Merge branch 'staging' into well-inventory-csv

Author: jirhiker

AGENTS.MD

@@ -21,7 +21,11 @@ these transfers, keep the following rules in mind to avoid hour-long runs:
   right instance before running destructive suites.
 - When done, `deactivate` to exit the venv and avoid polluting other shells.
 
+## 3. Data migrations must be idempotent
+- Data migrations should be safe to re-run without creating duplicate rows or corrupting data.
+- Use upserts or duplicate checks and update source fields only after successful inserts.
+
 Following this playbook keeps ETL runs measured in seconds/minutes instead of hours. EOF
 
 ## Activate python venv
-Always use `source .venv/bin/activate` to activate the venv running python
+Always use `source .venv/bin/activate` to activate the venv running python

cli/cli.py

@@ -13,42 +13,57 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ===============================================================================
-import click
+from enum import Enum
+from pathlib import Path
+
+import typer
 from dotenv import load_dotenv
 
 load_dotenv()
 
+cli = typer.Typer(help="Command line interface for managing the application.")
+water_levels = typer.Typer(help="Water-level utilities")
+data_migrations = typer.Typer(help="Data migration utilities")
+cli.add_typer(water_levels, name="water-levels")
+cli.add_typer(data_migrations, name="data-migrations")
+
 
-@click.group()
-def cli():
-    """Command line interface for managing the application."""
-    pass
+class OutputFormat(str, Enum):
+    json = "json"
 
 
-@cli.command()
+@cli.command("initialize-lexicon")
 def initialize_lexicon():
     from core.initializers import init_lexicon
 
     init_lexicon()
 
 
-@cli.command()
-@click.argument(
-    "root_directory",
-    type=click.Path(exists=True, file_okay=False, dir_okay=True, readable=True),
-)
-def associate_assets_command(root_directory: str):
+@cli.command("associate-assets")
+def associate_assets_command(
+    root_directory: str = typer.Argument(
+        ...,
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+    )
+):
     from cli.service_adapter import associate_assets
 
     associate_assets(root_directory)
 
 
-@cli.command()
-@click.argument(
-    "file_path",
-    type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True),
-)
-def well_inventory_csv(file_path: str):
+@cli.command("well-inventory-csv")
+def well_inventory_csv(
+    file_path: str = typer.Argument(
+        ...,
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        readable=True,
+    )
+):
     """
     parse and upload a csv to database
     """
@@ -58,38 +73,143 @@ def well_inventory_csv(file_path: str):
     well_inventory_csv(file_path)
 
 
-@cli.group()
-def water_levels():
-    """Water-level utilities"""
-    pass
-
-
 @water_levels.command("bulk-upload")
-@click.option(
-    "--file",
-    "file_path",
-    type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True),
-    required=True,
-    help="Path to CSV file containing water level rows",
-)
-@click.option(
-    "--output",
-    "output_format",
-    type=click.Choice(["json"], case_sensitive=False),
-    default=None,
-    help="Optional output format",
-)
-def water_levels_bulk_upload(file_path: str, output_format: str | None):
+def water_levels_bulk_upload(
+    file_path: str = typer.Option(
+        ...,
+        "--file",
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        readable=True,
+        help="Path to CSV file containing water level rows",
+    ),
+    output_format: OutputFormat | None = typer.Option(
+        None,
+        "--output",
+        help="Optional output format",
+    ),
+):
     """
     parse and upload a csv
     """
     # TODO: use the same helper function used by api to parse and upload a WL csv
     from cli.service_adapter import water_levels_csv
 
-    pretty_json = (output_format or "").lower() == "json"
+    pretty_json = output_format == OutputFormat.json
     water_levels_csv(file_path, pretty_json=pretty_json)
 
 
+@data_migrations.command("list")
+def data_migrations_list():
+    from data_migrations.registry import list_migrations
+
+    migrations = list_migrations()
+    if not migrations:
+        typer.echo("No data migrations registered.")
+        return
+    for migration in migrations:
+        repeatable = " (repeatable)" if migration.is_repeatable else ""
+        typer.echo(f"{migration.id}: {migration.name}{repeatable}")
+
+
+@data_migrations.command("status")
+def data_migrations_status():
+    from db.engine import session_ctx
+    from data_migrations.runner import get_status
+
+    with session_ctx() as session:
+        statuses = get_status(session)
+    if not statuses:
+        typer.echo("No data migrations registered.")
+        return
+    for status in statuses:
+        last_applied = (
+            status.last_applied_at.isoformat() if status.last_applied_at else "never"
+        )
+        typer.echo(
+            f"{status.id}: applied {status.applied_count} time(s), last={last_applied}"
+        )
+
+
+@data_migrations.command("run")
+def data_migrations_run(
+    migration_id: str = typer.Argument(...),
+    force: bool = typer.Option(
+        False, "--force", help="Re-run even if already applied."
+    ),
+):
+    from db.engine import session_ctx
+    from data_migrations.runner import run_migration_by_id
+
+    with session_ctx() as session:
+        ran = run_migration_by_id(session, migration_id, force=force)
+    typer.echo("applied" if ran else "skipped")
+
+
+@data_migrations.command("run-all")
+def data_migrations_run_all(
+    include_repeatable: bool = typer.Option(
+        False,
+        "--include-repeatable/--exclude-repeatable",
+        help="Whether to include repeatable migrations.",
+    ),
+    force: bool = typer.Option(
+        False, "--force", help="Re-run non-repeatable migrations."
+    ),
+):
+    from db.engine import session_ctx
+    from data_migrations.runner import run_all
+
+    with session_ctx() as session:
+        ran = run_all(session, include_repeatable=include_repeatable, force=force)
+    typer.echo(f"applied {len(ran)} migration(s)")
+
+
+@cli.command("alembic-upgrade-and-data")
+def alembic_upgrade_and_data(
+    revision: str = typer.Argument("head"),
+    include_repeatable: bool = typer.Option(
+        False,
+        "--include-repeatable/--exclude-repeatable",
+        help="Whether to include repeatable migrations.",
+    ),
+    force: bool = typer.Option(
+        False, "--force", help="Re-run non-repeatable migrations."
+    ),
+):
+    from alembic import command
+    from alembic.config import Config
+    from alembic.runtime.migration import MigrationContext
+    from alembic.script import ScriptDirectory
+    from db.engine import engine, session_ctx
+    from data_migrations.runner import run_all
+
+    root = Path(__file__).resolve().parents[1]
+    cfg = Config(str(root / "alembic.ini"))
+    cfg.set_main_option("script_location", str(root / "alembic"))
+
+    command.upgrade(cfg, revision)
+
+    with engine.connect() as conn:
+        context = MigrationContext.configure(conn)
+        heads = context.get_current_heads()
+        script = ScriptDirectory.from_config(cfg)
+        applied_revisions: set[str] = set()
+        for head in heads:
+            for rev in script.iterate_revisions(head, "base"):
+                applied_revisions.add(rev.revision)
+
+    with session_ctx() as session:
+        ran = run_all(
+            session,
+            include_repeatable=include_repeatable,
+            force=force,
+            allowed_alembic_revisions=applied_revisions,
+        )
+    typer.echo(f"applied {len(ran)} migration(s)")
+
+
 if __name__ == "__main__":
     cli()
 

data_migrations/__init__.py

@@ -0,0 +1 @@
+# Data migrations package

data_migrations/base.py

@@ -0,0 +1,29 @@
+# ===============================================================================
+# Copyright 2026 ross
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ===============================================================================
+from dataclasses import dataclass
+from typing import Callable
+
+from sqlalchemy.orm import Session
+
+
+@dataclass(frozen=True)
+class DataMigration:
+    id: str
+    alembic_revision: str
+    name: str
+    description: str
+    run: Callable[[Session], None]
+    is_repeatable: bool = False

data_migrations/migrations/20260205_0001_move_nma_location_notes.py

@@ -0,0 +1,94 @@
+# ===============================================================================
+# Copyright 2026 ross
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ===============================================================================
+from sqlalchemy import insert, select, update
+from sqlalchemy.orm import Session
+
+from data_migrations.base import DataMigration
+from db.location import Location
+from db.notes import Notes
+
+NOTE_TYPE = "General"
+BATCH_SIZE = 1000
+
+
+def _iter_location_notes(session: Session):
+    stmt = select(
+        Location.id,
+        Location.nma_location_notes,
+        Location.release_status,
+    ).where(Location.nma_location_notes.isnot(None))
+    for row in session.execute(stmt):
+        note = (row.nma_location_notes or "").strip()
+        if not note:
+            continue
+        yield row.id, note, row.release_status
+
+
+def run(session: Session) -> None:
+    buffer: list[tuple[int, str, str]] = []
+    for item in _iter_location_notes(session):
+        buffer.append(item)
+        if len(buffer) >= BATCH_SIZE:
+            _flush_batch(session, buffer)
+            buffer.clear()
+    if buffer:
+        _flush_batch(session, buffer)
+
+
+def _flush_batch(session: Session, batch: list[tuple[int, str, str]]) -> None:
+    location_ids = [row[0] for row in batch]
+    existing = session.execute(
+        select(Notes.target_id, Notes.content).where(
+            Notes.target_table == "location",
+            Notes.note_type == NOTE_TYPE,
+            Notes.target_id.in_(location_ids),
+        )
+    ).all()
+    existing_set = {(row.target_id, row.content) for row in existing}
+
+    inserts = []
+    for location_id, note, release_status in batch:
+        if (location_id, note) in existing_set:
+            continue
+        inserts.append(
+            {
+                "target_id": location_id,
+                "target_table": "location",
+                "note_type": NOTE_TYPE,
+                "content": note,
+                "release_status": release_status or "draft",
+            }
+        )
+
+    if inserts:
+        session.execute(insert(Notes), inserts)
+
+    session.execute(
+        update(Location)
+        .where(Location.id.in_(location_ids))
+        .values(nma_location_notes=None)
+    )
+    session.commit()
+
+
+MIGRATION = DataMigration(
+    id="20260205_0001_move_nma_location_notes",
+    alembic_revision="f0c9d8e7b6a5",
+    name="Move NMA location notes to Notes table",
+    description="Backfill polymorphic notes from Location.nma_location_notes.",
+    run=run,
+    is_repeatable=False,
+)

data_migrations/migrations/__init__.py

@@ -0,0 +1 @@
+# Data migrations live here.