diff --git a/.gitignore b/.gitignore index fb6f3e7..48d260a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,2 @@ .venv/ -src/__pycache__/ \ No newline at end of file +**/__pycache__/ \ No newline at end of file diff --git a/README.md b/README.md index 2dea3a5..966ca38 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,8 @@ - python 3.7 - postgresql 12 +# Known restrictions +- *models.py*, *schema.py*, and current representation of column headers in `headers` db table (as initialised by alembic migration script) **must** be kept in sync +- `SQALCHEMY_DATABASE_URL` in *database.py* and `sqlalchemy.url` in *alembic.ini* **must** be kept in sync + # Known issues -- ``` -ERROR: duplicate key value violates unique constraint "pg_type_typname_nsp_index" -DETAIL: Key (typname, typnamespace)=(headers, 2200) already exists. -``` -at the first database init. -https://www.postgresql.org/message-id/28194.1101582367%40sss.pgh.pa.us -Simple restart seems to fix it. -Use of Alembic might help \ No newline at end of file diff --git a/alembic.ini b/alembic.ini new file mode 100644 index 0000000..07b45c8 --- /dev/null +++ b/alembic.ini @@ -0,0 +1,105 @@ +# A generic, single database configuration. + +[alembic] +# path to migration scripts +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-dateutil library that can be +# installed by adding `alembic[tz]` to the pip requirements +# string value is passed to dateutil.tz.gettz() +# 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 migrations/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:migrations/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 = os # Use os.pathsep. Default configuration used for new projects. + +# the output encoding used when revision files +# are written from script.py.mako +# output_encoding = utf-8 + +sqlalchemy.url = postgresql+psycopg2://geodata:QAKvBKvLe4bS9U@postgres/geodata + + +[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 + +# Logging configuration +[loggers] +keys = root,sqlalchemy,alembic + +[handlers] +keys = console + +[formatters] +keys = generic + +[logger_root] +level = WARN +handlers = console +qualname = + +[logger_sqlalchemy] +level = WARN +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 diff --git a/migrations/README b/migrations/README new file mode 100644 index 0000000..98e4f9c --- /dev/null +++ b/migrations/README @@ -0,0 +1 @@ +Generic single-database configuration. \ No newline at end of file diff --git a/migrations/env.py b/migrations/env.py new file mode 100644 index 0000000..ecdd29a --- /dev/null +++ b/migrations/env.py @@ -0,0 +1,77 @@ +from logging.config import fileConfig + +from sqlalchemy import engine_from_config +from sqlalchemy import pool + +from alembic import context + +# 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 src.models import Base + +target_metadata = Base.metadata +# target_metadata = None + +# 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. + + +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() diff --git a/migrations/script.py.mako b/migrations/script.py.mako new file mode 100644 index 0000000..55df286 --- /dev/null +++ b/migrations/script.py.mako @@ -0,0 +1,24 @@ +"""${message} + +Revision ID: ${up_revision} +Revises: ${down_revision | comma,n} +Create Date: ${create_date} + +""" +from alembic import op +import sqlalchemy as sa +${imports if imports else ""} + +# revision identifiers, used by Alembic. +revision = ${repr(up_revision)} +down_revision = ${repr(down_revision)} +branch_labels = ${repr(branch_labels)} +depends_on = ${repr(depends_on)} + + +def upgrade() -> None: + ${upgrades if upgrades else "pass"} + + +def downgrade() -> None: + ${downgrades if downgrades else "pass"} diff --git a/migrations/versions/b76b7f791b3b_create_item_model.py b/migrations/versions/b76b7f791b3b_create_item_model.py new file mode 100644 index 0000000..25d9c9b --- /dev/null +++ b/migrations/versions/b76b7f791b3b_create_item_model.py @@ -0,0 +1,81 @@ +"""Create item model + +Revision ID: b76b7f791b3b +Revises: +Create Date: 2022-07-08 20:32:20.039600 + +""" +from alembic import op +import sqlalchemy as sa +from sqlalchemy.dialects import postgresql + +# revision identifiers, used by Alembic. +revision = "b76b7f791b3b" +down_revision = None +branch_labels = None +depends_on = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic ### + op.create_table( + "geodata", + sa.Column("id", sa.Integer(), nullable=False), + sa.Column("fadr", sa.String(), nullable=True), + sa.Column("internal_id", sa.String(), nullable=True), + sa.Column("x_coord", sa.String(), nullable=True), + sa.Column("y_coord", sa.String(), nullable=True), + sa.Column("gis_category", sa.String(), nullable=True), + sa.Column("category", sa.String(), nullable=True), + sa.Column("basin", sa.String(), nullable=True), + sa.Column("deposit", sa.String(), nullable=True), + sa.Column("well", sa.String(), nullable=True), + sa.Column("depth", sa.String(), nullable=True), + sa.Column("stratum", sa.String(), nullable=True), + sa.Column("owner", sa.String(), nullable=True), + sa.Column("org", sa.String(), nullable=True), + sa.Column("ownercontacts", sa.String(), nullable=True), + sa.Column("samplelist", sa.String(), nullable=True), + sa.Column("description", sa.String(), nullable=True), + sa.Column("form_dimentions", sa.String(), nullable=True), + sa.Column("datalist", sa.String(), nullable=True), + sa.Column("resolution", sa.String(), nullable=True), + sa.Column("date", sa.String(), nullable=True), + sa.Column("additional_info", sa.String(), nullable=True), + sa.Column("scanner", sa.String(), nullable=True), + sa.Column("comment", sa.String(), nullable=True), + sa.Column( + "geodata_search_ts", + postgresql.TSVECTOR(), + sa.Computed( + "to_tsvector('russian', coalesce(geodata.description, '') || ' ' || coalesce(geodata.additional_info, '') || ' ' || coalesce(geodata.comment, ''))", + persisted=True, + ), + nullable=True, + ), + sa.PrimaryKeyConstraint("id"), + ) + op.create_index( + "geodata_search_idx", + "geodata", + ["geodata_search_ts"], + unique=False, + postgresql_using="gin", + ) + op.create_index(op.f("ix_geodata_id"), "geodata", ["id"], unique=False) + op.create_table( + "headers", + sa.Column("database", sa.String(), nullable=False), + sa.Column("spreadsheet", sa.String(), nullable=True), + sa.PrimaryKeyConstraint("database"), + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table("headers") + op.drop_index(op.f("ix_geodata_id"), table_name="geodata") + op.drop_index("geodata_search_idx", table_name="geodata", postgresql_using="gin") + op.drop_table("geodata") + # ### end Alembic commands ### diff --git a/src/main.py b/src/main.py index 8f75d5b..37707b2 100644 --- a/src/main.py +++ b/src/main.py @@ -10,9 +10,6 @@ from . import crud, models, schemas, spreadsheet from .database import SessionLocal, engine -# TODO: switch for Alembic [2] -models.Base.metadata.create_all(bind=engine) - app = FastAPI() # Dependency diff --git a/src/requirements-dev.txt b/src/requirements-dev.txt index 13cac2b..9ee2a40 100644 --- a/src/requirements-dev.txt +++ b/src/requirements-dev.txt @@ -1,3 +1,4 @@ +alembic==1.8.0 anyio==3.5.0 asgiref==3.5.0 click==8.0.4 diff --git a/src/requirements.txt b/src/requirements.txt index f7ac231..5d244c8 100644 --- a/src/requirements.txt +++ b/src/requirements.txt @@ -1,3 +1,4 @@ +alembic==1.8.0 anyio==3.5.0 et-xmlfile==1.1.0 fastapi==0.74.1