add: alembic migration

v0.2
rrr-marble 4 years ago
parent 94570c0e0a
commit e91ebd714b

2
.gitignore vendored

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.venv/
src/__pycache__/
**/__pycache__/

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- 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

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# 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

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Generic single-database configuration.

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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()

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"""${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"}

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"""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 ###

@ -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

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alembic==1.8.0
anyio==3.5.0
asgiref==3.5.0
click==8.0.4

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alembic==1.8.0
anyio==3.5.0
et-xmlfile==1.1.0
fastapi==0.74.1

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