Merge pull request #16 from OpenDataServices/3-database

Save metadata about valid datasets to database

Author: tillywoodfield

README.md

@@ -7,6 +7,7 @@ A Python application to validate and store published OC4IDS datasets.
 ### Prerequisites
 
 - Python 3.12
+- Postgres
 
 ### Install Python requirements
 
@@ -16,6 +17,18 @@ source .venv/bin/activate
 pip install -r requirements_dev.txt
 ```
 
+### Set database enrivonment variable
+
+```
+export DATABASE_URL="postgresql://oc4ids_datastore@localhost/oc4ids_datastore"
+```
+
+### Run database migrations
+
+```
+alembic upgrade head
+```
+
 ### Run app
 
 ```
@@ -37,3 +50,9 @@ mypy oc4ids_datastore_pipeline/ tests/
 ```
 pytest
 ```
+
+### Generating new database migrations
+
+```
+alembic revision --autogenerate -m "<MESSAGE HERE>"
+```

alembic.ini

@@ -0,0 +1,116 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+# Use forward slashes (/) also on windows to provide an os agnostic path
+script_location = migrations
+
+# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
+# Uncomment the line below if you want the files to be prepended with date and time
+# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file
+# for all available tokens
+# file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python>=3.9 or backports.zoneinfo library and tzdata library.
+# Any required deps can installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to ZoneInfo()
+# leave blank for localtime
+# timezone =
+
+# max length of characters to apply to the "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; This defaults
+# to alembic/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "version_path_separator" below.
+# version_locations = %(here)s/bar:%(here)s/bat:alembic/versions
+
+# version path separator; As mentioned above, this is the character used to split
+# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep.
+# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas.
+# Valid values for version_path_separator are:
+#
+# version_path_separator = :
+# version_path_separator = ;
+# version_path_separator = space
+# version_path_separator = newline
+#
+# Use os.pathsep. Default configuration used for new projects.
+version_path_separator = os
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# new in Alembic version 1.10
+# recursive_version_locations = false
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 REVISION_SCRIPT_FILENAME
+
+# lint with attempts to fix using "ruff" - use the exec runner, execute a binary
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = %(here)s/.venv/bin/ruff
+# ruff.options = --fix REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARNING
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARNING
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migrations/README

@@ -0,0 +1 @@
+Generic single-database configuration.

migrations/env.py

@@ -0,0 +1,80 @@
+from logging.config import fileConfig
+import os
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+from alembic import context
+
+from oc4ids_datastore_pipeline.database import Base
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+target_metadata = Base.metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+config.set_main_option("sqlalchemy.url", os.environ["DATABASE_URL"])
+
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(connection=connection, target_metadata=target_metadata)
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

migrations/script.py.mako

@@ -0,0 +1,26 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision: str = ${repr(up_revision)}
+down_revision: Union[str, None] = ${repr(down_revision)}
+branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)}
+depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}

migrations/versions/aaabf849b37f_create_dataset_table.py

@@ -0,0 +1,39 @@
+"""create dataset table
+
+Revision ID: aaabf849b37f
+Revises:
+Create Date: 2025-02-04 17:14:46.411090
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "aaabf849b37f"
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "dataset",
+        sa.Column("dataset_id", sa.String(), nullable=False),
+        sa.Column("source_url", sa.String(), nullable=False),
+        sa.Column("publisher_name", sa.String(), nullable=False),
+        sa.Column("json_url", sa.String(), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), nullable=False),
+        sa.PrimaryKeyConstraint("dataset_id"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("dataset")
+    # ### end Alembic commands ###

oc4ids_datastore_pipeline/database.py

@@ -0,0 +1,42 @@
+import datetime
+import logging
+import os
+
+from sqlalchemy import (
+    DateTime,
+    Engine,
+    String,
+    create_engine,
+)
+from sqlalchemy.orm import DeclarativeBase, Mapped, Session, mapped_column
+
+logger = logging.getLogger(__name__)
+
+_engine = None
+
+
+class Base(DeclarativeBase):
+    pass
+
+
+class Dataset(Base):
+    __tablename__ = "dataset"
+
+    dataset_id: Mapped[str] = mapped_column(String, primary_key=True)
+    source_url: Mapped[str] = mapped_column(String)
+    publisher_name: Mapped[str] = mapped_column(String)
+    json_url: Mapped[str] = mapped_column(String)
+    updated_at: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True))
+
+
+def get_engine() -> Engine:
+    global _engine
+    if _engine is None:
+        _engine = create_engine(os.environ["DATABASE_URL"])
+    return _engine
+
+
+def save_dataset(dataset: Dataset) -> None:
+    with Session(get_engine()) as session:
+        session.merge(dataset)
+        session.commit()

oc4ids_datastore_pipeline/pipeline.py

@@ -1,3 +1,4 @@
+import datetime
 import json
 import logging
 import os
@@ -6,6 +7,8 @@
 import requests
 from libcoveoc4ids.api import oc4ids_json_output
 
+from oc4ids_datastore_pipeline.database import Dataset, save_dataset
+
 logger = logging.getLogger(__name__)
 
 
@@ -62,12 +65,34 @@ def write_json_to_file(file_name: str, json_data: Any) -> None:
         raise Exception("Error while writing to JSON file", e)
 
 
+def save_dataset_metadata(
+    dataset_name: str, source_url: str, publisher_name: str, file_name: str
+) -> None:
+    logger.info(f"Saving metadata for dataset {dataset_name}")
+    dataset = Dataset(
+        dataset_id=dataset_name,
+        source_url=source_url,
+        publisher_name=publisher_name,
+        json_url=file_name,
+        updated_at=datetime.datetime.now(datetime.UTC),
+    )
+    save_dataset(dataset)
+
+
 def process_dataset(dataset_name: str, dataset_url: str) -> None:
     logger.info(f"Processing dataset {dataset_name}")
     try:
         json_data = download_json(dataset_url)
         validate_json(dataset_name, json_data)
-        write_json_to_file(f"data/{dataset_name}.json", json_data)
+        file_name = f"data/{dataset_name}.json"
+        write_json_to_file(file_name, json_data)
+        publisher_name = json_data.get("publisher", {}).get("name", "")
+        save_dataset_metadata(
+            dataset_name=dataset_name,
+            source_url=dataset_url,
+            publisher_name=publisher_name,
+            file_name=file_name,
+        )
         logger.info(f"Processed dataset {dataset_name}")
     except Exception as e:
         logger.warning(f"Failed to process dataset {dataset_name} with error {e}")