From d212509e34f34d73bba30868db14ca83bbe8be69 Mon Sep 17 00:00:00 2001 From: Jun-te Kim Date: Thu, 27 Mar 2025 11:45:11 +0000 Subject: [PATCH 1/5] init alembic for db migration --- alembic.ini | 119 +++++++++++++++++++++++++++++++++++++++++ alembic/README | 1 + alembic/script.py.mako | 28 ++++++++++ poetry.lock | 113 +++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 5 files changed, 261 insertions(+), 1 deletion(-) create mode 100644 alembic.ini create mode 100644 alembic/README create mode 100644 alembic/script.py.mako diff --git a/alembic.ini b/alembic.ini new file mode 100644 index 0000000..6d91a48 --- /dev/null +++ b/alembic.ini @@ -0,0 +1,119 @@ +# A generic, single database configuration. + +[alembic] +# path to migration scripts +# Use forward slashes (/) also on windows to provide an os agnostic path +script_location = 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 + +# 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 + +sqlalchemy.url = driver://user:pass@localhost/dbname + + +[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 = check --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 diff --git a/alembic/README b/alembic/README new file mode 100644 index 0000000..98e4f9c --- /dev/null +++ b/alembic/README @@ -0,0 +1 @@ +Generic single-database configuration. \ No newline at end of file diff --git a/alembic/script.py.mako b/alembic/script.py.mako new file mode 100644 index 0000000..480b130 --- /dev/null +++ b/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, 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/poetry.lock b/poetry.lock index 7ffe6d7..f967653 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,25 @@ # This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +[[package]] +name = "alembic" +version = "1.15.1" +description = "A database migration tool for SQLAlchemy." +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "alembic-1.15.1-py3-none-any.whl", hash = "sha256:197de710da4b3e91cf66a826a5b31b5d59a127ab41bd0fc42863e2902ce2bbbe"}, + {file = "alembic-1.15.1.tar.gz", hash = "sha256:e1a1c738577bca1f27e68728c910cd389b9a92152ff91d902da649c192e30c49"}, +] + +[package.dependencies] +Mako = "*" +SQLAlchemy = ">=1.4.0" +typing-extensions = ">=4.12" + +[package.extras] +tz = ["tzdata"] + [[package]] name = "annotated-types" version = "0.7.0" @@ -700,6 +720,97 @@ traitlets = ">=5.3" docs = 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"f49b1428e8390de0d5989fcd7319d0f1e54d29127e967a3a7d9c07acd74e6d39" +content-hash = "c189101762db9561eb4fb22fdf0ecc5e88f537bbb82482435c6aaf953809e524" diff --git a/pyproject.toml b/pyproject.toml index b80566d..7561229 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,7 @@ dependencies = [ "sqlmodel (>=0.0.24,<0.0.25)", "psycopg2 (>=2.9.10,<3.0.0)", "pydantic-settings (>=2.8.1,<3.0.0)", + "alembic (>=1.15.1,<2.0.0)", ] [tool.poetry] From fd456762dd46114fe61e5e249a6173eae5adf69d Mon Sep 17 00:00:00 2001 From: Jun-te Kim Date: Fri, 28 Mar 2025 10:41:59 +0000 Subject: [PATCH 2/5] added ability for db migration --- alembic/versions/b650a366b88d_initla_db.py | 39 ++++++++++++++++++++++ migration_db.sh | 2 ++ 2 files changed, 41 insertions(+) create mode 100644 alembic/versions/b650a366b88d_initla_db.py create mode 100644 migration_db.sh diff --git a/alembic/versions/b650a366b88d_initla_db.py b/alembic/versions/b650a366b88d_initla_db.py new file mode 100644 index 0000000..b3100e1 --- /dev/null +++ b/alembic/versions/b650a366b88d_initla_db.py @@ -0,0 +1,39 @@ +"""initla db + +Revision ID: b650a366b88d +Revises: +Create Date: 2025-03-28 10:36:15.235350 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'b650a366b88d' +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: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('assessorinfo') + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('assessorinfo', + sa.Column('id', sa.UUID(), autoincrement=False, nullable=False), + sa.Column('accreditation_number', sa.VARCHAR(), autoincrement=False, nullable=False), + sa.Column('name', sa.VARCHAR(), autoincrement=False, nullable=False), + sa.Column('phone_number', sa.VARCHAR(), autoincrement=False, nullable=True), + sa.Column('email_address', sa.VARCHAR(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name='assessorinfo_pkey') + ) + # ### end Alembic commands ### diff --git a/migration_db.sh b/migration_db.sh new file mode 100644 index 0000000..b46bc72 --- /dev/null +++ b/migration_db.sh @@ -0,0 +1,2 @@ +poetry run alembic revision --autogenerate -m "some msg" +#poetry upgrade head From 0dc8d6bd938c8c8f13b1fd6412adc35db30b642f Mon Sep 17 00:00:00 2001 From: Jun-te Kim Date: Fri, 28 Mar 2025 10:59:58 +0000 Subject: [PATCH 3/5] check if test is run everytime --- poetry.lock | 832 ++++++++++++++++++++++++++----------------------- pyproject.toml | 1 + 2 files changed, 440 insertions(+), 393 deletions(-) diff --git a/poetry.lock b/poetry.lock index f967653..cc132fd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -262,7 +262,7 @@ 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"tzdata-2025.1-py2.py3-none-any.whl", hash = "sha256:7e127113816800496f027041c570f50bcd464a020098a3b6b199517772303639"}, - {file = "tzdata-2025.1.tar.gz", hash = "sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694"}, + {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"}, + {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"}, ] [[package]] @@ -1845,4 +1891,4 @@ files = [ [metadata] lock-version = "2.1" python-versions = ">=3.12" -content-hash = "c189101762db9561eb4fb22fdf0ecc5e88f537bbb82482435c6aaf953809e524" +content-hash = "09d7eba7676d047eac2f9f91f454617d48ee7b94348cb550941a271d776c1d39" diff --git a/pyproject.toml b/pyproject.toml index 7561229..8bc0fef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,7 @@ dependencies = [ "psycopg2 (>=2.9.10,<3.0.0)", "pydantic-settings (>=2.8.1,<3.0.0)", "alembic (>=1.15.1,<2.0.0)", + "pytest (>=8.3.5,<9.0.0)", ] [tool.poetry] From f45e7240b21876e5516d8808f2363e6ab2511a31 Mon Sep 17 00:00:00 2001 From: Jun-te Kim Date: Fri, 28 Mar 2025 11:01:03 +0000 Subject: [PATCH 4/5] add test --- .github/workflows/pytest.yml | 42 +++++++++++++++++++++++++++ etl/tests/test_pre_site_note_class.py | 21 ++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 .github/workflows/pytest.yml create mode 100644 etl/tests/test_pre_site_note_class.py diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 0000000..f5e484e --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,42 @@ +name: Run Pytest + +on: + push: + branches: + - '**' # Run on all branches + pull_request: + branches: + - main + +jobs: + test: + runs-on: ubuntu-22.04 + + steps: + - name: Checkout Repository + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.12' + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.12' + + - name: Install dependencies + run: | + pip install poetry + poetry install --no-root + + - name: Run Tests + run: | + poetry run pytest -W ignore::DeprecationWarning + env: + PYTHONPATH: ${{ github.workspace }} + + + + continue-on-error: ${{ github.event_name == 'push' && github.ref != 'refs/heads/main' }} diff --git a/etl/tests/test_pre_site_note_class.py b/etl/tests/test_pre_site_note_class.py new file mode 100644 index 0000000..a354cfa --- /dev/null +++ b/etl/tests/test_pre_site_note_class.py @@ -0,0 +1,21 @@ +# A very simple script to read a presite note and load to a postgres database +import os +from etl.surveyedData.surveryedData import surveyedDataProcessor +from etl.db.db import get_db_session, init_db +from etl.transform.types import AssessorInfo +import pytest + + +@pytest.fixture(scope="module") +def pre_site_note_path(): + """Fixture for the path to the example pre-site note.""" + return os.path.join(os.getcwd(), "example_data", "pre_site_note.pdf") + +@pytest.fixture(scope="module") +def local_survey(pre_site_note_path): + """Fixture to create a surveyedDataProcessor instance.""" + return surveyedDataProcessor("122 Fake Street", [pre_site_note_path]) + +def test_assessor_accreditation(local_survey): + """Test that the assessor accreditation number is correct.""" + assert local_survey.pre_site_note.assessor_information.accreditation_number == "QUID211435" \ No newline at end of file From 5b947a0d8aae58696e3dbc28369018c7a81192bb Mon Sep 17 00:00:00 2001 From: Jun-te Kim Date: Fri, 28 Mar 2025 11:02:04 +0000 Subject: [PATCH 5/5] unit tests --- .github/workflows/pytest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index f5e484e..7109d8f 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -9,7 +9,7 @@ on: - main jobs: - test: + etl-unit-tests: runs-on: ubuntu-22.04 steps: