From dc717b1135dd3b2f0bb03d6aa6c2cbe9ecdf9992 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 26 Sep 2024 19:06:06 -0600 Subject: [PATCH 1/5] Add support for database migrations and our first migration --- Dockerfile | 4 +- alembic.ini | 118 + compose.dev.yml | 1 + conda-lock.yml | 4023 ++++++++++------- doc/how-to/development.md | 41 + environment.yml | 2 + migrations/README | 1 + migrations/env.py | 86 + migrations/script.py.mako | 26 + ..._increase_length_of_description_columns.py | 55 + pyproject.toml | 1 + usaon_benefit_tool/util/db/connect.py | 44 +- 12 files changed, 2863 insertions(+), 1539 deletions(-) create mode 100644 alembic.ini create mode 100644 migrations/README create mode 100644 migrations/env.py create mode 100644 migrations/script.py.mako create mode 100644 migrations/versions/fafa3da67d5e_increase_length_of_description_columns.py diff --git a/Dockerfile b/Dockerfile index cd67b574..0820426b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -19,10 +19,12 @@ RUN micromamba install -y \ # Install source +COPY ./usaon_benefit_tool ./usaon_benefit_tool COPY ./pyproject.toml . COPY ./tasks ./tasks COPY ./scripts ./scripts -COPY ./usaon_benefit_tool ./usaon_benefit_tool +COPY ./migrations ./migrations +COPY ./alembic.ini . ENV FLASK_APP=usaon_benefit_tool diff --git a/alembic.ini b/alembic.ini new file mode 100644 index 00000000..bbb655f6 --- /dev/null +++ b/alembic.ini @@ -0,0 +1,118 @@ +# 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. +# 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 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 = newline +version_path_separator = os # Use os.pathsep. Default configuration used for new projects. + +# 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 + +# IMPORTANT: Populated in env.py dynamically +sqlalchemy.url = fakeurl + + +[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 = 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/compose.dev.yml b/compose.dev.yml index b46c3bd9..c19ddab1 100644 --- a/compose.dev.yml +++ b/compose.dev.yml @@ -31,6 +31,7 @@ services: user: "root" volumes: - "./usaon_benefit_tool:/usaon-benefit-tool/usaon_benefit_tool:ro" + - "./migrations:/usaon-benefit-tool/migrations:rw" - "./tasks:/usaon-benefit-tool/tasks:ro" ports: - "5000:5000" diff --git a/conda-lock.yml b/conda-lock.yml index 5e150461..6b0891e5 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -5,7 +5,7 @@ # available, unless you explicitly update the lock file. # # Install this environment as "YOURENV" with: -# conda-lock install -n YOURENV --file conda-lock.yml +# conda-lock install -n YOURENV conda-lock.yml # To update a single package to the latest version compatible with the version constraints in the source: # conda-lock lock --lockfile conda-lock.yml --update PACKAGE # To re-solve the entire environment, e.g. after changing a version constraint in the source file: @@ -13,8 +13,8 @@ version: 1 metadata: content_hash: - linux-64: 3da44b57daf299d306c853cd8176e59173bb5ae6df73a4333e849eb4747123ff - osx-64: be6d51e454ebe122b02a1b1304f362f5db37a669c24239db85b3e8e61757f9f4 + linux-64: a7e801de82070f5a60c7a2f75e7599f23f8423ad8a4d79e732a17845db2f762f + osx-64: 8ff94bd88c0cd6c04539047dc965d9b4bd6031bc54c6edbeb169737d2629cd7a channels: - url: conda-forge used_env_vars: [] @@ -48,6 +48,40 @@ package: sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22 category: main optional: false +- name: alembic + version: 1.13.3 + manager: conda + platform: linux-64 + dependencies: + importlib-metadata: '' + importlib_resources: '' + mako: '' + python: '>=3.8' + sqlalchemy: '>=1.3.0' + typing-extensions: '>=4' + url: https://conda.anaconda.org/conda-forge/noarch/alembic-1.13.3-pyhd8ed1ab_0.conda + hash: + md5: c81dc0d6ce99cf5c46e8b27dc37b5a75 + sha256: 7e61183ef0476f6e568e7021ba2abe0a566aaf1b9263575838fec6cb50d5eb42 + category: main + optional: false +- name: alembic + version: 1.13.3 + manager: conda + platform: osx-64 + dependencies: + importlib-metadata: '' + importlib_resources: '' + mako: '' + python: '>=3.8' + sqlalchemy: '>=1.3.0' + typing-extensions: '>=4' + url: https://conda.anaconda.org/conda-forge/noarch/alembic-1.13.3-pyhd8ed1ab_0.conda + hash: + md5: c81dc0d6ce99cf5c46e8b27dc37b5a75 + sha256: 7e61183ef0476f6e568e7021ba2abe0a566aaf1b9263575838fec6cb50d5eb42 + category: main + optional: false - name: amqp version: 5.2.0 manager: conda @@ -75,35 +109,59 @@ package: category: main optional: false - name: anyio - version: 4.3.0 + version: 4.6.0 manager: conda platform: linux-64 dependencies: exceptiongroup: '>=1.0.2' idna: '>=2.8' - python: '>=3.8' + python: '>=3.9' sniffio: '>=1.1' typing_extensions: '>=4.1' - url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.3.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.6.0-pyhd8ed1ab_1.conda hash: - md5: ac95aa8ed65adfdde51132595c79aade - sha256: 86aca4a31c09f9b4dbdb332cd9a6a7dbab62ca734d3f832651c0ab59c6a7f52e + md5: bc13891a047f50728b03595531f7f92e + sha256: d05493abca6ac1b0cb15f5d48c3117bddd73cc21e48bfcb460570cfa2ea2f909 category: main optional: false - name: anyio - version: 4.3.0 + version: 4.6.0 manager: conda platform: osx-64 dependencies: - python: '>=3.8' + python: '>=3.9' sniffio: '>=1.1' typing_extensions: '>=4.1' idna: '>=2.8' exceptiongroup: '>=1.0.2' - url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.3.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.6.0-pyhd8ed1ab_1.conda + hash: + md5: bc13891a047f50728b03595531f7f92e + sha256: d05493abca6ac1b0cb15f5d48c3117bddd73cc21e48bfcb460570cfa2ea2f909 + category: main + optional: false +- name: appdirs + version: 1.4.4 + manager: conda + platform: linux-64 + dependencies: + python: '' + url: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2 + hash: + md5: 5f095bc6454094e96f146491fd03633b + sha256: ae9fb8f68281f84482f2c234379aa12405a9e365151d43af20b3ae1f17312111 + category: main + optional: false +- name: appdirs + version: 1.4.4 + manager: conda + platform: osx-64 + dependencies: + python: '' + url: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2 hash: - md5: ac95aa8ed65adfdde51132595c79aade - sha256: 86aca4a31c09f9b4dbdb332cd9a6a7dbab62ca734d3f832651c0ab59c6a7f52e + md5: 5f095bc6454094e96f146491fd03633b + sha256: ae9fb8f68281f84482f2c234379aa12405a9e365151d43af20b3ae1f17312111 category: main optional: false - name: appnope @@ -151,14 +209,15 @@ package: manager: conda platform: linux-64 dependencies: + __glibc: '>=2.17,<3.0.a0' cffi: '>=1.0.1' - libgcc-ng: '>=12' + libgcc: '>=13' python: '>=3.11,<3.12.0a0' python_abi: 3.11.* - url: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-21.2.0-py311h459d7ec_4.conda + url: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-21.2.0-py311h9ecbd09_5.conda hash: - md5: de5b16869a430949b02161b04b844a30 - sha256: 104194af519b4e667aa5341068b94b521a791aaaa05ec0091f8f0bdba43a60ac + md5: 18143eab7fcd6662c604b85850f0db1e + sha256: d1af1fbcb698c2e07b0d1d2b98384dd6021fa55c8bcb920e3652e0b0c393881b category: main optional: false - name: argon2-cffi-bindings @@ -166,13 +225,14 @@ package: manager: conda platform: osx-64 dependencies: + __osx: '>=10.13' cffi: '>=1.0.1' python: '>=3.11,<3.12.0a0' python_abi: 3.11.* - url: https://conda.anaconda.org/conda-forge/osx-64/argon2-cffi-bindings-21.2.0-py311h2725bcf_4.conda + url: https://conda.anaconda.org/conda-forge/osx-64/argon2-cffi-bindings-21.2.0-py311h3336109_5.conda hash: - md5: e2aba0ad0f533ee73f9d4330d2e32549 - sha256: be27659496bcb660fc9c3f5f74128a7bb090336897e9c7cfbcc55ae66f13b8d8 + md5: 29b46bd410067f668c4cef7fdc78fe25 + sha256: fa5eb633b320e10fc2138f3d842d8a8ca72815f106acbab49a68ec9783e4d70d category: main optional: false - name: arrow @@ -256,27 +316,27 @@ package: category: main optional: false - name: attrs - version: 23.2.0 + version: 24.2.0 manager: conda platform: linux-64 dependencies: python: '>=3.7' - url: https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda hash: - md5: 5e4c0743c70186509d1412e03c2d8dfa - sha256: 77c7d03bdb243a048fff398cedc74327b7dc79169ebe3b4c8448b0331ea55fea + md5: 6732fa52eb8e66e5afeb32db8701a791 + sha256: 28dba85a7e0f7fb57d7315e13f603d1e41b83c5b88aa2a602596b52c833a2ff8 category: main optional: false - name: attrs - version: 23.2.0 + version: 24.2.0 manager: conda platform: osx-64 dependencies: python: '>=3.7' - url: https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda hash: - md5: 5e4c0743c70186509d1412e03c2d8dfa - sha256: 77c7d03bdb243a048fff398cedc74327b7dc79169ebe3b4c8448b0331ea55fea + md5: 6732fa52eb8e66e5afeb32db8701a791 + sha256: 28dba85a7e0f7fb57d7315e13f603d1e41b83c5b88aa2a602596b52c833a2ff8 category: main optional: false - name: babel @@ -307,6 +367,56 @@ package: sha256: 8584e3da58e92b72641c89ff9b98c51f0d5dbe76e527867804cbdf03ac91d8e6 category: main optional: false +- name: backports + version: '1.0' + manager: conda + platform: linux-64 + dependencies: + python: '>=3' + url: https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_4.conda + hash: + md5: 67bdebbc334513034826e9b63f769d4c + sha256: 31b51537ce7d2ba8b5b3d0095f1813711884304ac1701bc55938ca75f6c82e19 + category: main + optional: false +- name: backports + version: '1.0' + manager: conda + platform: osx-64 + dependencies: + python: '>=3' + url: https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_4.conda + hash: + md5: 67bdebbc334513034826e9b63f769d4c + sha256: 31b51537ce7d2ba8b5b3d0095f1813711884304ac1701bc55938ca75f6c82e19 + category: main + optional: false +- name: backports.tarfile + version: 1.0.0 + manager: conda + platform: linux-64 + dependencies: + backports: '' + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/backports.tarfile-1.0.0-pyhd8ed1ab_1.conda + hash: + md5: c747b1d79f136013c3b7ebcba876afa6 + sha256: 7ba30f32daad2e7ca251508525185ba170eedc14123572611c2acf261c7956b3 + category: main + optional: false +- name: backports.tarfile + version: 1.0.0 + manager: conda + platform: osx-64 + dependencies: + backports: '' + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/backports.tarfile-1.0.0-pyhd8ed1ab_1.conda + hash: + md5: c747b1d79f136013c3b7ebcba876afa6 + sha256: 7ba30f32daad2e7ca251508525185ba170eedc14123572611c2acf261c7956b3 + category: main + optional: false - name: backports.zoneinfo version: 0.2.1 manager: conda @@ -314,10 +424,10 @@ package: dependencies: python: '>=3.11,<3.12.0a0' python_abi: 3.11.* - url: https://conda.anaconda.org/conda-forge/linux-64/backports.zoneinfo-0.2.1-py311h38be061_8.conda + url: https://conda.anaconda.org/conda-forge/linux-64/backports.zoneinfo-0.2.1-py311h38be061_9.conda hash: - md5: 5384590f14dfe6ccd02811236afc9f8e - sha256: 1708c5e6729567f30ccde7761492cb43ee72fa2f7d5065b9102785278718505b + md5: 6ba5ba862ef1fa30e87292df09e6b73b + sha256: 93421eeeeb909cd8c8339afdb3fc2fcfe438219e6528c8593d555906e0eac511 category: main optional: false - name: backports.zoneinfo @@ -327,10 +437,10 @@ package: dependencies: python: '>=3.11,<3.12.0a0' python_abi: 3.11.* - url: https://conda.anaconda.org/conda-forge/osx-64/backports.zoneinfo-0.2.1-py311h6eed73b_8.conda + url: https://conda.anaconda.org/conda-forge/osx-64/backports.zoneinfo-0.2.1-py311h6eed73b_9.conda hash: - md5: 82f37234dbc0254423c109e9e21ce332 - sha256: f6064fc69833fed6d02738d29132bc87a6195098ec74257f53044de306694ff3 + md5: bad08123d75515ac39d82dbca34ca8fc + sha256: d503a07b251d4ce7bc372ec9ce7617c349919d96222e6c8127c09c7bf5939d04 category: main optional: false - 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Migrations themselves live in +`migrations/versions/` directories. They are named with unique identifiers, and they are +**not in chronological order**. The migration script itself contains information about +its dependencies. Each migration depends on the one before it. + +**When the data model changes, you must +[create a database migration (a.k.a. "revision")](https://alembic.sqlalchemy.org/en/latest/tutorial.html#create-a-migration-script). +Each release should contain either 0 or 1 database migrations.** If you make multiple +changes within a single release cycle, combine them all into one migration. + +Create each revision with a descriptive name, following the convention you would use +when creating a Git commit. + +:::{.callout-important} +These commands are executed within the Docker stack by prefixing `docker compose run +--rm usaon-benefit-tool` to the `alembic` command. The database must be running. +::: + +```bash +docker compose run --rm usaon-benefit-tool alembic revision --autogenerate --message "Add new criticality rationale field" +``` + +This will scan the database and data model for changes and produce an automated +migration, creating a new file in `migrations/versions/` directory. **Review and test +this migration carefully.** Remember, the data in the database needs to be changed, not +just the columns. + +To generate an empty migration and manually populate the behaviors, omit +`--autogenerate`. + +To apply all migrations and bring the DB to the latest state: + +```bash +docker compose run --rm usaon-benefit-tool alembic upgrade head # or replace "head" with a migration id +``` + + ### Third-party services See diff --git a/environment.yml b/environment.yml index 9e090ceb..4ec8a860 100644 --- a/environment.yml +++ b/environment.yml @@ -10,6 +10,7 @@ dependencies: # Dev dependencies: - pre-commit + - conda-lock - bump-my-version ~=0.9.3 # TODO: For some reason, with later versions, imports within invoke tasks stop working - invoke ~=2.0.0 @@ -30,6 +31,7 @@ dependencies: - flask-login ~=0.6.2 - sqlalchemy ~=1.4 - psycopg2 ~=2.9 + - alembic ~=1.13.3 - flask-sqlalchemy ~=3.0 - markdown ~=3.5 - matplotlib-base ~=3.8.3 diff --git a/migrations/README b/migrations/README new file mode 100644 index 00000000..2500aa1b --- /dev/null +++ b/migrations/README @@ -0,0 +1 @@ +Generic single-database configuration. diff --git a/migrations/env.py b/migrations/env.py new file mode 100644 index 00000000..9ead4f4f --- /dev/null +++ b/migrations/env.py @@ -0,0 +1,86 @@ +from logging.config import fileConfig + +from alembic import context +from sqlalchemy import engine_from_config, pool + +from usaon_benefit_tool.models.tables import BaseModel +from usaon_benefit_tool.util.db.connect import db_connstr + +# 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 = BaseModel.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', + # NOTE: Passing None is technically not permitted by the type signature of this + # function, but it allows us to avoid initializing a Flask app object. Migrations + # won't work when running with a SQLite DB. I don't think there's a good reason to + # support the SQLite DB anymore. + db_connstr(None), +) + + +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 00000000..fbc4b07d --- /dev/null +++ b/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"} diff --git a/migrations/versions/fafa3da67d5e_increase_length_of_description_columns.py b/migrations/versions/fafa3da67d5e_increase_length_of_description_columns.py new file mode 100644 index 00000000..038815b5 --- /dev/null +++ b/migrations/versions/fafa3da67d5e_increase_length_of_description_columns.py @@ -0,0 +1,55 @@ +"""Increase length of description columns. + +Revision ID: fafa3da67d5e +Revises: +Create Date: 2024-09-27 01:03:09.472099 +""" + +from collections.abc import Sequence + +import sqlalchemy as sa +from alembic import op + +# revision identifiers, used by Alembic. +revision: str = 'fafa3da67d5e' +down_revision: str | None = None +branch_labels: str | Sequence[str] | None = None +depends_on: str | Sequence[str] | None = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.alter_column( + 'assessment', + 'description', + existing_type=sa.VARCHAR(length=512), + type_=sa.String(length=4096), + existing_nullable=True, + ) + op.alter_column( + 'node', + 'description', + existing_type=sa.VARCHAR(length=512), + type_=sa.String(length=4096), + existing_nullable=True, + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.alter_column( + 'node', + 'description', + existing_type=sa.String(length=4096), + type_=sa.VARCHAR(length=512), + existing_nullable=True, + ) + op.alter_column( + 'assessment', + 'description', + existing_type=sa.String(length=4096), + type_=sa.VARCHAR(length=512), + existing_nullable=True, + ) + # ### end Alembic commands ### diff --git a/pyproject.toml b/pyproject.toml index 719b59e7..040b69e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -94,6 +94,7 @@ ignore = [ "usaon_benefit_tool/forms.py" = ["N802"] "usaon_benefit_tool/routes/__init__.py" = ["F401", "I001"] "usaon_benefit_tool/__init__.py" = ["E501", "PLR0915"] +"migrations/*" = ["INP001"] [tool.ruff.isort] known-third-party = ["luigi"] diff --git a/usaon_benefit_tool/util/db/connect.py b/usaon_benefit_tool/util/db/connect.py index 1a280a25..8d200af9 100644 --- a/usaon_benefit_tool/util/db/connect.py +++ b/usaon_benefit_tool/util/db/connect.py @@ -5,6 +5,8 @@ from usaon_benefit_tool.util.envvar import envvar_is_true +DB_NAME = "usaon-benefit-tool" + @cache def db_connstr(app: Flask) -> str: @@ -20,25 +22,31 @@ def db_connstr(app: Flask) -> str: If not provided, default to local sqlite? """ sqlite_db = envvar_is_true('USAON_BENEFIT_TOOL_DB_SQLITE') - db_name = "usaon-benefit-tool" if sqlite_db: - if not (app.config["TESTING"] or app.config["DEBUG"]): - raise RuntimeError( - f"Production application config detected with SQLite DB. {app.config=}", - ) - db_path = f"/db/{db_name}.db" - connstr = f"sqlite:///{db_path}" - app.logger.warning( - f"Using a local file database for development: {connstr}." - " You should never see this logged in production!", - ) - return connstr + return _sqlite_db_connstr(app) else: - host = os.environ['USAON_BENEFIT_TOOL_DB_HOST'] - port = os.environ['USAON_BENEFIT_TOOL_DB_PORT'] - user = os.environ['USAON_BENEFIT_TOOL_DB_USER'] - password = os.environ['USAON_BENEFIT_TOOL_DB_PASSWORD'] + return _postgres_db_connstr() + + +def _postgres_db_connstr() -> str: + host = os.environ['USAON_BENEFIT_TOOL_DB_HOST'] + port = os.environ['USAON_BENEFIT_TOOL_DB_PORT'] + user = os.environ['USAON_BENEFIT_TOOL_DB_USER'] + password = os.environ['USAON_BENEFIT_TOOL_DB_PASSWORD'] + + return f'postgresql://{user}:{password}@{host}:{port}/{DB_NAME}' + + +def _sqlite_db_connstr(app: Flask) -> str: + if not (app.config["TESTING"] or app.config["DEBUG"]): + raise RuntimeError( + f"Production application config detected with SQLite DB. {app.config=}", + ) - connstr = f'postgresql://{user}:{password}@{host}:{port}/{db_name}' - return connstr + connstr = f"sqlite:////db/{DB_NAME}.db" + app.logger.warning( + f"Using a local file database for development: {connstr}." + " You should never see this logged in production!", + ) + return connstr From 51052266d712d3f4e02cf3f708d7e4d582d000cd Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 26 Sep 2024 19:11:06 -0600 Subject: [PATCH 2/5] Update CHANGELOG --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f1a45052..85dee94d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,11 @@ +## NEXT_VERSION + +* Increase length of description columns to 4096 chars. + + ## v2.0.2 (2024-06-07) -* Change all sankey nodes to gray color +* Change all sankey nodes to gray color. ## v2.0.1 (2024-03-21) From 69f1c99e3812b5eae05ba98d9a7df0c4a14918b7 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 26 Sep 2024 19:48:07 -0600 Subject: [PATCH 3/5] Add post-deploy migration script --- deploy/post/v2.1.0 | 17 +++++++++++++++++ doc/how-to/development.md | 3 +++ 2 files changed, 20 insertions(+) create mode 100755 deploy/post/v2.1.0 diff --git a/deploy/post/v2.1.0 b/deploy/post/v2.1.0 new file mode 100755 index 00000000..0f097a99 --- /dev/null +++ b/deploy/post/v2.1.0 @@ -0,0 +1,17 @@ +#!/bin/bash + +set -euo pipefail + +# TODO: figure out better way +echo "Waiting 10 seconds for the new stack to come up..." +sleep 10 + +docker compose run --rm usaon-benefit-tool alembic upgrade head + +# confirm the expected migration was applied +current=$(docker compose run --rm usaon-benefit-tool alembic current 2>/dev/null) +if [ "fafa3da67d5e (head)" = "${current}" ]; then + echo "Data migration successful. On expected revision ${current}." +else + echo "Data migration failed. On unexpected revision ${current}." +fi diff --git a/doc/how-to/development.md b/doc/how-to/development.md index 0595081b..b974faef 100644 --- a/doc/how-to/development.md +++ b/doc/how-to/development.md @@ -181,6 +181,9 @@ To apply all migrations and bring the DB to the latest state: docker compose run --rm usaon-benefit-tool alembic upgrade head # or replace "head" with a migration id ``` +Finally, create an executable post-deploy script matching the release which should +include the new migration in `deploy/post/` directory, e.g. `deploy/post/v2.1.0`. + ### Third-party services From 8e2175dcc192cab5a9909d85582cca5894ad7cec Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 26 Sep 2024 19:48:38 -0600 Subject: [PATCH 4/5] Bump -> v2.1.0 --- CHANGELOG.md | 2 +- CITATION.cff | 4 ++-- VERSION.env | 2 +- pyproject.toml | 4 ++-- usaon_benefit_tool/constants/version.py | 2 +- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 85dee94d..b2417bbd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -## NEXT_VERSION +## v2.1.0 (2024-09-26) * Increase length of description columns to 4096 chars. diff --git a/CITATION.cff b/CITATION.cff index 45a915f5..f73b769d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -10,8 +10,8 @@ type: "software" # https://github.com/zenodo/zenodo/issues/2515 license: "MIT" -version: 2.0.2 -date-released: "2024-06-07" +version: 2.1.0 +date-released: "2024-09-26" url: "https://github.com/nsidc/usaon-benefit-tool" authors: diff --git a/VERSION.env b/VERSION.env index 482aef28..51494bfb 100644 --- a/VERSION.env +++ b/VERSION.env @@ -1 +1 @@ -export USAON_BENEFIT_TOOL_VERSION="v2.0.2" +export USAON_BENEFIT_TOOL_VERSION="v2.1.0" diff --git a/pyproject.toml b/pyproject.toml index 040b69e8..f91ed146 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] name = "usaon_benefit_tool" description = "Gather data for US AON's Value Tree Analysis (Benefit Tool) process" -version = "2.0.2" +version = "2.1.0" url = "git@github.com:nsidc/usaon-benefit-tool.git" authors = [ {name = "National Snow and Ice Data Center", email = "nsidc@nsidc.org"}, @@ -106,7 +106,7 @@ max-complexity = 8 inline-quotes = "double" [tool.bumpversion] -current_version = "2.0.2" +current_version = "2.1.0" commit = false tag = false diff --git a/usaon_benefit_tool/constants/version.py b/usaon_benefit_tool/constants/version.py index 311aff26..127c148a 100644 --- a/usaon_benefit_tool/constants/version.py +++ b/usaon_benefit_tool/constants/version.py @@ -1 +1 @@ -VERSION = "2.0.2" +VERSION = "2.1.0" From 859706d53623229b4b94784e15b3093b6a684e8d Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Fri, 27 Sep 2024 17:39:58 -0600 Subject: [PATCH 5/5] Hack: Re-source envvars in post-deploy script --- deploy/post/v2.1.0 | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/deploy/post/v2.1.0 b/deploy/post/v2.1.0 index 0f097a99..115b8a2c 100755 --- a/deploy/post/v2.1.0 +++ b/deploy/post/v2.1.0 @@ -2,6 +2,13 @@ set -euo pipefail +# HACK: Garrison doesn't see these variables that were exported in main deploy +# script, which is unintuitive. NOTE that sourcing VERSION.env is not +# compatible with integration, but this script doesn't receive the environment +# as a parameter. Garrison needs some extra thought here. +source /etc/profile.d/envvars.sh +source VERSION.env + # TODO: figure out better way echo "Waiting 10 seconds for the new stack to come up..." sleep 10