From aab0cd355a490f7cfbb2a314622f99e5d1946624 Mon Sep 17 00:00:00 2001 From: Ubuntu Date: Sun, 3 May 2026 00:04:18 +0000 Subject: [PATCH] feat(alembic): add initial schema migration for all SQLAlchemy models Initializes Alembic with autogenerated migration covering all 11 tables (tasks, users, projects, project_files, ontologies, graphs, simulations, reports, system_config, invitation_tokens, password_reset_tokens). Adds *.db to .gitignore to exclude local SQLite dev database. Co-Authored-By: Claude Sonnet 4.6 --- .gitignore | 3 + backend/alembic.ini | 149 ++++++++++++++ backend/alembic/README | 1 + backend/alembic/env.py | 48 +++++ backend/alembic/script.py.mako | 28 +++ .../versions/fef526537305_initial_schema.py | 183 ++++++++++++++++++ 6 files changed, 412 insertions(+) create mode 100644 backend/alembic.ini create mode 100644 backend/alembic/README create mode 100644 backend/alembic/env.py create mode 100644 backend/alembic/script.py.mako create mode 100644 backend/alembic/versions/fef526537305_initial_schema.py diff --git a/.gitignore b/.gitignore index 01976b09..adec5c25 100644 --- a/.gitignore +++ b/.gitignore @@ -58,6 +58,9 @@ backend/uploads/ # Docker 数据 data/ + +# SQLite local dev database +*.db # Git worktrees .worktrees/ diff --git a/backend/alembic.ini b/backend/alembic.ini new file mode 100644 index 00000000..bc496bd8 --- /dev/null +++ b/backend/alembic.ini @@ -0,0 +1,149 @@ +# A generic, single database configuration. + +[alembic] +# path to migration scripts. +# this is typically a path given in POSIX (e.g. forward slashes) +# format, relative to the token %(here)s which refers to the location of this +# ini file +script_location = %(here)s/alembic + +# 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 +# Or organize into date-based subdirectories (requires recursive_version_locations = true) +# file_template = %%(year)d/%%(month).2d/%%(day).2d_%%(hour).2d%%(minute).2d_%%(second).2d_%%(rev)s_%%(slug)s + +# sys.path path, will be prepended to sys.path if present. +# defaults to the current working directory. for multiple paths, the path separator +# is defined by "path_separator" below. +prepend_sys_path = . + + +# timezone to use when rendering the date within the migration file +# as well as the filename. +# If specified, requires the tzdata library which can be 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 /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 "path_separator" +# below. +# version_locations = %(here)s/bar:%(here)s/bat:%(here)s/alembic/versions + +# path_separator; This indicates what character is used to split lists of file +# paths, including version_locations and prepend_sys_path within configparser +# files such as alembic.ini. +# The default rendered in new alembic.ini files is "os", which uses os.pathsep +# to provide os-dependent path splitting. +# +# Note that in order to support legacy alembic.ini files, this default does NOT +# take place if path_separator is not present in alembic.ini. If this +# option is omitted entirely, fallback logic is as follows: +# +# 1. Parsing of the version_locations option falls back to using the legacy +# "version_path_separator" key, which if absent then falls back to the legacy +# behavior of splitting on spaces and/or commas. +# 2. Parsing of the prepend_sys_path option falls back to the legacy +# behavior of splitting on spaces, commas, or colons. +# +# Valid values for path_separator are: +# +# path_separator = : +# path_separator = ; +# path_separator = space +# path_separator = newline +# +# Use os.pathsep. Default configuration used for new projects. +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 + +# database URL. This is consumed by the user-maintained env.py script only. +# other means of configuring database URLs may be customized within the env.py +# file. +sqlalchemy.url = sqlite:///mirofish_dev.db + + +[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 module runner, against the "ruff" module +# hooks = ruff +# ruff.type = module +# ruff.module = ruff +# ruff.options = check --fix REVISION_SCRIPT_FILENAME + +# Alternatively, use the exec runner to execute a binary found on your PATH +# hooks = ruff +# ruff.type = exec +# ruff.executable = ruff +# ruff.options = check --fix REVISION_SCRIPT_FILENAME + +# Logging configuration. This is also consumed by the user-maintained +# env.py script only. +[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 diff --git a/backend/alembic/README b/backend/alembic/README new file mode 100644 index 00000000..98e4f9c4 --- /dev/null +++ b/backend/alembic/README @@ -0,0 +1 @@ +Generic single-database configuration. \ No newline at end of file diff --git a/backend/alembic/env.py b/backend/alembic/env.py new file mode 100644 index 00000000..d880d84f --- /dev/null +++ b/backend/alembic/env.py @@ -0,0 +1,48 @@ +# backend/alembic/env.py +import os +import sys +from logging.config import fileConfig +from sqlalchemy import engine_from_config, pool +from alembic import context + +# Afegir el backend al path perquè els imports funcionin +sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..')) + +from app.db import Base +import app.models.db_models # noqa: F401 — registra tots els models al Base + +config = context.config + +# Llegir DATABASE_URL de l'entorn (prioritat sobre alembic.ini) +db_url = os.environ.get('DATABASE_URL', config.get_main_option('sqlalchemy.url')) +config.set_main_option('sqlalchemy.url', db_url) + +if config.config_file_name is not None: + fileConfig(config.config_file_name) + +target_metadata = Base.metadata + + +def run_migrations_offline(): + url = config.get_main_option("sqlalchemy.url") + context.configure(url=url, target_metadata=target_metadata, literal_binds=True) + with context.begin_transaction(): + context.run_migrations() + + +def run_migrations_online(): + 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/backend/alembic/script.py.mako b/backend/alembic/script.py.mako new file mode 100644 index 00000000..11016301 --- /dev/null +++ b/backend/alembic/script.py.mako @@ -0,0 +1,28 @@ +"""${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, Sequence[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: + """Upgrade schema.""" + ${upgrades if upgrades else "pass"} + + +def downgrade() -> None: + """Downgrade schema.""" + ${downgrades if downgrades else "pass"} diff --git a/backend/alembic/versions/fef526537305_initial_schema.py b/backend/alembic/versions/fef526537305_initial_schema.py new file mode 100644 index 00000000..b347eb68 --- /dev/null +++ b/backend/alembic/versions/fef526537305_initial_schema.py @@ -0,0 +1,183 @@ +"""initial_schema + +Revision ID: fef526537305 +Revises: +Create Date: 2026-05-03 00:03:51.173534 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'fef526537305' +down_revision: Union[str, Sequence[str], None] = None +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('tasks', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('task_type', sa.String(length=100), nullable=False), + sa.Column('entity_type', sa.String(length=50), nullable=True), + sa.Column('entity_id', sa.String(length=36), nullable=True), + sa.Column('status', sa.String(length=20), nullable=False), + sa.Column('progress', sa.Integer(), nullable=False), + sa.Column('message', sa.Text(), nullable=True), + sa.Column('result', sa.JSON(), nullable=True), + sa.Column('error', sa.Text(), nullable=True), + sa.Column('progress_detail', sa.JSON(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.Column('updated_at', sa.DateTime(), nullable=False), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('users', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('email', sa.String(length=255), nullable=False), + sa.Column('name', sa.String(length=255), nullable=False), + sa.Column('password_hash', sa.Text(), nullable=True), + sa.Column('role', sa.String(length=20), nullable=False), + sa.Column('status', sa.String(length=20), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.Column('updated_at', sa.DateTime(), nullable=False), + sa.PrimaryKeyConstraint('id'), + sa.UniqueConstraint('email') + ) + op.create_table('invitation_tokens', + sa.Column('token', sa.String(length=36), nullable=False), + sa.Column('user_id', sa.String(length=36), nullable=False), + sa.Column('expires_at', sa.DateTime(), nullable=False), + sa.Column('used_at', sa.DateTime(), nullable=True), + sa.ForeignKeyConstraint(['user_id'], ['users.id'], ondelete='CASCADE'), + sa.PrimaryKeyConstraint('token') + ) + op.create_table('password_reset_tokens', + sa.Column('token', sa.String(length=36), nullable=False), + sa.Column('user_id', sa.String(length=36), nullable=False), + sa.Column('expires_at', sa.DateTime(), nullable=False), + sa.Column('used_at', sa.DateTime(), nullable=True), + sa.ForeignKeyConstraint(['user_id'], ['users.id'], ondelete='CASCADE'), + sa.PrimaryKeyConstraint('token') + ) + op.create_table('projects', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('user_id', sa.String(length=36), nullable=True), + sa.Column('name', sa.String(length=255), nullable=False), + sa.Column('status', sa.String(length=50), nullable=False), + sa.Column('analysis_summary', sa.Text(), nullable=True), + sa.Column('simulation_requirement', sa.Text(), nullable=True), + sa.Column('chunk_size', sa.Integer(), nullable=False), + sa.Column('chunk_overlap', sa.Integer(), nullable=False), + sa.Column('active_task_id', sa.String(length=36), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.Column('updated_at', sa.DateTime(), nullable=False), + sa.ForeignKeyConstraint(['active_task_id'], ['tasks.id'], ondelete='SET NULL'), + sa.ForeignKeyConstraint(['user_id'], ['users.id'], ondelete='CASCADE'), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('system_config', + sa.Column('key', sa.String(length=100), nullable=False), + sa.Column('value', sa.Text(), nullable=True), + sa.Column('value_type', sa.String(length=20), nullable=False), + sa.Column('group', sa.String(length=50), nullable=False), + sa.Column('label', sa.String(length=255), nullable=False), + sa.Column('description', sa.Text(), nullable=False), + sa.Column('is_secret', sa.Boolean(), nullable=False), + sa.Column('updated_at', sa.DateTime(), nullable=False), + sa.Column('updated_by', sa.String(length=36), nullable=True), + sa.ForeignKeyConstraint(['updated_by'], ['users.id'], ondelete='SET NULL'), + sa.PrimaryKeyConstraint('key') + ) + op.create_table('ontologies', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('project_id', sa.String(length=36), nullable=False), + sa.Column('version', sa.Integer(), nullable=False), + sa.Column('entity_types', sa.JSON(), nullable=True), + sa.Column('edge_types', sa.JSON(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.ForeignKeyConstraint(['project_id'], ['projects.id'], ondelete='CASCADE'), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('project_files', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('project_id', sa.String(length=36), nullable=False), + sa.Column('original_name', sa.String(length=255), nullable=False), + sa.Column('storage_path', sa.Text(), nullable=False), + sa.Column('size', sa.Integer(), nullable=False), + sa.Column('mime_type', sa.String(length=100), nullable=False), + sa.Column('file_type', sa.String(length=30), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.ForeignKeyConstraint(['project_id'], ['projects.id'], ondelete='CASCADE'), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('graphs', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('project_id', sa.String(length=36), nullable=False), + sa.Column('ontology_id', sa.String(length=36), nullable=True), + sa.Column('backend', sa.String(length=20), nullable=False), + sa.Column('external_id', sa.Text(), nullable=True), + sa.Column('status', sa.String(length=20), nullable=False), + sa.Column('node_count', sa.Integer(), nullable=True), + sa.Column('edge_count', sa.Integer(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.Column('updated_at', sa.DateTime(), nullable=False), + sa.ForeignKeyConstraint(['ontology_id'], ['ontologies.id'], ondelete='SET NULL'), + sa.ForeignKeyConstraint(['project_id'], ['projects.id'], ondelete='CASCADE'), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('simulations', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('project_id', sa.String(length=36), nullable=False), + sa.Column('graph_id', sa.String(length=36), nullable=True), + sa.Column('status', sa.String(length=30), nullable=False), + sa.Column('platform', sa.String(length=20), nullable=False), + sa.Column('config', sa.JSON(), nullable=True), + sa.Column('profiles_path', sa.Text(), nullable=True), + sa.Column('db_path', sa.Text(), nullable=True), + sa.Column('actions_path', sa.Text(), nullable=True), + sa.Column('rounds_total', sa.Integer(), nullable=True), + sa.Column('rounds_completed', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.Column('updated_at', sa.DateTime(), nullable=False), + sa.ForeignKeyConstraint(['graph_id'], ['graphs.id'], ondelete='SET NULL'), + sa.ForeignKeyConstraint(['project_id'], ['projects.id'], ondelete='CASCADE'), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('reports', + sa.Column('id', sa.String(length=36), nullable=False), + sa.Column('project_id', sa.String(length=36), nullable=False), + sa.Column('simulation_id', sa.String(length=36), nullable=True), + sa.Column('graph_id', sa.String(length=36), nullable=True), + sa.Column('status', sa.String(length=30), nullable=False), + sa.Column('outline', sa.JSON(), nullable=True), + sa.Column('storage_prefix', sa.Text(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.Column('updated_at', sa.DateTime(), nullable=False), + sa.ForeignKeyConstraint(['graph_id'], ['graphs.id'], ondelete='SET NULL'), + sa.ForeignKeyConstraint(['project_id'], ['projects.id'], ondelete='CASCADE'), + sa.ForeignKeyConstraint(['simulation_id'], ['simulations.id'], ondelete='SET NULL'), + sa.PrimaryKeyConstraint('id') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('reports') + op.drop_table('simulations') + op.drop_table('graphs') + op.drop_table('project_files') + op.drop_table('ontologies') + op.drop_table('system_config') + op.drop_table('projects') + op.drop_table('password_reset_tokens') + op.drop_table('invitation_tokens') + op.drop_table('users') + op.drop_table('tasks') + # ### end Alembic commands ###