From 93b88cf2b2928f8d36718f4b9bb0e3f8ece9fd48 Mon Sep 17 00:00:00 2001 From: rbpatt2019 Date: Mon, 12 Jul 2021 10:12:24 +0100 Subject: [PATCH] feat(repo): initiate repository Migrates source code to independent repository. --- .gitignore | 135 ++ .pre-commit-config.yaml | 42 + CODE_OF_CONDUCT.md | 132 ++ CONTRIBUTING.md | 138 ++ LICENSE | 7 + README.md | 61 + docs/coc.md | 2 + docs/conf.py | 33 + docs/contributing.md | 2 + docs/custom_temp_file.md | 7 + docs/data_handling.md | 20 + docs/data_handling_tests.md | 18 + docs/index.md | 28 + docs/logging.md | 13 + docs/logging_tests.md | 13 + docs/multithreading.md | 27 + docs/multithreading_tests.md | 12 + docs/readme.md | 2 + docs/source.md | 29 + docs/testing.md | 22 + gtexquery/__init__.py | 1 + gtexquery/data_handling/__init__.py | 2 + gtexquery/data_handling/biomart.py | 139 ++ gtexquery/data_handling/process.py | 76 + gtexquery/data_handling/request.py | 50 + gtexquery/logs/__init__.py | 2 + gtexquery/logs/get_logger.py | 49 + gtexquery/multithreading/__init__.py | 2 + gtexquery/multithreading/biomart.py | 67 + gtexquery/multithreading/process.py | 134 ++ gtexquery/multithreading/request.py | 143 ++ noxfile.py | 133 ++ poetry.lock | 2504 ++++++++++++++++++++++++++ pyproject.toml | 104 ++ requirements.txt | 126 ++ tests/__init__.py | 2 + tests/custom_tmp_file.py | 123 ++ tests/data_handling/__init__.py | 2 + tests/data_handling/test_process.py | 91 + tests/data_handling/test_request.py | 25 + tests/logs/__init__.py | 2 + tests/logs/test_get_logger.py | 29 + tests/multithreading/__init__.py | 2 + tests/multithreading/test_biomart.py | 16 + whitelist.txt | 5 + 45 files changed, 4572 insertions(+) create mode 100644 .gitignore create mode 100644 .pre-commit-config.yaml create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.md create mode 100644 LICENSE create mode 100644 README.md create mode 100644 docs/coc.md create mode 100644 docs/conf.py create mode 100644 docs/contributing.md create mode 100644 docs/custom_temp_file.md create mode 100644 docs/data_handling.md create mode 100644 docs/data_handling_tests.md create mode 100644 docs/index.md create mode 100644 docs/logging.md create mode 100644 docs/logging_tests.md create mode 100644 docs/multithreading.md create mode 100644 docs/multithreading_tests.md create mode 100644 docs/readme.md create mode 100644 docs/source.md create mode 100644 docs/testing.md create mode 100644 gtexquery/__init__.py create mode 100644 gtexquery/data_handling/__init__.py create mode 100644 gtexquery/data_handling/biomart.py create mode 100644 gtexquery/data_handling/process.py create mode 100644 gtexquery/data_handling/request.py create mode 100644 gtexquery/logs/__init__.py create mode 100644 gtexquery/logs/get_logger.py create mode 100644 gtexquery/multithreading/__init__.py create mode 100644 gtexquery/multithreading/biomart.py create mode 100644 gtexquery/multithreading/process.py create mode 100644 gtexquery/multithreading/request.py create mode 100644 noxfile.py create mode 100644 poetry.lock create mode 100644 pyproject.toml create mode 100644 requirements.txt create mode 100644 tests/__init__.py create mode 100644 tests/custom_tmp_file.py create mode 100644 tests/data_handling/__init__.py create mode 100644 tests/data_handling/test_process.py create mode 100644 tests/data_handling/test_request.py create mode 100644 tests/logs/__init__.py create mode 100644 tests/logs/test_get_logger.py create mode 100644 tests/multithreading/__init__.py create mode 100644 tests/multithreading/test_biomart.py create mode 100644 whitelist.txt diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9e74edb --- /dev/null +++ b/.gitignore @@ -0,0 +1,135 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.envrc +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# Local things +.DS_store +Makefile +.conda/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..7c3b949 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,42 @@ +default_language_version: + python: python3.9 +default_stages: [commit] + +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.0.1 + hooks: + - id: check-yaml + - id: check-toml + - id: fix-encoding-pragma + - id: end-of-file-fixer + - id: trailing-whitespace + - id: check-added-large-files +- repo: https://github.com/PyCQA/isort + rev: 5.8.0 + hooks: + - id: isort +- repo: https://github.com/psf/black + rev: 21.5b1 + hooks: + - id: black +- repo: https://github.com/pre-commit/mirrors-mypy + rev: v0.812 + hooks: + - id: mypy + args: ['--ignore-missing-imports', '--disable-error-code', 'name-defined'] +- repo: https://github.com/PyCQA/flake8 + rev: 3.9.2 + hooks: + - id: flake8 + entry: pflake8 + additional_dependencies: + - flake8-annotations + - flake8-bandit + - flake8-bugbear + - flake8-comprehensions + - flake8-docstrings + - flake8-pytest-style + - flake8-spellcheck + - darglint + - pyproject-flake8 diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..0122e1e --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,132 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, caste, color, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +- Demonstrating empathy and kindness toward other people +- Being respectful of differing opinions, viewpoints, and experiences +- Giving and gracefully accepting constructive feedback +- Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +- Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +- The use of sexualized language or imagery, and sexual attention or + advances of any kind +- Trolling, insulting or derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or email + address, without their explicit permission +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement email at +rb.patterson.cross@gmail.com. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available +at [https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..5f618dd --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,138 @@ +# Contributing + +````{admonition} TLDR +:class: tip + +Create a virtual environment with your preferred tool. +Both `pyproject.toml` and `requirements.txt` are provided. +Then run `pre-commit install --install-hooks`. +Then commit with `cz commit`, +and everything should take care of itself! +```` + +Welcome, friend! +Open-source software isn't open open-source without the community. +We appreciate your interest and welcome all contributions. +While your here, +we respectfully ask that you abide by our [code of conduct](CODE_OF_CONDUCT.md). +To help keep everything moving smoothly, +we have a few guidelines. + +## Bugs + +If you think you've found a bug, +let us know [here][issues]. +We'll do our best to deal with it ASAP, +but please be patient as we also work many other projects! + +## Developing + +If you think you can fix one of the bugs, +or would like to submit a new feature, +then let's get coding! + +Once you've cloned the repository, +fork it, +and get your development environment set up. +We use [poetry][poetry], +[nox][nox], +and [pre-commit][pre-commit] +to handle environments, testing, and linting. +Between them, +they make sure that all checks run in isolated environments. +If you don't have `poetry`, +please see the installation instructions [here][poetry_install]. +Once you have poetry, +you can get set up with: + +```{code-block} shell +poetry install +poetry run pre-commit install --install-hooks +``` + +Now, +you don't even have to think about linting or testing. +When you commit a change, +pre-commit will automatically run [black][black], +[isort][isort], +[mypy][mypy], +and a suite of [flake8][flake8]-based linters. +When you push a change, +github actions will trigger a more robust suit using Nox, +including security check and automated documentation building. + +### Commits + +We use a GitHub action for +[python-semantic-release][psr] +to manage our version numbers. +This automatically parses your commit messages to determine if a new release is nesessary, +and, if so, what kind (ie. major, minor, patch). +So your commit message is very important! + +But we also don't want you stressing about how to format your commit message. +To that end, +we use a python implementation of +[commitizen][cz] +to handle that for you! +Just commit using `cz commit` instead of `git commit`, +and enjoy the magic! + +### Documentation and Testing + +Speaking of documentation and testing - +if you add new code, +please add documentation and tests for it as well. +We use [napoleon numpy][docstrings] +for our docstrings, +and [sphinx][sphinx] for automatic documentation. +Our testing suite is [pytest][pytest] with a directory structure +that matches the project structure. +Please put your tests in the relevant spot! + +## Review + +Once your happy with your code, +open a pull-request, +and we will reveiw ASAP. +If you pull-request is not passing on github actions, +or something else confuses us +(we are, after all, only human!), +we might ask for some small changes. +Once everything is looking good, +we will merges in your changes! + +## From the Command-Line + +```{admonition} :fireworks: Optional fun! + +None of this section is required, but we find it useful and hope you do, too! +``` + +If you haven't heard of it already, +give a peek to to [gh][gh], +GitHub's official CLI. +It allows to manage all of the above steps from the command-line, +from forking, +to raising issues, +and checking on the status of your pull request. +Not a necessity, +but for you terminal warriors out there, +it just might help! + +[conduct]: CODE_OF_CONDUCT.md "Code of conduct" +[issues]: HOLDING "Issues" +[gh]: https://github.com/cli/cli "GH CLI" +[poetry]: https://python-poetry.org/ "Poetry" +[poetry_install]: https://python-poetry.org/docs/#installation "Poetry Installation Instructions" +[nox]: https://nox.thea.codes/en/stable/ "Nox" +[pre-commit]: https://pre-commit.com/ "Pre-commit" +[black]: https://github.com/psf/black "Black" +[isort]: https://pycqa.github.io/isort/ "iSort" +[mypy]: https://mypy.readthedocs.io/en/stable/index.html "Mypy" +[flake8]: https://flake8.pycqa.org/en/latest/ "Flake8" +[psr]: https://github.com/relekang/python-semantic-release "Python Semantic Release" +[cz]: https://commitizen-tools.github.io/commitizen/index.html "Commitizen" +[docstrings]: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html "Numpy Napoleon Docstrings" +[sphinx]: https://www.sphinx-doc.org/en/master/index.html "Sphinx" +[pytest]: https://docs.pytest.org/en/6.2.x/ "pytest" diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..3a8a22c --- /dev/null +++ b/LICENSE @@ -0,0 +1,7 @@ +Copyright 2021 IMS-MRL Bioinformatics and Biostatistics Core + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..3189d51 --- /dev/null +++ b/README.md @@ -0,0 +1,61 @@ +# GTExQuery + +[![MIT License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) +[![Python 3.9](https://img.shields.io/badge/Python-3.9-brightgreen.svg)](https://docs.python.org/3/whatsnew/3.9.html) +[![Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) +[![Codestyle: Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) + +[//]: # (HOLDING actions badge) + +[//]: # (HOLDING coverage badge) + +[//]: # (HOLDING docs badge) + +[//]: # (HOLDING stars badge) + +```{admonition} For use with GTExSnake +:class: tip + +This repository houses the code, tests, etc., +that run the nuts and bolts of the Snakemake pipeline +[GTExSnake][GTExSnake] +``` + +GTExSnake is a fully concurrent pipeline for querying +transcript-level GTEx data in specific tissues. +This package handles all the code needed for +multithreading, +data handling, +and file manipulation necessary for so-said pipeline. + +If you find the project useful, +leaves us a star on [github][stars]! + +If you want to contribute, +please see the [guide on contributing](./CONTRIBUTING.md) + +## Motivation + +There are a number of circumstances where transcript level expressed data for a +specific tissue is highly valuable. +For tissue-dependent expression data, +there are few resources better than GTEx. +In this case, the `medianTranscriptExpression` query provides the necessary data. +It returns the median expression of each transcript for a gene in a given tissue. + +As the code and tests necessary to handle the multithreading and data grew, +maintaining both the pipeline and the source code in a single repository +became quite the challenge. +To help alleviate this, +it was decided to refactor the source code into its own repository, +allowing both the pipeline and the code to more easily adhere to best practices. + +## Further Information + +For more information about the source code, +see our [documentation][docs] on ReadTheDocs. +You can learn more about the pipeline this code supports [here][GTExSnake]. + +[GTExSnake]: HOLDING "GTExSnake Snakemake Pipeline" +[stars]: HOLDING "Stargazers" +[docs]: HOLDING "Package Documentation" diff --git a/docs/coc.md b/docs/coc.md new file mode 100644 index 0000000..1c46998 --- /dev/null +++ b/docs/coc.md @@ -0,0 +1,2 @@ +```{include} ../CODE_OF_CONDUCT.md +``` diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..a58e180 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,33 @@ +# -*- coding: utf-8 -*- +"""Sphinx configuration.""" +import os +import sys + +import sphinx_rtd_theme + +sys.path.insert(0, os.path.abspath("../")) +sys.path.insert(0, os.path.abspath("../tests/")) +sys.path.insert(0, os.path.abspath("../gtexquery/")) + +project = "GTExQuery" +author = "Ryan B Patterson-Cross" +copyright = "2021, IMS-MRL Bioinformatics and Biostatistic Core" +version = "0.1.0" +extensions = [ + "sphinx_rtd_theme", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "myst_parser", +] + +napoleon_google_docstrings = False +napoleon_numpy_docstrings = True +napoleon_use_param = False + +html_theme = "sphinx_rtd_theme" + +source_suffix = { + '.rst': 'restructuredtext', + '.md': 'markdown', +} +myst_heading_anchors = 2 diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 0000000..78caf34 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,2 @@ +```{include} ../CONTRIBUTING.md +``` diff --git a/docs/custom_temp_file.md b/docs/custom_temp_file.md new file mode 100644 index 0000000..b0518e6 --- /dev/null +++ b/docs/custom_temp_file.md @@ -0,0 +1,7 @@ +```{eval-rst} +Custom TempFile "Fixture +======================== + +.. automodule:: tests.custom_tmp_file + :members: +``` diff --git a/docs/data_handling.md b/docs/data_handling.md new file mode 100644 index 0000000..bb4b52e --- /dev/null +++ b/docs/data_handling.md @@ -0,0 +1,20 @@ +```{eval-rst} +data_handling Module +==================== + +.. automodule:: gtexquery.data_handling + +data_handling.request +--------------------- + +.. automodule:: gtexquery.data_handling.request + :members: + :private-members: + +data_handling.process +--------------------- + +.. automodule:: gtexquery.data_handling.process + :members: + :private-members: +``` diff --git a/docs/data_handling_tests.md b/docs/data_handling_tests.md new file mode 100644 index 0000000..8206281 --- /dev/null +++ b/docs/data_handling_tests.md @@ -0,0 +1,18 @@ +```{eval-rst} +Tests for the data_handling Module +================================== + +.. automodule:: tests.data_handling + +Tests for the data_handling.request Submodule +--------------------------------------------- + +.. automodule:: tests.data_handling.test_request + :members: + +Tests for the data_handling.process Submodule +--------------------------------------------- + +.. automodule:: tests.data_handling.test_process + :members: +``` diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..e22531e --- /dev/null +++ b/docs/index.md @@ -0,0 +1,28 @@ +# Welcome to GTExQuery + +The source code for the [GTExSnake][gtexsnake] pipeline. + +While you are here, +we'd kindly ask you to abide by our [code of conduct](./coc.md). +If you'd like to learn more about the project, +please see the [README](./readme.md). +For information about the source code, +please see the [documentation](./source.md). +If testing is your passion, +take a peek at [testing](./testing.md). +Finally, +if you are interested in contributing, +please see our guide for [contributors](./contributing.md) + +[gtexsnake]: HOLDING + +```{toctree} +:hidden: +:maxdepth: 3 + +coc +readme +source +testing +contributing +``` diff --git a/docs/logging.md b/docs/logging.md new file mode 100644 index 0000000..efd0652 --- /dev/null +++ b/docs/logging.md @@ -0,0 +1,13 @@ +```{eval-rst} +logs Module +=========== + +.. automodule:: gtexquery.logs + +logs.get_logger +--------------- + +.. automodule:: gtexquery.logs.get_logger + :members: + :private-members: +``` diff --git a/docs/logging_tests.md b/docs/logging_tests.md new file mode 100644 index 0000000..dd40eca --- /dev/null +++ b/docs/logging_tests.md @@ -0,0 +1,13 @@ +```{eval-rst} +Tests for the logs Module +========================= + +.. automodule:: tests.logs + :members: + +Tests for the logs.get_logger Submodule +--------------------------------------- + +.. automodule:: tests.logs.test_get_logger + :members: +``` diff --git a/docs/multithreading.md b/docs/multithreading.md new file mode 100644 index 0000000..9032aa5 --- /dev/null +++ b/docs/multithreading.md @@ -0,0 +1,27 @@ +```{eval-rst} +multithreading Module +===================== + +.. automodule:: gtexquery.multithreading + +multithreading.request +---------------------- + +.. automodule:: gtexquery.multithreading.request + :members: + :private-members: + +multithreading.biomart +---------------------- + +.. automodule:: gtexquery.multithreading.biomart + :members: + :private-members: + +multithreading.process +---------------------- + +.. automodule:: gtexquery.multithreading.process + :members: + :private-members: +``` diff --git a/docs/multithreading_tests.md b/docs/multithreading_tests.md new file mode 100644 index 0000000..ea9027e --- /dev/null +++ b/docs/multithreading_tests.md @@ -0,0 +1,12 @@ +```{eval-rst} +Tests for the multithreading Module +=================================== + +.. automodule:: tests.multithreading + +Tests for the multithreading.biomart Submodule +---------------------------------------------- + +.. automodule:: tests.multithreading.test_biomart + :members: +``` diff --git a/docs/readme.md b/docs/readme.md new file mode 100644 index 0000000..451beda --- /dev/null +++ b/docs/readme.md @@ -0,0 +1,2 @@ +```{include} ../README.md +``` diff --git a/docs/source.md b/docs/source.md new file mode 100644 index 0000000..12de830 --- /dev/null +++ b/docs/source.md @@ -0,0 +1,29 @@ +# Source Code + +```{admonition} Warning: Refactoring Underway! +:class: warning + +The source code continues to undergo refactoring to separate data_handling +from multithreading as much as possible. +I'm endeavouring to do so without a breaking change, +but there are no quarantees. +``` + + +The source code is currently divided into 3 modules: + +- `logs` submodule, containing code related to logging configuration. + See [logs](./logging.md). +- `data_handling` contains the code for manipulating query data. + See [data_handling](./data_handling.md). +- `multithreading` submodule, containing code related to concurrency. + See [multithreading](./multithreading.md). + +```{toctree} +:hidden: +:maxdepth: 3 + +logging +data_handling +multithreading +``` diff --git a/docs/testing.md b/docs/testing.md new file mode 100644 index 0000000..3ff166f --- /dev/null +++ b/docs/testing.md @@ -0,0 +1,22 @@ +# Testing + +Each module within the source code has its own module for unit testing. +Please see [logging_tests](./logging_tests.md), +[data_handling_tests](./data_handling_tests.md), +and [multithreading_tests](./multithreading_tests.md) for more information. +Additionally, +there is a class-based "fixture" - +well it's not really a fixture, +pytest doesn't allow class based fixtures - +for creating custom temporary file. +Please see [custom_temp_file](./custom_temp_file.md). + +```{toctree} +:hidden: +:maxdepth: 3 + +logging_tests +data_handling_tests +multithreading_tests +custom_temp_file +``` diff --git a/gtexquery/__init__.py b/gtexquery/__init__.py new file mode 100644 index 0000000..b794fd4 --- /dev/null +++ b/gtexquery/__init__.py @@ -0,0 +1 @@ +__version__ = '0.1.0' diff --git a/gtexquery/data_handling/__init__.py b/gtexquery/data_handling/__init__.py new file mode 100644 index 0000000..e3349ed --- /dev/null +++ b/gtexquery/data_handling/__init__.py @@ -0,0 +1,2 @@ +# -*- coding: utf-8 -*- +"""Functions for handling data.""" diff --git a/gtexquery/data_handling/biomart.py b/gtexquery/data_handling/biomart.py new file mode 100644 index 0000000..8e3d8d1 --- /dev/null +++ b/gtexquery/data_handling/biomart.py @@ -0,0 +1,139 @@ +# -*- coding: utf-8 -*- +"""Data handling for *biomart* step.""" +import logging +import threading +from dataclasses import dataclass +from io import StringIO +from time import sleep + +import pandas as pd +from bioservices import BioMart + +thread_local = threading.local() +logger = logging.getLogger(__name__) + + +@dataclass() +class BMSession: + """A pipeline for requesting multiple transcripts from BioMart. + + Parameters + ---------- + transcripts : list[str] + A list of *version-less* ENST IDs + output : str + Where to save the csv results file + """ + + transcripts: list[str] + output: str + + def __post_init__(self) -> None: + """Initialise thread local BioMart session.""" + self._s = self._get_biomart() + + def _get_biomart(self) -> BioMart: + """Instantiate a thread local BioMart session. + + Returns + ------- + BioMart + + """ + # session still worth it - re-used by each thread + if not hasattr(thread_local, "bm"): + thread_local.bm = BioMart(host="www.ensembl.org", verbose=False, cache=True) + logger.info(f"Generated BioMart with host {thread_local.bm.host}") + return thread_local.bm + + def _prepare_query(self, transcript: str) -> tuple[BioMart, str]: + """Prepare a BioMart query. + + Using the thread_local session provided during post-initialisation, + prepare a BioMart query by adding the appropriate attributes. + + Note + ---- + Calling this will erase the attributes of any previous query. + + Parameters + ---------- + transcript : str + A *version-less* ENST ID + + Returns + ------- + tuple[BioMart, str] + A tuple consisting of the prepared, thread_local sesssion with the correct + attributes and the xml content of the query. + """ + self._s.new_query() + self._s.add_dataset_to_xml("hsapiens_gene_ensembl") + self._s.add_filter_to_xml("ensembl_transcript_id", transcript) + self._s.add_attribute_to_xml("hgnc_symbol") + self._s.add_attribute_to_xml("ensembl_gene_id") + self._s.add_attribute_to_xml("ensembl_transcript_id") + self._s.add_attribute_to_xml("refseq_mrna") + xml = self._s.get_xml() + return self._s, xml + + def _query_biomart(self, transcript: str) -> pd.DataFrame: + """Reguest data on a transcript from BioMart. + + A thread-local session is provided during post-initialisation. + + With the BioMart interface, simultaneous requests for multiple transcripts only + return data for the last transcript. Ergo, this function must be mapped over all + input transcipts individually. + + Parameters + ---------- + transcript : str + A *version-less* ENST ID + + Returns + ------- + pd.DataFrame + Containing the geneSymbol, gencodeId, transcriptId, and refseq ID of the + transcript. If refseq is NA, then there is no corresponding ID in BioMart. + + Raises + ------ + TimeoutError + When BioMart cannot be reached after 5 tries + + """ + s, xml = self._prepare_query(transcript) + + logger.info(f"Requesting transcript {transcript}") + + i = 0 + # Bioservices does not raise error, so we must check manually. + # This can probably be improved... + while "ERROR" in (message := s.query(xml)): + logger.warning(f"Query error for {transcript}. Trying again in 0.1 s.") + i += 1 + try: + if i > 5: + raise TimeoutError + except TimeoutError: + logger.exception( + f"Query for {transcript} failed. Likely a BioMart connection issue." + ) + raise + else: + sleep(0.1) + else: + data = pd.read_csv( + StringIO(message), + sep="\t", + header=None, + names=["geneSymbol", "gencodeId", "transcriptId", "refseq"], + ) + return data + + def biomart_request(self) -> None: + """Request data on multiple ENST IDs from BioMart.""" + data = pd.concat([self._query_biomart(t) for t in self.transcripts]) + data.to_csv(self.output, index=False) + logger.info(f"Data saved to {self.output}") diff --git a/gtexquery/data_handling/process.py b/gtexquery/data_handling/process.py new file mode 100644 index 0000000..301e679 --- /dev/null +++ b/gtexquery/data_handling/process.py @@ -0,0 +1,76 @@ +# -*- coding: utf-8 -*- +"""Data handling for *process* step. + +Attributes +---------- +Pathlike : TypeVar + A custom type to unify string and Path +""" +import logging +from pathlib import Path +from typing import TypeVar + +import pandas as pd + +logger = logging.getLogger(__name__) + + +Pathlike = TypeVar("Pathlike", Path, str) + + +def merge_data( + gtex_path: Pathlike, bm_path: Pathlike, mane: pd.DataFrame +) -> pd.DataFrame: + """Merge the data from previous pipeline queries. + + Parameters + ---------- + gtex_path : Pathlike + Path to the file containing GTEx query data. + bm_path : Pathlike + Path to the file containing BioMart query data. + mane : pd.DataFrame + A DataFrame containing MANE annotations + + Returns + ------- + pd.DataFrame + The merged DataFrame, containing the GTEx query, + the BioMart query, and the MANE annotations. + + """ + gtex = pd.read_csv(gtex_path, header=0, index_col=None) + bm = pd.read_csv(bm_path, header=0, index_col=None) + data = ( + gtex.merge(bm, on=["geneSymbol", "gencodeId", "transcriptId"], how="outer") + .merge( + mane, + on=["geneSymbol", "gencodeId", "transcriptId", "refseq"], + how="left", + ) + .sort_values(["median", "MANE_status"]) + ) + return data + + +def write_data(data: pd.DataFrame, writer: pd.ExcelWriter) -> None: + """Write a DataFrame to an Excel file. + + Note + ---- + This function is best used within a ``with`` block, so that: + + #. The ``ExcelWriter`` is already open. + #. It will be properly closed. + + Parameters + ---------- + data : pd.DataFrame + The DataFrame to be written. + writer : pd.ExcelWriter + An **open** pandas ExcelWriter. + + """ + gene = data["geneSymbol"].unique()[0] + data.to_excel(writer, index=False, sheet_name=gene) + logger.info(f"{gene} add to output file.") diff --git a/gtexquery/data_handling/request.py b/gtexquery/data_handling/request.py new file mode 100644 index 0000000..afa7d41 --- /dev/null +++ b/gtexquery/data_handling/request.py @@ -0,0 +1,50 @@ +# -*- coding: utf-8 -*- +"""Data handling for *request* step.""" +import contextlib +import logging +from typing import Optional + +import pandas as pd + +logger = logging.getLogger(__name__) + + +def lut_check(gene: str, lut: pd.DataFrame) -> Optional[str]: # type: ignore + """Check that a gene is found in the Gencode annotations. + + If the gene is found, then it is converted to its Ensembl ID. + If it is not found, then None is returned to signal to downstream processing + that the gene is not in Gencode. + + `contextlib suppress `_ + is used rather than the more verbose ``try/except`` + as we are only interested in returning ``none`` for this specific case. + Any and all other cases should fail fast and hard. + + Note + ---- + It's likely that your gene is in Gencode even if it is not found. + Common reasons (at least for me!) that a gene might not be found include + spelling errors and name errors (ie. using NGN2 instead of NEUROG2). + + Parameters + ---------- + gene : str + The gene name to be queried + lut : pd.DataFrame + The dataframe containing the name-to-id conversion for the genes + + Returns + ------- + Optional[str] + + Example + ------- + >>> lut = pd.DataFrame.from_dict({"name": ["ASCL1"], "id": ["ENSG00000139352.3"]}) + >>> lut_check("ASCL1", lut) + 'ENSG00000139352.3' + >>> lut_check("NotAGene", lut) + + """ + with contextlib.suppress(IndexError): + return lut.loc[lut["name"] == gene, "id"].values[0] diff --git a/gtexquery/logs/__init__.py b/gtexquery/logs/__init__.py new file mode 100644 index 0000000..4522b02 --- /dev/null +++ b/gtexquery/logs/__init__.py @@ -0,0 +1,2 @@ +# -*- coding: utf-8 -*- +"""Functions for logging.""" diff --git a/gtexquery/logs/get_logger.py b/gtexquery/logs/get_logger.py new file mode 100644 index 0000000..dde8c0c --- /dev/null +++ b/gtexquery/logs/get_logger.py @@ -0,0 +1,49 @@ +# -*- coding: utf-8 -*- +"""Configure logger. + +This takes advantage of the parent-child relationship between modules to configure +logging. +This only needs to be called once, +in the top module - +here, the analysis scripts - +for these effects to be propagated to all modules that configure logging using: + +.. code-block:: python + + import logging + logger = logging.getLogger(__name__) + +And then log using one of the standard levels. +""" +import logging + + +def get_logger(module: str, file: str) -> logging.Logger: + """Configure a file logger for use in a script. + + Parameters + ---------- + module : str + The name of the module from which the logger is called + file : str + The name of the log file to which the logger will write + + + Returns + ------- + logging.Logger + The configured logger instance. + """ + handler = logging.FileHandler(file) + formatter = logging.Formatter( + "{asctime} :: {levelname} :: {name} :: {message}", style="{" + ) + + handler.setLevel(logging.INFO) + handler.setFormatter(formatter) + + logging.basicConfig(level=logging.INFO, handlers=[handler]) + + logger = logging.getLogger(module) + + return logger diff --git a/gtexquery/multithreading/__init__.py b/gtexquery/multithreading/__init__.py new file mode 100644 index 0000000..d29213b --- /dev/null +++ b/gtexquery/multithreading/__init__.py @@ -0,0 +1,2 @@ +# -*- coding: utf-8 -*- +"""Code handling the concurrency of data analysis.""" diff --git a/gtexquery/multithreading/biomart.py b/gtexquery/multithreading/biomart.py new file mode 100644 index 0000000..5f64b51 --- /dev/null +++ b/gtexquery/multithreading/biomart.py @@ -0,0 +1,67 @@ +# -*- coding: utf-8 -*- +"""Classes and functions for concurrent BioMart requests. + +.. warning:: + + Though every effort has been made to ensure thread safety, + the concurrency is, as of yet, untested. + +.. note:: + + This module will likely undergo significant refactoring to generalise + the concurrency pipeline and move all data handling code to a separate + model. + +Any API query is likely to be an I/O bound process, +particularly if there are many to make. +As this is a many in, many out process, +a call to ``concurrency.futures.ThreadPoolExecutor.map`` is sufficient, +though this call occurs in the analysis script. + +To simplify the multi-step process for mapping, +and allow for multiple transcripts to be queried, +a ``BMSession`` class is provided. +""" +import logging +import threading + +import pandas as pd + +from ..data_handling.biomart import BMSession + +thread_local = threading.local() +logger = logging.getLogger(__name__) + + +def concurrent_biomart(file: str, output: str) -> None: + """Given an input file, extract the ENST IDs and query BioMart. + + Note + ---- + For use with ``concurrency.futures.ThreadPoolExecutor.map``. + + This is designed to allow concurrency within the given pipeline, + as reading files and querying an external API are inherently I/O + bound processes. Given the nature of this pipeline, the function + expects the input file to contain a column `transcriptId` that + contains a list of *version-less* ENST IDs from GTEx. + + Parameters + ---------- + file : str + Where to read the data from + output : str + Where to write the results to + + Raises + ------ + IndexError + If there are no transcipts to process in ``file`` + """ + logger.info(f"Processing file {file}") + df = pd.read_csv(file, index_col=None) + if len(transcripts := df.loc[:, "transcriptId"].unique().tolist()) == 0: + logging.error(f"There are no transcripts for {file}. Raising index error") + raise IndexError + s = BMSession(transcripts, output) + s.biomart_request() diff --git a/gtexquery/multithreading/process.py b/gtexquery/multithreading/process.py new file mode 100644 index 0000000..15b4158 --- /dev/null +++ b/gtexquery/multithreading/process.py @@ -0,0 +1,134 @@ +# -*- coding: utf-8 -*- +"""A simple queue for data processing. + +.. warning:: + + Though every effort has been made to ensure thread safety, + the concurrency is, as of yet, untested. + +.. note:: + + This module will likely undergo significant refactoring to generalise + the concurrency pipeline and move all data handling code to a separate + model. + +Combining the relevant data is a massively I/O bound process. +That is, +the file reading/writing takes more time than the data processing, +making this an ideal candidate for concurrency. +Additionally, +as this is a "many in, one out" situation, +a queue is a useful structure. +Here, +a common producer-consumer queue is structured as a class to simplify calls +to the queue. +""" +import logging +import queue +from concurrent.futures import ThreadPoolExecutor +from dataclasses import dataclass +from typing import Union + +import pandas as pd +from data_handling.process import merge_data, write_data + +logger = logging.getLogger(__name__) + + +@dataclass() +class Pipeline: + """A class-based implementation of a simple queue. + + This pipeline takes a list of files, performs basic data processing on them, + and then concatenates the output to a single excel file. As such a process is + IO bound (a quick check with pprofile suggests the majority of the time is + writing to Excel), it is an excellent choice for concurrency. + + We take advantage of the ``dataclass __post_init__`` method to initialise the queue + with user-specified parameters, + and to mark the end of the files with None. + + Using joining has the interesting problem that that the consumer can finish + before all items have been processed by the producer. Instead, we trigger + each to return by marking the last item as None. + + Attributes + ---------- + gtex : list[str] + The list of gtex data to iterate over. + bm : list[str] + The list of BioMart data to iterate over. + writer : pd.ExcelWriter + The *open* pd.ExcelWriter instance. + This should be opened, preferably with a `with` block before instantiating + the class. + mane : pd.DataFrame + The MANE reference data to be used. + maxworkers : int + The maximum number of workers to use. + maxsize : int, default: 0 + The maximum size of the queue. + Defaults to no limit. + """ + + gtex: list[Union[str, None]] + bm: list[Union[str, None]] + writer: pd.ExcelWriter + mane: pd.DataFrame + maxworkers: int + maxsize: int = 0 + + def __post_init__(self) -> None: + """Initialise queue from given values and end lists with ``None``.""" + self.gtex += [None] + self.bm += [None] + self._q: queue.Queue = queue.Queue(maxsize=self.maxsize) + + def _producer(self) -> None: + """Initialise the queue's producer. + + The producer will return when all files have been iterated over, as indicated + by the presence of `None` appended in `__post_init__`. This works by popping + from 0 instead of -1. + + Additionally, the None signal is sent to the consumer to indicate when there are + no more items to process. + """ + while (gtex_path := self.gtex.pop(0)) is not None and ( + bm_path := self.bm.pop(0) + ) is not None: + data = merge_data(gtex_path, bm_path, self.mane) + self._q.put(data) + logger.info(f"Contents of file {gtex_path} added to queue") + else: + self._q.put(None) # Send end signal to consumer + logger.info("All files added. None signal sent. Producer returns") + return + + def _consumer(self) -> None: + """Initialise the queue's consumer. + + The consumer will return when producer sends None. This works as the default + queue is a FIFO queue. + """ + while (data := self._q.get()) is not None: + write_data(data, self.writer) + self._q.task_done() + else: + logging.info("None received. Queue consumed.") + self._q.task_done() + return + + def run(self) -> None: + """Run the queue. + + The producer will return when there are no more files, and the consumer + will return when the producer sends `None`. This prevent the interesting, + and entirely common, situation of the consumer returning before the producer + finishes the known number of inputs. A call to `join` is still used, however, + to insure the queue locks till done. + """ + with ThreadPoolExecutor(max_workers=self.maxworkers) as ex: + ex.submit(self._producer) + ex.submit(self._consumer) + self._q.join() diff --git a/gtexquery/multithreading/request.py b/gtexquery/multithreading/request.py new file mode 100644 index 0000000..baffc3f --- /dev/null +++ b/gtexquery/multithreading/request.py @@ -0,0 +1,143 @@ +# -*- coding: utf-8 -*- +"""Functions for concurrent GTEx requests. + +.. warning:: + + Though every effort has been made to ensure thread safety, + the concurrency is, as of yet, untested. + +.. note:: + + This module will likely undergo significant refactoring to generalise + the concurrency pipeline and move all data handling code to a separate + model. + +Any API query is likely to be an I/O bound process, +particularly if there are many to make. +As this is a single step, +many in, many out process, +concurrency can be easily achieved with a thread local ``requests.session`` +and mapping with ``concurrent.futures.ThreadPoolExecutor.map``. +The call to ``concurrent.futures.ThreadPoolExecutor.map`` is handled in the analysis +script. +""" +import csv +import logging +import threading +from io import StringIO + +import pandas as pd +import requests + +thread_local = threading.local() +logger = logging.getLogger(__name__) + + +def _get_session(region: str) -> requests.Session: + """Instantiate a thread local session. + + The requests session is not thread safe, + per `this thread `_. + To circumvent this, we create a thread local session. This means each session + will still make multiple requests but remain isolated to its calling thread. + + Parameters + ---------- + region : str + The GTEx region to query. + + Returns + ------- + requests.Session + """ + # session still worth it - re-used by each thread + if not hasattr(thread_local, "session"): + thread_local.session = requests.Session() + thread_local.session.headers.update({"Accept": "text/html"}) + thread_local.session.params.update( # type: ignore + { + "datasetId": "gtex_v8", + "tissueSiteDetailId": region, + "format": "tsv", + } + ) + return thread_local.session + + +def gtex_request(region: str, gene: str, output: str) -> None: + """Make a thead-safe gtex request against medianTranscriptExpression. + + If gene is a str, then a query is made to GTEx; however, if gene is None, then + a blank file is created and no query is performed. + + A thread local session is provided by a call to ``_get_session``. + This allows the reuse of sessions, which, among other things, + provides significant speed ups. + + Parameters + ---------- + region : str + The GTEx region to query. + gene : str + The ENSG to query. + output : str + Where to save the output file. + + Raises + ------ + requests.HTTPError + When the GET request returns an error + Exception + Any other errors + """ + s = _get_session(region) + + # If gene is None, write blank file + if gene is None: + with open(output, "w") as file: + writer = csv.writer(file) + writer.writerow( + [ + "gencodeId", + "geneSymbol", + "tissueSiteDetailId", + "transcriptId", + "median", + "unit", + "datasetId", + ] + ) + logger.warning( + "A gene was not found in Gencode. An empty file has been created." + ) + exit() + + response = s.get( + "https://gtexportal.org/rest/v1/expression/medianTranscriptExpression", + params={ + "gencodeId": gene, + }, + ) + + try: + response.raise_for_status() + except requests.HTTPError: + logger.exception( + f"An HTTP Error occurred on gene {gene}. A detailed report follows" + ) + raise + except Exception: + logger.exception( + f"A non-HTTP Error occurred on gene {gene}. A detailed report follows" + ) + raise + else: + logger.info( + f"GET request for {gene} successful! Details: \n\t{response.headers}" + ) + data = pd.read_csv(StringIO(response.text), sep="\t") + data = data.loc[data["median"] > 0, :].sort_values("median", ascending=False) + data.loc[:, ["gencodeId", "transcriptId"]] = data.loc[ + :, ["gencodeId", "transcriptId"] + ].apply(lambda x: x.str.split(".").str.get(0)) + data.to_csv(output, index=False) diff --git a/noxfile.py b/noxfile.py new file mode 100644 index 0000000..722ef0a --- /dev/null +++ b/noxfile.py @@ -0,0 +1,133 @@ +# -*- coding: utf-8 -*- +"""Nox session configuration.""" +import tempfile +from typing import Any, List + +import nox +from nox.sessions import Session + +PACKAGE: str = "gtexquery" +LOCATIONS: List[str] = [ + PACKAGE, + "noxfile.py", + "tests", +] +VERSIONS: List[str] = ["3.9",] + +nox.options.stop_on_first_error = True +nox.options.reuse_existing_virtualenvs = True + + +def constrained_install(session: Session, *args: str, **kwargs: Any) -> None: + """Install packages with poetry version constraint.""" + with tempfile.NamedTemporaryFile() as reqs: + session.run( + "poetry", + "export", + "--dev", + "--without-hashes", + "--format=requirements.txt", + f"--output={reqs.name}", + external=True, + ) + session.install(f"--constraint={reqs.name}", *args, **kwargs) + + +@nox.session(python="3.9") +def form(session: Session) -> None: + """Format code with isort and black.""" + args = session.posargs or LOCATIONS + constrained_install(session, "isort", "black") + session.run("isort", *args) + session.run("black", *args) + + +@nox.session(python=VERSIONS) +def lint(session: Session) -> None: + """Lint files with flake8.""" + args = session.posargs or LOCATIONS[:2] + constrained_install( + session, + "flake8", + "flake8-annotations", + "flake8-bandit", + "flake8-bugbear", + "flake8-comprehensions", + "flake8-docstrings", + "flake8-pytest-style", + "flake8-spellcheck", + "darglint", + ) + session.run("flake8", *args) + + +@nox.session(python=VERSIONS) +def type(session: Session) -> None: + """Type check files with mypy.""" + args = session.posargs or LOCATIONS + constrained_install(session, "mypy") + session.run("mypy", "--ignore-missing-imports", *args) + + +@nox.session(python=VERSIONS) +def security(session: Session) -> None: + """Check security safety.""" + constrained_install(session, "safety") + with tempfile.NamedTemporaryFile() as reqs: + session.run( + "poetry", + "export", + "--dev", + "--without-hashes", + "--format=requirements.txt", + f"--output={reqs.name}", + external=True, + ) + session.run("safety", "check", f"--file={reqs.name}", "--full-report") + + +@nox.session(python=VERSIONS) +def tests(session: Session) -> None: + """Run the test suite with pytest.""" + args = session.posargs or [] + session.run("poetry", "install", "--no-dev", external=True) + constrained_install( # These are required for tests. Don't clutter w/ all dependencies! + session, + "coverage", + "pytest", + "pytest-clarity", + "pytest-sugar", + "pytest-mock", + "pytest-cov", + "typeguard", # Though typing, run best in pytest + "six", + ) + session.run("pytest", *args) + + +@nox.session(python=VERSIONS) +def doc_tests(session: Session) -> None: + """Test docstrings with xdoctest.""" + args = session.posargs or ["all"] + session.run("poetry", "install", "--no-dev", external=True) + constrained_install(session, "xdoctest") + session.run( + "python", + "-m", + "xdoctest", + "--verbose", + "2", + "--report", + "cdiff", + "--nocolor", + PACKAGE, + *args, + ) + + +@nox.session(python="3.9") +def doc_build(session: Session) -> None: + """Build the documentation.""" + session.run("poetry", "install", "--no-dev", external=True) + constrained_install(session, "sphinx", "sphinx-rtd-theme", "myst-parser", "pytest") + session.run("sphinx-build", "docs", "docs/_build") diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..42835ea --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2504 @@ +[[package]] +name = "aiohttp" +version = "3.7.4.post0" +description = "Async http client/server framework (asyncio)" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +async-timeout = ">=3.0,<4.0" +attrs = ">=17.3.0" +chardet = ">=2.0,<5.0" +multidict = ">=4.5,<7.0" +typing-extensions = ">=3.6.5" +yarl = ">=1.0,<2.0" + +[package.extras] +speedups = ["aiodns", "brotlipy", "cchardet"] + +[[package]] +name = "alabaster" +version = "0.7.12" +description = "A configurable sidebar-enabled Sphinx theme" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "argcomplete" +version = "1.12.3" +description = "Bash tab completion 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python_version < "4.0" +flake8-polyfill==1.0.2 +flake8-pytest-style==1.5.0; python_version >= "3.6" and python_version < "4.0" +flake8-spellcheck==0.24.0 +flake8==3.9.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") +gevent==21.1.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" +gitdb==4.0.7; python_version >= "3.6" +gitpython==3.1.18; python_version >= "3.6" +greenlet==1.1.0; python_version >= "2.7" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" or python_full_version >= "3.5.0" and platform_python_implementation == "CPython" +grequests==0.6.0 +identify==2.2.10; python_full_version >= "3.6.1" +idna==2.10; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6" +imagesize==1.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +iniconfig==1.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +isort==5.9.2; python_full_version >= "3.6.1" and python_version < "4.0" +itsdangerous==2.0.1; python_version >= "3.6" and python_version < "4.0" +jinja2==3.0.1; python_full_version >= "3.6.1" and python_full_version < "4.0.0" and python_version >= "3.6" +lxml==4.6.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") +markdown-it-py==1.1.0; python_version >= "3.6" and python_version < "4.0" +markupsafe==2.0.1; python_full_version >= "3.6.1" and python_full_version < "4.0.0" and python_version >= "3.6" +mccabe==0.6.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" +mdit-py-plugins==0.2.8; python_version >= "3.6" and python_version < "4.0" +multidict==5.1.0; python_version >= "3.6" +mypy-extensions==0.4.3; python_version >= "3.5" and python_full_version >= "3.6.2" +mypy==0.910; python_version >= "3.5" +myst-parser==0.15.1; python_version >= "3.6" +nodeenv==1.6.0; python_full_version >= "3.6.1" +nox==2021.6.12; python_version >= "3.6" +numpy==1.21.0; python_version >= "3.7" and python_full_version >= "3.7.1" +openpyxl==3.0.7; python_version >= "3.6" +packaging==20.9; python_full_version >= "3.6.1" and python_version >= "3.6" and python_full_version < "4.0.0" and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0") +pandas==1.3.0; python_full_version >= "3.7.1" +pathspec==0.8.1; python_full_version >= "3.6.2" +pbr==5.6.0; python_version >= "3.6" +pexpect==4.8.0 +pluggy==0.13.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +pprintpp==0.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" +pre-commit==2.13.0; python_full_version >= "3.6.1" +prompt-toolkit==3.0.19; python_full_version >= "3.6.1" and python_full_version < "4.0.0" +ptyprocess==0.7.0 +py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +pycodestyle==2.7.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" +pycparser==2.20; python_version >= "2.7" and python_full_version < "3.0.0" and platform_python_implementation == "CPython" and sys_platform == "win32" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0") or platform_python_implementation == "CPython" and sys_platform == "win32" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0") and python_full_version >= "3.4.0" +pydocstyle==6.1.1; python_version >= "3.6" +pyflakes==2.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" +pygments==2.9.0; python_version >= "3.6" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0") +pyparsing==2.4.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +pyproject-flake8==0.0.1a2 +pytest-clarity==1.0.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") +pytest-cov==2.12.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") +pytest-mock==3.6.1; python_version >= "3.6" +pytest-sugar==0.9.4 +pytest==6.2.4; python_version >= "3.6" +python-dateutil==2.8.1; python_full_version >= "3.7.1" +pytz==2021.1; python_full_version >= "3.7.1" and python_version >= "3.6" +pyyaml==5.4.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0") +questionary==1.6.0; python_full_version >= "3.6.1" and python_full_version < "4.0.0" +regex==2021.7.6; python_full_version >= "3.6.2" +requests-cache==0.7.0; python_version >= "3.6" and python_version < "4.0" +requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0") +rich==10.5.0; python_version >= "3.6" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0") +safety==1.10.3; python_version >= "3.5" +six==1.16.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0") +smmap==4.0.0; python_version >= "3.6" +snowballstemmer==2.1.0; python_version >= "3.6" +soupsieve==2.2.1; python_version >= "3.6" +sphinx-rtd-theme==0.5.2 +sphinx==4.0.3; python_version >= "3.6" +sphinxcontrib-applehelp==1.0.2; python_version >= "3.6" +sphinxcontrib-devhelp==1.0.2; python_version >= "3.6" +sphinxcontrib-htmlhelp==2.0.0; python_version >= "3.6" +sphinxcontrib-jsmath==1.0.1; python_version >= "3.6" +sphinxcontrib-qthelp==1.0.3; python_version >= "3.6" +sphinxcontrib-serializinghtml==1.1.5; python_version >= "3.6" +stevedore==3.3.0; python_version >= "3.6" +suds-jurko==0.6 +termcolor==1.1.0; python_full_version >= "3.6.1" and python_full_version < "4.0.0" +toml==0.10.2; python_full_version >= "3.6.2" and python_version >= "3.5" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0") and (python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.5") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") +tomlkit==0.7.2; python_full_version >= "3.6.1" and python_full_version < "4.0.0" +typeguard==2.12.1; python_full_version >= "3.5.3" +typing-extensions==3.10.0.0; python_version >= "3.6" +url-normalize==1.4.3; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.0" +urllib3==1.26.6; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" +virtualenv==20.4.7; python_full_version >= "3.6.1" and python_version >= "3.6" +wcwidth==0.2.5; python_full_version >= "3.6.1" and python_full_version < "4.0.0" +wrapt==1.12.1 +xdoctest==0.15.5 +xmltodict==0.12.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" +yarl==1.6.3; python_version >= "3.6" +zope.event==4.5.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" +zope.interface==5.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e297f85 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,2 @@ +# -*- coding: utf-8 -*- +"""Tests for source code.""" diff --git a/tests/custom_tmp_file.py b/tests/custom_tmp_file.py new file mode 100644 index 0000000..18b07bb --- /dev/null +++ b/tests/custom_tmp_file.py @@ -0,0 +1,123 @@ +# -*- coding: utf-8 -*- +"""Pytest fixtures. + +Well, sort of. +Pytest does not allow for class based fixtures, +so the best alternative in this case is to create a module local to the tests +that can easily imported and used within them. + +This module contains the code for a ``CustomTempFile`` class, +as well as several variables representing longer file contents needed in some tests. + +Attributes +---------- +BIOMART_CONTENTS : str + Example response from a BioMart query. +GTEX_CONTENTS : str + Example response from a GTEx query. +MANE_CONTENTS : str + Minimal MANE file contents. +""" + +from __future__ import annotations + +import os +from tempfile import NamedTemporaryFile +from types import TracebackType +from typing import Optional, Type + +BIOMART_CONTENTS = """ +geneSymbol,gencodeId,transcriptId,refseq +DLX1,ENSG00000144355,ENST00000341900,NM_001038493 +DLX1,ENSG00000144355,ENST00000361725,NM_178120 +DLX1,ENSG00000144355,ENST00000409492, +DLX1,ENSG00000144355,ENST00000475989, +DLX1,ENSG00000144355,ENST00000550686, +DLX1,ENSG00000144355,ENST00000361609, +""" + +GTEX_CONTENTS = """ +gencodeId,geneSymbol,tissueSiteDetailId,transcriptId,median,unit,datasetId +ENSG00000144355,DLX1,Brain_Hypothalamus,ENST00000341900,5.184999942779541,read count,gtex_v8 +ENSG00000144355,DLX1,Brain_Hypothalamus,ENST00000361725,3.1599998474121094,read count,gtex_v8 +ENSG00000144355,DLX1,Brain_Hypothalamus,ENST00000409492,1.2300000190734863,read count,gtex_v8 +ENSG00000144355,DLX1,Brain_Hypothalamus,ENST00000475989,1.225000023841858,read count,gtex_v8 +ENSG00000144355,DLX1,Brain_Hypothalamus,ENST00000550686,0.4699999988079071,read count,gtex_v8 +ENSG00000144355,DLX1,Brain_Hypothalamus,ENST00000361609,0.2399999946355819,read count,gtex_v8 +""" + +MANE_CONTENTS = """ +#NCBI_GeneID,gencodeId,HGNC_ID,geneSymbol,name,refseq,RefSeq_prot,transcriptId,Ensembl_prot,MANE_status,GRCh38_chr,chr_start,chr_end,chr_strand +GeneID:1745,ENSG00000144355,HGNC:2914,DLX1,distal-less homeobox 1,NM_178120,NP_835221.2,ENST00000361725,ENSP00000354478.4,MANE Select,2,172085507,172089674,+ +""" + + +class CustomTempFile: + """Create a temporary file with custom content. + + This is best used within a context manager to insure proper file clean up. + + Adapted from a StackOverflow `answer `_. + + Parameters + ---------- + content : str + Content of created temporary file. + + Examples + -------- + >>> with CustomTempFile('Hello World') as tmp: + >>> with open(tmp.filename, 'r') as file: + >>> assert file.read() == 'Hello World' + + """ + + def __init__(self, content: str) -> None: + self.file = NamedTemporaryFile(mode="w", delete=False) + with self.file as file: + file.write(content) + + @property + def filename(self) -> str: + """Return the filename of the created file. + + Returns + ------- + str + The filename. + """ + return self.file.name + + def __enter__(self) -> CustomTempFile: + """Call on entry into ``with`` statement. + + Returns + ------- + CustomTempFile + Instance of self + """ + return self + + def __exit__( + self, + ex_type: Optional[Type[BaseException]], + ex_val: Optional[BaseException], + tb: Optional[TracebackType], + ) -> None: + """Call on exit from with statement. + + Typing via `mypy`_. + + .. _mypy: https://github.com/python/mypy/issues/4885 + + Parameters + ---------- + ex_type : Optional[Type[BaseException]] + Exception type + ex_val : Optional[BaseException] + Exception value + tb : Optional[TracebackType] + Traceback + + """ + os.unlink(self.filename) diff --git a/tests/data_handling/__init__.py b/tests/data_handling/__init__.py new file mode 100644 index 0000000..78e9c98 --- /dev/null +++ b/tests/data_handling/__init__.py @@ -0,0 +1,2 @@ +# -*- coding: utf-8 -*- +"""Tests for the data_handling submodule.""" diff --git a/tests/data_handling/test_process.py b/tests/data_handling/test_process.py new file mode 100644 index 0000000..1043d92 --- /dev/null +++ b/tests/data_handling/test_process.py @@ -0,0 +1,91 @@ +# -*- coding: utf-8 -*- +"""Tests for the scripts.data_handling.process submodule. + +These unit tests are designed to test that the results of the query +are handled correctly. +They assume the data returned by the API query is formatted correctly, +as tests of data returned by realworld API queries are best left to integrations tests. +As such, +representative data is included in the tests.data module. + +Attributes +---------- +MANE : pd.DataFrame + A minimal MANE dataset +""" +from io import StringIO + +import pandas as pd + +from gtexquery.data_handling.process import merge_data + +from ..custom_tmp_file import ( + BIOMART_CONTENTS, + GTEX_CONTENTS, + MANE_CONTENTS, + CustomTempFile, +) + +MANE: pd.DataFrame = pd.read_csv(StringIO(MANE_CONTENTS)) + + +def test_returns_dataframe() -> None: + """It returns a DataFrame.""" + results = merge_data( + CustomTempFile(GTEX_CONTENTS).filename, + CustomTempFile(BIOMART_CONTENTS).filename, + MANE, + ) + assert type(results) == pd.DataFrame + + +def test_results_columns() -> None: + """Its columns are named correctly .""" + columns = [ + "gencodeId", + "geneSymbol", + "tissueSiteDetailId", + "transcriptId", + "median", + "unit", + "datasetId", + "refseq", + "#NCBI_GeneID", + "HGNC_ID", + "name", + "RefSeq_prot", + "Ensembl_prot", + "MANE_status", + "GRCh38_chr", + "chr_start", + "chr_end", + "chr_strand", + ] + results = merge_data( + CustomTempFile(GTEX_CONTENTS).filename, + CustomTempFile(BIOMART_CONTENTS).filename, + MANE, + ) + assert all(x in columns for x in results.columns), "Found an unexpected column." + assert len(results.columns) == len( + columns + ), f"There should be {len(columns)} columns" + + +def test_sorted_results() -> None: + """The results are sorted by median. + + As the ``merge_data`` function technically sorts on "MANE_status" as well, + it would be ideal to test that sort, too. + However, it it impossible to know in advance how many will have this status, + so we cannot check count. + Additionally, we cannot check the sort as most values are NaN, + and knowing the correct order would require prior knowledge about the number + of GTEx transcripts and the number with MANE status. + """ + results = merge_data( + CustomTempFile(GTEX_CONTENTS).filename, + CustomTempFile(BIOMART_CONTENTS).filename, + MANE, + ) + assert results["median"].is_monotonic diff --git a/tests/data_handling/test_request.py b/tests/data_handling/test_request.py new file mode 100644 index 0000000..d71619a --- /dev/null +++ b/tests/data_handling/test_request.py @@ -0,0 +1,25 @@ +# -*- coding: utf-8 -*- +"""Tests for the scripts.data_handling.request submodule. + +These unit tests are designed to test that genes are passed to the query correctly. +They do not test the API, +as tests of data returned by realworld API queries are best left to integrations tests. +""" + +import pandas as pd + +from gtexquery.data_handling.request import lut_check + +lut = pd.DataFrame.from_dict({"name": ["abc", "def"], "id": ["a1", "a2"]}) + + +def test_return_none() -> None: + """It returns None when the gene is not found.""" + result = lut_check("ghi", lut) + assert result is None + + +def test_return_str() -> None: + """It returns the id when the gene is found.""" + result = lut_check("abc", lut) + assert result == "a1" diff --git a/tests/logs/__init__.py b/tests/logs/__init__.py new file mode 100644 index 0000000..16c0be1 --- /dev/null +++ b/tests/logs/__init__.py @@ -0,0 +1,2 @@ +# -*- coding: utf-8 -*- +"""Tests for the logs module.""" diff --git a/tests/logs/test_get_logger.py b/tests/logs/test_get_logger.py new file mode 100644 index 0000000..c013590 --- /dev/null +++ b/tests/logs/test_get_logger.py @@ -0,0 +1,29 @@ +# -*- coding: utf-8 -*- +"""Tests for scripts.logs.get_logger. + +Frustratingly, because of the way PyTest, logging, and the parent/child relationship +interact, it is difficult to test the undelying handler. For the time being, we suffice +to test that the logger exists, is enabled, and has the correct name. +""" +import logging +from pathlib import Path + +from gtexquery.logs.get_logger import get_logger + + +def test_returns_logger(tmpdir: Path) -> None: + """It returns a logger.""" + logger = get_logger(__name__, str(tmpdir / "tmp.log")) + assert type(logger) == logging.Logger + + +def test_logger_enabled(tmpdir: Path) -> None: + """It returns an enabled logger.""" + logger = get_logger(__name__, str(tmpdir / "tmp.log")) + assert not logger.disabled + + +def test_logger_named(tmpdir: Path) -> None: + """It returns a logger with the correct name.""" + logger = get_logger(__name__, str(tmpdir / "tmp.log")) + assert logger.name == __name__ diff --git a/tests/multithreading/__init__.py b/tests/multithreading/__init__.py new file mode 100644 index 0000000..57fb3e1 --- /dev/null +++ b/tests/multithreading/__init__.py @@ -0,0 +1,2 @@ +# -*- coding: utf-8 -*- +"""Tests for the multithreading module.""" diff --git a/tests/multithreading/test_biomart.py b/tests/multithreading/test_biomart.py new file mode 100644 index 0000000..d57576f --- /dev/null +++ b/tests/multithreading/test_biomart.py @@ -0,0 +1,16 @@ +# -*- coding: utf-8 -*- +"""Tests for the multithreading.biomart submodule.""" + +from pathlib import Path + +import pytest + +from gtexquery.multithreading.biomart import concurrent_biomart + +from ..custom_tmp_file import CustomTempFile + + +def test_raises_index_error(tmpdir: Path) -> None: + """It raises an IndexError when there are no transcripts.""" + with pytest.raises(IndexError), CustomTempFile("transcriptId") as file: + concurrent_biomart(file.filename, str(tmpdir)) diff --git a/whitelist.txt b/whitelist.txt new file mode 100644 index 0000000..bf1281f --- /dev/null +++ b/whitelist.txt @@ -0,0 +1,5 @@ +Bioservices +bioservices +snakemake +conda +nox