | CREATE INDEX target_obj_id_input_catalog_id_idx ON public.target USING btree (obj_id, input_catalog_id) |
 | target_input_catalog_id_idx | CREATE INDEX target_input_catalog_id_idx ON public.target USING btree (input_catalog_id) |
 | target_proposal_id_obj_id_idx | CREATE INDEX target_proposal_id_obj_id_idx ON public.target USING btree (proposal_id, obj_id) |
 | target_q3c_ang2ipix_idx | CREATE INDEX target_q3c_ang2ipix_idx ON public.target USING btree (q3c_ang2ipix(ra, "dec")) |
+| target_proposal_id_idx | CREATE INDEX target_proposal_id_idx ON public.target USING btree (proposal_id) |
+| target_obj_id_input_catalog_id_idx | CREATE INDEX target_obj_id_input_catalog_id_idx ON public.target USING btree (obj_id, input_catalog_id) |
 
 ## Relations
 
diff --git a/pyproject.toml b/pyproject.toml
index 5b0c4d8..e436c65 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,13 +45,19 @@ source = "https://github.com/Subaru-PFS/ets_target_database"
 pfs-targetdb-cli = "targetdb.cli.cli_main:app"
 
 [project.optional-dependencies]
-dev = ["ipython", "pytest", "black", "ruff", "setuptools-scm>=8.0"]
+dev = ["ipython", "pytest", "pytest-cov", "black", "ruff", "setuptools-scm>=8.0"]
 doc = ["mkdocs<2", "mkdocs-material[imaging]"]
 
 [build-system]
 requires = ["setuptools>=64", "setuptools-scm>=8.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+markers = [
+  "integration: tests requiring a PostgreSQL container via Docker",
+]
+
 [tool.black]
 line-length = 88
 
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..2ec181a
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+
+import shutil
+import subprocess
+from functools import lru_cache
+from pathlib import Path
+
+import pytest
+
+INTEGRATION_TESTS_DIR = Path(__file__).parent / "integration"
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--keep-db",
+        action="store_true",
+        default=False,
+        help=(
+            "Do not tear down the PostgreSQL test container after the "
+            "integration test session. Useful for inspecting the database "
+            "after a failure, e.g. with "
+            "`psql -h localhost -p 15433 -U postgres -d test_targetdb`."
+        ),
+    )
+
+
+@lru_cache(maxsize=1)
+def docker_available_reason():
+    """
+    Check whether a usable Docker daemon is available.
+
+    Returns
+    -------
+    reason : str or None
+        None if Docker is available and responsive, otherwise a short
+        string explaining why it is not, suitable for a pytest skip reason.
+    """
+    if shutil.which("docker") is None:
+        return "docker executable not found on PATH"
+
+    try:
+        result = subprocess.run(
+            ["docker", "info"],
+            capture_output=True,
+            timeout=10,
+        )
+    except (OSError, subprocess.TimeoutExpired) as e:
+        return f"docker info failed to run: {e}"
+
+    if result.returncode != 0:
+        return "docker daemon is not reachable (`docker info` failed)"
+
+    return None
+
+
+def pytest_configure(config):
+    config.addinivalue_line(
+        "markers",
+        "integration: tests requiring a PostgreSQL container via Docker",
+    )
+
+
+def pytest_collection_modifyitems(config, items):
+    reason = docker_available_reason()
+
+    for item in items:
+        try:
+            item.path.relative_to(INTEGRATION_TESTS_DIR)
+        except ValueError:
+            continue
+
+        item.add_marker(pytest.mark.integration)
+
+        if reason is not None:
+            item.add_marker(pytest.mark.skip(reason=f"Docker unavailable: {reason}"))
diff --git a/tests/docker/Dockerfile b/tests/docker/Dockerfile
new file mode 100644
index 0000000..d549c60
--- /dev/null
+++ b/tests/docker/Dockerfile
@@ -0,0 +1,9 @@
+# PostgreSQL image with the Q3C extension pre-installed, mirroring the
+# packages installed on-the-fly in .github/workflows/test_database.yml.
+# Building this once and reusing the image is much faster than the CI
+# approach of installing q3c into a freshly-started container every run.
+FROM postgres:16
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends postgresql-16-q3c \
+    && rm -rf /var/lib/apt/lists/*
diff --git a/tests/docker/docker-compose.test.yml b/tests/docker/docker-compose.test.yml
new file mode 100644
index 0000000..be67075
--- /dev/null
+++ b/tests/docker/docker-compose.test.yml
@@ -0,0 +1,26 @@
+# Standalone PostgreSQL + Q3C stack used by the pytest integration tests
+# (tests/integration/). Kept separate from examples/docker/, which is a
+# developer-facing, persistent local database and not meant to be
+# started/stopped/discarded by the test suite.
+name: targetdb-test
+
+services:
+  postgres:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: postgres
+    ports:
+      - "${TARGETDB_TEST_PG_PORT:-15433}:5432"
+    # Data lives in tmpfs: each test session starts from a clean database
+    # and nothing is left on disk after teardown.
+    tmpfs:
+      - /var/lib/postgresql/data
+    healthcheck:
+      test: ["CMD", "pg_isready", "-U", "postgres"]
+      interval: 2s
+      timeout: 5s
+      retries: 30
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py
new file mode 100644
index 0000000..0aaad31
--- /dev/null
+++ b/tests/integration/conftest.py
@@ -0,0 +1,266 @@
+#!/usr/bin/env python3
+"""
+Session-scoped fixture pipeline that reproduces, locally, the sequence of
+`pfs-targetdb-cli` commands run by .github/workflows/test_database.yml:
+
+    postgres_service -> db_config -> database -> q3c_installed -> schema
+        -> master_data -> fluxstd_data
+        -> master_data -> target_data -> pointing_data
+
+Each fixture requests the one(s) it depends on, so a test only needs to
+request the fixture for the stage it cares about (and pytest builds
+everything upstream automatically). All of it is torn down once per test
+session (or left running with `--keep-db`).
+
+Unlike the CI workflow, output files (prep-fluxstd output, transferred
+target lists) are written under a pytest-managed temporary directory
+instead of into the repository, so running the suite never leaves the
+working tree dirty.
+"""
+
+import subprocess
+from pathlib import Path
+
+import pandas as pd
+import pytest
+from astropy.table import Table
+from sqlalchemy import create_engine, text
+from typer.testing import CliRunner
+
+from targetdb.cli.cli_main import app
+from targetdb.utils import get_url_object, load_config
+
+REPO_ROOT = Path(__file__).resolve().parents[2]
+DOCKER_DIR = REPO_ROOT / "tests" / "docker"
+COMPOSE_FILE = DOCKER_DIR / "docker-compose.test.yml"
+
+EXAMPLES_DATA = REPO_ROOT / "examples" / "data"
+TARGETS_DATA_DIR = EXAMPLES_DATA / "targets"
+FLUXSTD_INPUT_DIR = EXAMPLES_DATA / "fluxstd" / "Fstar_v3.3" / "feather-original"
+
+# Master tables inserted in the same order as the "Insert example data" CI step.
+MASTER_TABLE_FILES = [
+    ("target_type", "target_types.csv"),
+    ("filter_name", "filter_names.csv"),
+    ("partner", "partner.csv"),
+    ("pfs_arm", "pfs_arm.csv"),
+    ("proposal_category", "proposal_category.csv"),
+    ("proposal", "proposals.csv"),
+    ("input_catalog", "input_catalogs.csv"),
+]
+
+PG_PORT = 15433
+
+_cli_runner = CliRunner()
+
+
+def run_cli(*args):
+    """
+    Invoke the ``pfs-targetdb-cli`` Typer app in-process and assert success.
+
+    Running in-process (rather than via subprocess) means failures surface
+    as normal Python tracebacks/output in the pytest report instead of an
+    opaque non-zero exit code.
+    """
+    result = _cli_runner.invoke(app, [str(a) for a in args], catch_exceptions=False)
+    assert result.exit_code == 0, (
+        f"CLI command {args!r} failed with exit code {result.exit_code}\n"
+        f"Output:\n{result.output}"
+    )
+    return result
+
+
+def count_rows(engine, table):
+    with engine.connect() as conn:
+        return conn.execute(text(f"SELECT count(*) FROM {table}")).scalar_one()
+
+
+def csv_row_count(path):
+    return len(pd.read_csv(path))
+
+
+def ecsv_row_count(path):
+    return len(Table.read(path, format="ascii.ecsv"))
+
+
+def _run_compose(*args):
+    cmd = ["docker", "compose", "-f", str(COMPOSE_FILE), *args]
+    result = subprocess.run(cmd, cwd=DOCKER_DIR, capture_output=True, text=True)
+    if result.returncode != 0:
+        raise RuntimeError(
+            f"Command failed: {' '.join(cmd)}\n"
+            f"stdout:\n{result.stdout}\nstderr:\n{result.stderr}"
+        )
+    return result
+
+
+@pytest.fixture(scope="session")
+def postgres_service(request):
+    """Bring up the PostgreSQL+Q3C container for the whole test session."""
+    _run_compose("up", "-d", "--build", "--wait", "--wait-timeout", "120")
+    try:
+        yield {"host": "localhost", "port": PG_PORT}
+    finally:
+        if request.config.getoption("--keep-db"):
+            print(
+                f"\n--keep-db: leaving the test PostgreSQL container running "
+                f"on port {PG_PORT}. Stop it manually with:\n"
+                f"  docker compose -f {COMPOSE_FILE} down -v"
+            )
+        else:
+            _run_compose("down", "-v", "--remove-orphans")
+
+
+@pytest.fixture(scope="session")
+def work_dir(tmp_path_factory):
+    """Scratch directory for generated config/data files, unique per session."""
+    return tmp_path_factory.mktemp("targetdb-integration")
+
+
+@pytest.fixture(scope="session")
+def db_config(postgres_service, work_dir):
+    """Write a test dbconf.toml pointing at the container and return its path."""
+    config_path = work_dir / "test_db_config.toml"
+    config_path.write_text(
+        f"""\
+[targetdb.db]
+dialect = "postgresql"
+user = "postgres"
+password = "postgres"
+host = "{postgres_service["host"]}"
+port = {postgres_service["port"]}
+dbname = "test_targetdb"
+
+[uploader]
+host = "localhost"
+data_dir = "{EXAMPLES_DATA / "uploader"}"
+"""
+    )
+    return config_path
+
+
+@pytest.fixture(scope="session")
+def engine(database, db_config):
+    config = load_config(str(db_config))
+    eng = create_engine(get_url_object(config))
+    yield eng
+    eng.dispose()
+
+
+@pytest.fixture(scope="session")
+def database(db_config):
+    run_cli("create-db", "-c", db_config)
+
+
+@pytest.fixture(scope="session")
+def q3c_installed(database, db_config):
+    run_cli("install-q3c", "-c", db_config)
+
+
+@pytest.fixture(scope="session")
+def schema(q3c_installed, db_config):
+    run_cli("create-schema", "-c", db_config)
+
+
+@pytest.fixture(scope="session")
+def master_data(schema, db_config):
+    """Insert the master/reference tables shared by every downstream stage."""
+    for table, filename in MASTER_TABLE_FILES:
+        run_cli(
+            "insert", EXAMPLES_DATA / filename, "-c", db_config, "-t", table, "--commit"
+        )
+    # input_catalog entry required by the flux standard star catalog.
+    run_cli(
+        "insert",
+        EXAMPLES_DATA / "input_catalog_fluxstd.csv",
+        "-c",
+        db_config,
+        "-t",
+        "input_catalog",
+        "--commit",
+    )
+
+
+@pytest.fixture(scope="session")
+def fluxstd_data(master_data, db_config, work_dir):
+    """Run prep-fluxstd and insert the resulting rows into the fluxstd table."""
+    output_dir = work_dir / "fluxstd_feather"
+    run_cli(
+        "prep-fluxstd",
+        FLUXSTD_INPUT_DIR,
+        output_dir,
+        "--version",
+        "3.3",
+        "--input_catalog_id",
+        "3006",
+        "--rename-cols",
+        '{"fstar_gaia": "is_fstar_gaia"}',
+        "--format",
+        "feather",
+    )
+    generated_files = sorted(output_dir.glob("*.feather"))
+    assert generated_files, f"prep-fluxstd produced no feather files in {output_dir}"
+
+    for f in generated_files:
+        run_cli("insert", f, "-c", db_config, "-t", "fluxstd", "--commit")
+
+    return {"output_dir": output_dir, "files": generated_files}
+
+
+@pytest.fixture(scope="session")
+def target_data(master_data, db_config, work_dir):
+    """Insert proposals/catalogs for the target examples, then transfer and insert targets."""
+    run_cli(
+        "insert",
+        TARGETS_DATA_DIR / "example_proposals.csv",
+        "-c",
+        db_config,
+        "-t",
+        "proposal",
+        "--commit",
+    )
+    run_cli(
+        "insert",
+        TARGETS_DATA_DIR / "example_input_catalogs.csv",
+        "-c",
+        db_config,
+        "-t",
+        "input_catalog",
+        "--commit",
+        "--fetch",
+    )
+
+    local_dir = work_dir / "targets"
+    run_cli(
+        "transfer-targets",
+        TARGETS_DATA_DIR / "example_input_catalogs.csv",
+        "-c",
+        db_config,
+        "--local-dir",
+        local_dir,
+        "--force",
+    )
+    run_cli(
+        "insert-targets",
+        TARGETS_DATA_DIR / "example_input_catalogs.csv",
+        "-c",
+        db_config,
+        "--data-dir",
+        local_dir,
+        "--commit",
+    )
+
+    return {"local_dir": local_dir}
+
+
+@pytest.fixture(scope="session")
+def pointing_data(target_data, db_config):
+    run_cli(
+        "insert-pointings",
+        TARGETS_DATA_DIR / "example_input_catalogs.csv",
+        "-c",
+        db_config,
+        "--data-dir",
+        target_data["local_dir"],
+        "--commit",
+    )
diff --git a/tests/integration/test_catalog_active.py b/tests/integration/test_catalog_active.py
new file mode 100644
index 0000000..c669f42
--- /dev/null
+++ b/tests/integration/test_catalog_active.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+"""Verify update-catalog-active only changes the targeted input_catalog row."""
+
+from sqlalchemy import text
+
+from .conftest import run_cli
+
+TARGET_CATALOG_ID = 1004
+
+
+def _read_active_flags(engine):
+    with engine.connect() as conn:
+        rows = conn.execute(text("SELECT input_catalog_id, active FROM input_catalog"))
+        return dict(rows.all())
+
+
+def test_update_catalog_active_only_affects_target_row(engine, master_data, db_config):
+    before = _read_active_flags(engine)
+    assert TARGET_CATALOG_ID in before, (
+        f"expected input_catalog_id={TARGET_CATALOG_ID} from examples/data/input_catalogs.csv"
+    )
+
+    run_cli(
+        "update-catalog-active",
+        TARGET_CATALOG_ID,
+        "true",
+        "-c",
+        db_config,
+        "--verbose",
+        "--commit",
+    )
+
+    after = _read_active_flags(engine)
+
+    assert after[TARGET_CATALOG_ID] is True
+
+    unaffected_before = {k: v for k, v in before.items() if k != TARGET_CATALOG_ID}
+    unaffected_after = {k: v for k, v in after.items() if k != TARGET_CATALOG_ID}
+    assert unaffected_after == unaffected_before
diff --git a/tests/integration/test_fluxstd.py b/tests/integration/test_fluxstd.py
new file mode 100644
index 0000000..8b2619b
--- /dev/null
+++ b/tests/integration/test_fluxstd.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+"""Verify prep-fluxstd output and the resulting fluxstd table contents."""
+
+import pandas as pd
+from sqlalchemy import text
+
+from .conftest import FLUXSTD_INPUT_DIR, count_rows
+
+INPUT_FEATHER = FLUXSTD_INPUT_DIR / "ra354.8_354.9_dec-40.0_90.0.feather"
+
+
+def test_prep_fluxstd_generates_output_files(fluxstd_data):
+    assert fluxstd_data["files"], "expected at least one generated feather file"
+    for f in fluxstd_data["files"]:
+        assert f.exists()
+
+
+def test_fluxstd_row_count_matches_input(engine, fluxstd_data):
+    expected = len(pd.read_feather(INPUT_FEATHER))
+    assert count_rows(engine, "fluxstd") == expected
+
+
+def test_fluxstd_rows_tagged_with_catalog_and_version(engine, fluxstd_data):
+    with engine.connect() as conn:
+        rows = conn.execute(
+            text("SELECT DISTINCT input_catalog_id, version FROM fluxstd")
+        ).fetchall()
+    assert rows == [(3006, "3.3")]
+
+
+def test_fluxstd_rename_cols_applied(fluxstd_data):
+    df = pd.read_feather(fluxstd_data["files"][0])
+    assert "is_fstar_gaia" in df.columns
+    assert "fstar_gaia" not in df.columns
diff --git a/tests/integration/test_master_tables.py b/tests/integration/test_master_tables.py
new file mode 100644
index 0000000..130d22e
--- /dev/null
+++ b/tests/integration/test_master_tables.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+"""Verify the master/reference tables inserted from examples/data/*.csv."""
+
+import pytest
+from sqlalchemy import text
+
+from .conftest import EXAMPLES_DATA, MASTER_TABLE_FILES, count_rows, csv_row_count
+
+# input_catalog receives an extra insert (input_catalog_fluxstd.csv) on top of
+# input_catalogs.csv, so it is checked separately below rather than via the
+# generic 1:1 CSV-to-table comparison.
+SIMPLE_MASTER_TABLES = [
+    (table, filename) for table, filename in MASTER_TABLE_FILES if table != "input_catalog"
+]
+
+
+@pytest.mark.parametrize("table, filename", SIMPLE_MASTER_TABLES)
+def test_master_table_row_count(engine, master_data, table, filename):
+    expected = csv_row_count(EXAMPLES_DATA / filename)
+    assert count_rows(engine, table) == expected
+
+
+def test_input_catalog_row_count(engine, master_data):
+    expected = csv_row_count(EXAMPLES_DATA / "input_catalogs.csv") + csv_row_count(
+        EXAMPLES_DATA / "input_catalog_fluxstd.csv"
+    )
+    assert count_rows(engine, "input_catalog") == expected
+
+
+def test_fluxstd_input_catalog_registered(engine, master_data):
+    with engine.connect() as conn:
+        row = conn.execute(
+            text(
+                "SELECT input_catalog_name FROM input_catalog "
+                "WHERE input_catalog_id = 3006"
+            )
+        ).fetchone()
+    assert row is not None
+    assert row[0] == "Fstar_v3.3"
diff --git a/tests/integration/test_pointings.py b/tests/integration/test_pointings.py
new file mode 100644
index 0000000..84b4e1d
--- /dev/null
+++ b/tests/integration/test_pointings.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+"""Verify insert-pointings only creates user_pointing rows for catalogs
+flagged with is_user_pointing=True, and that the row count and catalog
+linkage are correct."""
+
+import pandas as pd
+from sqlalchemy import text
+
+from .conftest import TARGETS_DATA_DIR, count_rows, ecsv_row_count
+
+INPUT_CATALOGS_CSV = TARGETS_DATA_DIR / "example_input_catalogs.csv"
+
+
+def test_user_pointing_only_for_flagged_catalogs(engine, pointing_data, target_data):
+    catalogs_df = pd.read_csv(INPUT_CATALOGS_CSV)
+    flagged = catalogs_df[catalogs_df["is_user_pointing"]]
+    not_flagged = catalogs_df[~catalogs_df["is_user_pointing"]]
+    assert len(flagged) > 0, "test fixture data must include a user-pointing catalog"
+
+    local_dir = target_data["local_dir"]
+
+    with engine.connect() as conn:
+        for _, row in flagged.iterrows():
+            upload_dir = next(local_dir.glob(f"????????-??????-{row['upload_id']}"))
+            expected = ecsv_row_count(upload_dir / f"ppc_{row['upload_id']}.ecsv")
+
+            actual = conn.execute(
+                text(
+                    "SELECT count(*) FROM user_pointing up "
+                    "JOIN input_catalog c ON up.input_catalog_id = c.input_catalog_id "
+                    "WHERE c.upload_id = :upload_id"
+                ),
+                {"upload_id": row["upload_id"]},
+            ).scalar_one()
+            assert actual == expected
+
+        for _, row in not_flagged.iterrows():
+            actual = conn.execute(
+                text(
+                    "SELECT count(*) FROM user_pointing up "
+                    "JOIN input_catalog c ON up.input_catalog_id = c.input_catalog_id "
+                    "WHERE c.upload_id = :upload_id"
+                ),
+                {"upload_id": row["upload_id"]},
+            ).scalar_one()
+            assert actual == 0
+
+
+def test_user_pointing_total_matches_flagged_catalogs(engine, pointing_data, target_data):
+    catalogs_df = pd.read_csv(INPUT_CATALOGS_CSV)
+    flagged = catalogs_df[catalogs_df["is_user_pointing"]]
+
+    local_dir = target_data["local_dir"]
+    total_expected = 0
+    for _, row in flagged.iterrows():
+        upload_dir = next(local_dir.glob(f"????????-??????-{row['upload_id']}"))
+        total_expected += ecsv_row_count(upload_dir / f"ppc_{row['upload_id']}.ecsv")
+
+    assert count_rows(engine, "user_pointing") == total_expected
diff --git a/tests/integration/test_setup.py b/tests/integration/test_setup.py
new file mode 100644
index 0000000..a38041c
--- /dev/null
+++ b/tests/integration/test_setup.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+"""Verify the initial database setup: q3c extension and table creation."""
+
+from sqlalchemy import text
+
+from targetdb import models
+
+
+def test_q3c_extension_installed(engine, q3c_installed):
+    with engine.connect() as conn:
+        extnames = {row[0] for row in conn.execute(text("SELECT extname FROM pg_extension"))}
+    assert "q3c" in extnames
+
+
+def test_all_model_tables_created(engine, schema):
+    with engine.connect() as conn:
+        existing_tables = {
+            row[0]
+            for row in conn.execute(
+                text(
+                    "SELECT table_name FROM information_schema.tables "
+                    "WHERE table_schema = 'public'"
+                )
+            )
+        }
+
+    expected_tables = set(models.Base.metadata.tables.keys())
+    missing = expected_tables - existing_tables
+    assert not missing, f"Tables missing after create-schema: {sorted(missing)}"
diff --git a/tests/integration/test_targets.py b/tests/integration/test_targets.py
new file mode 100644
index 0000000..bdbbddd
--- /dev/null
+++ b/tests/integration/test_targets.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+"""
+Verify transfer-targets + insert-targets: local data is fetched for every
+catalog, and the resulting `target` rows match the transferred ECSV files
+and reference valid input_catalog/proposal/target_type rows.
+"""
+
+import pandas as pd
+import pytest
+from sqlalchemy import text
+
+from .conftest import TARGETS_DATA_DIR, count_rows, ecsv_row_count
+
+INPUT_CATALOGS_CSV = TARGETS_DATA_DIR / "example_input_catalogs.csv"
+
+
+@pytest.fixture(scope="module")
+def catalogs_df():
+    return pd.read_csv(INPUT_CATALOGS_CSV)
+
+
+def test_transfer_targets_downloads_all_catalogs(target_data, catalogs_df):
+    local_dir = target_data["local_dir"]
+    for upload_id in catalogs_df["upload_id"]:
+        matches = list(local_dir.glob(f"????????-??????-{upload_id}"))
+        assert len(matches) == 1, (
+            f"expected exactly one transferred data dir for upload_id={upload_id}, "
+            f"got {matches}"
+        )
+
+
+def test_input_catalogs_registered_with_upload_id(engine, target_data, catalogs_df):
+    with engine.connect() as conn:
+        rows = conn.execute(
+            text(
+                "SELECT input_catalog_name, upload_id FROM input_catalog "
+                "WHERE upload_id IS NOT NULL"
+            )
+        ).fetchall()
+    registered = {name: upload_id for name, upload_id in rows}
+
+    for _, row in catalogs_df.iterrows():
+        assert registered.get(row["input_catalog_name"]) == row["upload_id"]
+
+
+def test_target_row_count_matches_ecsv_inputs(engine, target_data):
+    local_dir = target_data["local_dir"]
+    total_expected = 0
+    for upload_dir in sorted(local_dir.glob("????????-??????-*")):
+        upload_id = upload_dir.name.split("-", 2)[2]
+        total_expected += ecsv_row_count(upload_dir / f"target_{upload_id}.ecsv")
+
+    assert count_rows(engine, "target") == total_expected
+
+
+def test_targets_reference_valid_foreign_keys(engine, target_data):
+    with engine.connect() as conn:
+        orphan_catalog = conn.execute(
+            text(
+                "SELECT count(*) FROM target t "
+                "LEFT JOIN input_catalog c ON t.input_catalog_id = c.input_catalog_id "
+                "WHERE c.input_catalog_id IS NULL"
+            )
+        ).scalar_one()
+        orphan_proposal = conn.execute(
+            text(
+                "SELECT count(*) FROM target t "
+                "LEFT JOIN proposal p ON t.proposal_id = p.proposal_id "
+                "WHERE t.proposal_id IS NOT NULL AND p.proposal_id IS NULL"
+            )
+        ).scalar_one()
+        orphan_target_type = conn.execute(
+            text(
+                "SELECT count(*) FROM target t "
+                "LEFT JOIN target_type tt ON t.target_type_id = tt.target_type_id "
+                "WHERE t.target_type_id IS NOT NULL AND tt.target_type_id IS NULL"
+            )
+        ).scalar_one()
+
+    assert orphan_catalog == 0
+    assert orphan_proposal == 0
+    assert orphan_target_type == 0
diff --git a/uv.lock b/uv.lock
index afcfb7d..b09118d 100644
--- a/uv.lock
+++ b/uv.lock
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 ]
 
+[[package]]
+name = "coverage"
+version = "7.15.3"
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