From be013976ecc599594aa2f51def5514f679991ca6 Mon Sep 17 00:00:00 2001 From: Kenneth Domingo Date: Sun, 11 Sep 2022 23:15:45 +0800 Subject: [PATCH] Revamp backend (#72) * Replace Django with Flask and initial custom exceptions for CLI * revise task definitions, file watchers, format isort * add types * revise build tasks * FE cleanup * Restore GA * fix tests --- Dockerfile | 58 +- Dockerfile.build | 18 - Taskfile.yml | 36 +- build.Dockerfile | 20 + cloudbuild.yaml | 2 +- docker-compose.yml | 37 +- gunicorn.conf.py | 10 + poetry.lock | 1241 ++ primerdriver/__init__.py | 1 + primerdriver/__main__.py | 35 +- {sdm => primerdriver/__tests__}/__init__.py | 0 .../test_characterize.py} | 18 +- primerdriver/checks.py | 103 +- primerdriver/exceptions.py | 2 + primerdriver/input_handler.py | 5 +- primerdriver/output_handler.py | 17 +- primerdriver/primer_design.py | 401 +- primerdriver/version.py | 1 - primerx/app.py | 85 + primerx/asgi.py | 16 - primerx/cache/__init__.py | 1 + primerx/cache/cache.py | 11 + primerx/config.py | 12 + primerx/jinja2.py | 28 - primerx/log/__init__.py | 1 + primerx/log/log.py | 1 + primerx/settings.py | 150 - primerx/tasks.py | 16 + primerx/urls.py | 12 - primerx/wsgi.py | 18 +- proxy/nginx.conf | 81 +- pyproject.toml | 47 + requirements.dev.txt | 10 - requirements.txt | 35 - sdm/admin.py | 3 - sdm/apps.py | 5 - sdm/migrations/__init__.py | 0 sdm/models.py | 1 - sdm/tests.py | 118 - sdm/urls.py | 9 - sdm/views.py | 65 - setup.py | 1 - web/app/Dockerfile | 2 +- web/app/package.json | 29 +- web/app/setup.js | 19 + web/app/src/App.css | 18 +- .../src/{utils/Endpoints.js => api/index.js} | 4 +- web/app/src/components/Landing.js | 4 +- web/app/src/components/Station.js | 28 +- .../src/components/form/AdvancedSettings.js | 8 +- .../src/components/form/DnaSequenceInput.js | 2 +- web/app/src/components/form/Form.js | 4 +- .../src/components/form/MutationSelector.js | 2 +- .../components/form/ProteinSequenceInput.js | 2 +- web/app/src/components/menu/Characterize.js | 14 +- web/app/src/components/menu/DnaView.js | 23 +- web/app/src/components/menu/Menu.js | 4 +- web/app/src/components/menu/ProteinView.js | 70 +- web/app/src/components/menu/Result.js | 165 +- web/app/src/contexts/PrimerDriverContext.js | 2 +- web/app/src/index.css | 8 +- web/app/src/reportWebVitals.js | 2 +- web/app/src/setupTests.js | 2 +- web/app/src/utils/ErrorBoundary.js | 2 +- web/app/src/utils/GAUtil.js | 25 + web/app/yarn.lock | 10416 ++++++---------- 66 files changed, 6302 insertions(+), 7284 deletions(-) delete mode 100644 Dockerfile.build create mode 100644 build.Dockerfile create mode 100644 gunicorn.conf.py create mode 100644 poetry.lock rename {sdm => primerdriver/__tests__}/__init__.py (100%) rename primerdriver/{tests.py => __tests__/test_characterize.py} (71%) create mode 100644 primerdriver/exceptions.py create mode 100644 primerx/app.py delete mode 100644 primerx/asgi.py create mode 100644 primerx/cache/__init__.py create mode 100644 primerx/cache/cache.py create mode 100644 primerx/config.py delete mode 100644 primerx/jinja2.py create mode 100644 primerx/log/__init__.py create mode 100644 primerx/log/log.py delete mode 100644 primerx/settings.py create mode 100644 primerx/tasks.py delete mode 100644 primerx/urls.py delete mode 100644 requirements.dev.txt delete mode 100644 requirements.txt delete mode 100644 sdm/admin.py delete mode 100644 sdm/apps.py delete mode 100644 sdm/migrations/__init__.py delete mode 100644 sdm/models.py delete mode 100644 sdm/tests.py delete mode 100644 sdm/urls.py delete mode 100644 sdm/views.py create mode 100644 web/app/setup.js rename web/app/src/{utils/Endpoints.js => api/index.js} (81%) create mode 100644 web/app/src/utils/GAUtil.js diff --git a/Dockerfile b/Dockerfile index 7b01a89..f2a623c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,55 +1,51 @@ -FROM python:3.9.7-bullseye as base +FROM python:3.10-bullseye as base ENV PYTHONUNBUFFERED 1 +ENV PYTHONDONTWRITEBYTECODE 1 +ENV POETRY_VERSION 1.1.12 -COPY requirements.txt /tmp/requirements.txt - -RUN python -m pip install -U pip setuptools - -RUN pip install --no-cache-dir -r /tmp/requirements.txt +RUN pip install poetry==$POETRY_VERSION FROM base as dev -COPY requirements.dev.txt /tmp/requirements.dev.txt -COPY requirements.txt /tmp/requirements.txt +WORKDIR /primerdriver -RUN pip install --no-cache-dir -r /tmp/requirements.dev.txt +COPY pyproject.toml poetry.lock ./ -WORKDIR /primerdriver +RUN poetry install -ENTRYPOINT python manage.py migrate && \ - SHORT_SHA=$(git show --format="%h" --no-patch) gunicorn primerx.wsgi \ - -b 0.0.0.0:5000 \ - --workers 2 \ - --threads 4 \ - --log-file - \ - --capture-output \ - --reload +ENTRYPOINT ["poetry", "run", "flask", "run", "-h", "0.0.0.0", "-p", "5000", "--reload"] -FROM node:16-alpine as build +FROM node:16-alpine as web_build WORKDIR /web -COPY ./web/app/ ./ +COPY ./web/app/public ./public +COPY ./web/app/src ./src +COPY ./web/app/package.json ./web/app/yarn.lock ./ -RUN yarn install --prod - -RUN yarn build +RUN yarn install && yarn build FROM base as prod +ARG SHORT_SHA=$SHORT_SHA +ENV SHORT_SHA $SHORT_SHA + +WORKDIR /tmp + +COPY pyproject.toml poetry.lock ./ + +RUN poetry export -f requirements.txt | pip install --no-cache-dir -r /dev/stdin + WORKDIR /primerdriver COPY ./primerdriver/ ./primerdriver/ COPY ./primerx/ ./primerx/ COPY ./sdm/ ./sdm/ -COPY ./manage.py ./manage.py -COPY --from=build /web/build ./web/app/ +COPY ./*.py ./ +COPY ./*.sh ./ +COPY --from=web_build /web/build ./web/app/ -ARG SHORT_SHA=$SHORT_SHA - -ENV SHORT_SHA $SHORT_SHA +EXPOSE $PORT -ENTRYPOINT python manage.py collectstatic --noinput && \ - python manage.py migrate && \ - gunicorn primerx.wsgi -b 0.0.0.0:$PORT --workers 1 --threads 2 --log-file - +ENTRYPOINT [ "gunicorn", "-b", "0.0.0.0:$PORT", "-c", "./gunicorn.conf.py" ] \ No newline at end of file diff --git a/Dockerfile.build b/Dockerfile.build deleted file mode 100644 index 80f75b0..0000000 --- a/Dockerfile.build +++ /dev/null @@ -1,18 +0,0 @@ -FROM python:3.9.7-bullseye - -RUN apt-get update -RUN apt-get install upx-ucl libgfortran-10-dev libquadmath0 -y - -ENV PYTHONUNBUFFERED 1 -ENV PYTHONDONTWRITEBYTECODE 1 - -COPY requirements.dev.txt /tmp/requirements.dev.txt -COPY requirements.txt /tmp/requirements.txt - -RUN pip install --no-cache-dir -r /tmp/requirements.dev.txt - -RUN sh -c "$(curl --location https://taskfile.dev/install.sh)" -- -d -b /bin - -WORKDIR /primerdriver - -ENTRYPOINT [ "/bin/task", "build" ] diff --git a/Taskfile.yml b/Taskfile.yml index 2c2fabb..261e615 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -1,21 +1,28 @@ version: '3' +env: + NAME: primerdriver-dev + SHORT_SHA: + sh: git show --format="%h" --no-patch + tasks: default: cmds: - - docker compose up -d --build --remove-orphans + - docker compose -p $NAME up -d --build --remove-orphans {{.CLI_ARGS}} + - task logs logs: cmds: - - docker compose logs --follow + - docker compose -p $NAME logs --follow {{.CLI_ARGS}} - make-builder: + test: cmds: - - docker build -t kvdomingo/primerdriver-makelinux:latest -f Dockerfile.build . + - poetry run python -m unittest {{.CLI_ARGS}} - publish-builder: + make-builder: cmds: - - docker push kvdomingo/primerdriver-makelinux:latest + - docker build -t kvdomingo/primerdriver-makelinux:latest -f build.Dockerfile . + - docker push kvdomingo/primerdriver-makelinux:latest build-linux: cmds: @@ -23,20 +30,25 @@ tasks: build: cmds: - - pyinstaller --clean -F --name primerdriver setup.py + - poetry run pyinstaller --clean -F --name primerdriver setup.py + + build-all: + cmds: + - task build + - task build-linux shutdown: cmds: - - docker compose stop + - docker compose -p $NAME stop {{.CLI_ARGS}} restart: cmds: - - docker compose restart + - docker compose -p $NAME restart {{.CLI_ARGS}} - restart-proxy: + reload-proxy: cmds: - - docker compose restart proxy + - docker compose -p $NAME exec -- proxy nginx -s reload clean: cmds: - - docker compose down -v --remove-orphans + - docker compose -p $NAME down -v --remove-orphans diff --git a/build.Dockerfile b/build.Dockerfile new file mode 100644 index 0000000..4cf71eb --- /dev/null +++ b/build.Dockerfile @@ -0,0 +1,20 @@ +FROM python:3.10-bullseye + +ENV PYTHONUNBUFFERED 1 +ENV PYTHONDONTWRITEBYTECODE 1 +ENV POETRY_VERSION 1.1.13 + +RUN apt-get update && apt-get install upx-ucl libgfortran-10-dev libquadmath0 -y + +RUN pip install "poetry==$POETRY_VERSION" + +RUN sh -c "$(curl --location https://taskfile.dev/install.sh)" -- -d -b /bin + +WORKDIR /primerdriver + +COPY pyproject.toml poetry.lock ./ + +RUN poetry config virtualenvs.create false && poetry install --no-interaction --no-ansi + + +ENTRYPOINT [ "/bin/task", "build" ] diff --git a/cloudbuild.yaml b/cloudbuild.yaml index f1fd69a..de6953d 100644 --- a/cloudbuild.yaml +++ b/cloudbuild.yaml @@ -35,7 +35,7 @@ steps: id: Deploy entrypoint: gcloud -timeout: 900s +timeout: 1500s images: - '$_GCR_HOSTNAME/$PROJECT_ID/$REPO_NAME/$_SERVICE_NAME:$COMMIT_SHA' diff --git a/docker-compose.yml b/docker-compose.yml index dfc91aa..6ec7e7a 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,7 +1,11 @@ version: "3.8" +networks: + gateway: + external: true + services: - apiserver: + backend: build: context: . target: dev @@ -15,20 +19,29 @@ services: context: ./web/app target: dev image: kvdomingo/primerdriver-app:latest - env_file: ./web/app/.env + environment: + - HOST=0.0.0.0 + - PORT=3000 + - NODE_ENV=development + - CHOKIDAR_USEPOLLING=true + - TSC_WATCHFILE=UseFsEventsWithFallbackDynamicPolling + - WDS_SOCKET_PORT=0 volumes: - ./web:/web proxy: - image: nginx:latest - ports: - - 8000:8000 - command: - - nginx - - "-g" - - daemon off; + image: bitnami/nginx:1.21.6 + environment: + - NGINX_HTTP_PORT_NUMBER=8000 volumes: - - ./proxy/nginx.conf:/etc/nginx/nginx.conf:ro - depends_on: - - apiserver + - ./proxy/nginx.conf:/opt/bitnami/nginx/conf/server_blocks/primerdriver.conf:ro + labels: + - "traefik.enable=true" + - "traefik.http.routers.primerdriver.rule=Host(`primerdriver.localhost`)" + - "traefik.http.routers.primerdriver.entrypoints=http" + - "traefik.docker.network=gateway" + - "traefik.http.services.primerdriver.loadbalancer.server.port=8000" restart: unless-stopped + networks: + - default + - gateway \ No newline at end of file diff --git a/gunicorn.conf.py b/gunicorn.conf.py new file mode 100644 index 0000000..822ba1d --- /dev/null +++ b/gunicorn.conf.py @@ -0,0 +1,10 @@ +wsgi_app = "primerx.wsgi" + +worker_class = "gthread" +workers = 1 +threads = 2 + +errorlog = "-" +accesslog = "-" +capture_output = True +loglevel = "error" diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..d152bbb --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1241 @@ +[[package]] +name = "alabaster" +version = "0.7.12" +description = "A configurable sidebar-enabled Sphinx theme" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "altgraph" +version = "0.17.2" +description = "Python graph (network) package" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "async-generator" +version = "1.10" +description = "Async generators and context managers for Python 3.5+" +category = "dev" +optional = false +python-versions = ">=3.5" + +[[package]] +name = "attrs" +version = "22.1.0" +description = "Classes Without Boilerplate" +category = "dev" +optional = false +python-versions = ">=3.5" + +[package.extras] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] +docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"] + +[[package]] +name = "babel" +version = "2.10.3" +description = "Internationalization utilities" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +pytz = ">=2015.7" + +[[package]] +name = "biopython" +version = "1.76" +description = "Freely available tools for computational molecular biology." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +numpy = "*" + +[[package]] +name = "black" +version = "22.8.0" +description = "The uncompromising code formatter." +category = "dev" +optional = false +python-versions = ">=3.6.2" + +[package.dependencies] +click = ">=8.0.0" +mypy-extensions = ">=0.4.3" +pathspec = ">=0.9.0" +platformdirs = ">=2" +tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""} + +[package.extras] +colorama = ["colorama (>=0.4.3)"] +d = ["aiohttp (>=3.7.4)"] +jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] +uvloop = ["uvloop (>=0.15.2)"] + +[[package]] +name = "cachelib" +version = "0.9.0" +description = "A collection of cache libraries in the same API interface." +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "certifi" +version = "2022.6.15.1" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "cffi" +version = "1.15.1" +description = "Foreign Function Interface for Python calling C code." +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +pycparser = "*" + +[[package]] +name = "charset-normalizer" +version = "2.1.1" +description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" +optional = false +python-versions = ">=3.6.0" + +[package.extras] +unicode_backport = ["unicodedata2"] + +[[package]] +name = "click" +version = "8.1.3" +description = "Composable command line interface toolkit" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + +[[package]] +name = "colorama" +version = "0.4.5" +description = "Cross-platform colored terminal text." +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[[package]] +name = "docutils" +version = "0.19" +description = "Docutils -- Python Documentation Utilities" +category = "dev" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "flask" +version = "2.2.2" +description = "A simple framework for building complex web applications." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +click = ">=8.0" +itsdangerous = ">=2.0" +Jinja2 = ">=3.0" +Werkzeug = ">=2.2.2" + +[package.extras] +async = ["asgiref (>=3.2)"] +dotenv = ["python-dotenv"] + +[[package]] +name = "flask-caching" +version = "1.11.1" +description = "Adds caching support to Flask applications." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +cachelib = "*" +Flask = "*" + +[[package]] +name = "future" +version = "0.18.2" +description = "Clean single-source support for Python 3 and 2" +category = "dev" +optional = false +python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" + +[[package]] +name = "gunicorn" +version = "20.1.0" +description = "WSGI HTTP Server for UNIX" +category = "main" +optional = false +python-versions = ">=3.5" + +[package.extras] +eventlet = ["eventlet (>=0.24.1)"] +gevent = ["gevent (>=1.4.0)"] +setproctitle = ["setproctitle"] +tornado = ["tornado (>=0.2)"] + +[[package]] +name = "h11" +version = "0.13.0" +description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" +category = "dev" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "idna" +version = "3.3" +description = "Internationalized Domain Names in Applications (IDNA)" +category = "main" +optional = false +python-versions = ">=3.5" + +[[package]] +name = "imagesize" +version = "1.4.1" +description = "Getting image size from png/jpeg/jpeg2000/gif file" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[[package]] +name = "isort" +version = "5.10.1" +description = "A Python utility / library to sort Python imports." +category = "dev" +optional = false +python-versions = ">=3.6.1,<4.0" + +[package.extras] +pipfile_deprecated_finder = ["pipreqs", "requirementslib"] +requirements_deprecated_finder = ["pipreqs", "pip-api"] +colors = ["colorama (>=0.4.3,<0.5.0)"] +plugins = ["setuptools"] + +[[package]] +name = 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+python-versions = ">=3.6" + +[package.extras] +plugins = ["importlib-metadata"] + +[[package]] +name = "pyinstaller" +version = "5.4.1" +description = "PyInstaller bundles a Python application and all its dependencies into a single package." +category = "dev" +optional = false +python-versions = "<3.11,>=3.7" + +[package.dependencies] +altgraph = "*" +macholib = {version = ">=1.8", markers = "sys_platform == \"darwin\""} +pefile = {version = ">=2022.5.30", markers = "sys_platform == \"win32\""} +pyinstaller-hooks-contrib = ">=2021.4" +pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""} + +[package.extras] +encryption = ["tinyaes (>=1.0.0)"] +hook_testing = ["pytest (>=2.7.3)", "execnet (>=1.5.0)", "psutil"] + +[[package]] +name = "pyinstaller-hooks-contrib" +version = "2022.10" +description = "Community maintained hooks for PyInstaller" +category = "dev" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "pyparsing" +version = "3.0.9" 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"sha256:ad565f26ecb92588a3e43bc3d96164de84cd9902482b130d0ddbaa9664a85065"}, +] diff --git a/primerdriver/__init__.py b/primerdriver/__init__.py index e69de29..c68196d 100644 --- a/primerdriver/__init__.py +++ b/primerdriver/__init__.py @@ -0,0 +1 @@ +__version__ = "1.2.0" diff --git a/primerdriver/__main__.py b/primerdriver/__main__.py index f50b816..3c14d16 100644 --- a/primerdriver/__main__.py +++ b/primerdriver/__main__.py @@ -1,7 +1,12 @@ import sys from argparse import ArgumentParser -from .input_handler import * -from .output_handler import * + +from primerx.log import logger + +from .input_handler import interactive_handler, single_command_handler +from .output_handler import interactive_saver, single_command_saver +from .primer_design import MutationType, OperationMode, PrimerDesign +from .version import __version__ @logger.catch @@ -10,11 +15,11 @@ def main(): f""" ---. .------------. ||||\\ /||||||||||||||\\ - Primer · Driver + Primer · Driver \\|||||||||||/ \\||||||| `---------` `------ -PrimerDriver v{version} +PrimerDriver v{__version__} (c) 2020 Kenneth V. Domingo & Numeriano Amer E. Gutierrez """ ) @@ -23,11 +28,16 @@ def main(): parser.add_argument( "-M", "--mode", - help="Choose between 'dna' (DNA), 'pro' (protein), or 'char' (primer characterization) mode", + help="Operation mode. Choose between 'dna' (DNA), 'pro' (protein), or 'char' (primer characterization) mode", type=str, ) parser.add_argument("-s", "--sequence", help="Template DNA sequence", type=str) - parser.add_argument("-m", "--mutation-type", help="Mutation type", type=str) + parser.add_argument( + "-m", + "--mutation-type", + help="Mutation type. Choose between 'S' (substitution), 'I' (insertion), or 'D' (deletion)", + type=str, + ) parser.add_argument("-t", "--target", help="Target base", type=str) parser.add_argument("-r", "--replacement", help="Replacement for target base", type=str) parser.add_argument("-p", "--position", help="Target base position", type=int) @@ -46,8 +56,13 @@ def main(): args_dict = single_command_handler(args) res = PrimerDesign(**args_dict) - if args_dict["mode"].upper() == "CHAR": - res.characterize_primer(args_dict["sequence"], args_dict["mutation_type"], [1], args_dict["mismatched_bases"]) + if OperationMode(args_dict["mode"].upper()) == OperationMode.CHARACTERIZATION: + res.characterize_primer( + sequence=args_dict["sequence"], + mutation_type=MutationType(args_dict["mutation_type"].upper()), + mismatched_bases=args_dict["mismatched_bases"], + replacement=None, + ) else: res.main() @@ -55,9 +70,7 @@ def main(): interactive_saver(res.df) else: if res.savename is not None: - single_command_saver(res, res.df, res.savename) - - return 0 + single_command_saver(res.df, res.savename) if __name__ == "__main__": diff --git a/sdm/__init__.py b/primerdriver/__tests__/__init__.py similarity index 100% rename from sdm/__init__.py rename to primerdriver/__tests__/__init__.py diff --git a/primerdriver/tests.py b/primerdriver/__tests__/test_characterize.py similarity index 71% rename from primerdriver/tests.py rename to primerdriver/__tests__/test_characterize.py index 261b6a5..124cea7 100644 --- a/primerdriver/tests.py +++ b/primerdriver/__tests__/test_characterize.py @@ -1,12 +1,15 @@ import io from contextlib import redirect_stdout -from django.test import TestCase -from .primer_design import * +from unittest import TestCase + +from pandas import DataFrame + +from primerdriver.primer_design import MutationType, PrimerDesign class CharacterizeTestCase(TestCase): databases = [] - pd = PrimerDesign("char", "GATTACA", "sub", 1, "T", "A", 4) + pd = PrimerDesign("char", "GATTACA", "SUB", 1, "T", "A", 4) def test_gc_content(self): """Calculate GC content""" @@ -27,18 +30,21 @@ def test_gc_end(self): def test_calculate_Tm(self): """Calculate melting temperature""" self.assertAlmostEqual( - self.pd.calculate_Tm( + self.pd.calculate_melting_temperature( self.pd.sequence, self.pd.mutation_type, self.pd.replacement, 0.286, self.pd.mismatched_bases ), -103.449, 3, ) - def test_characterization_is_dataframe(self): + def test_characterization_returns_dataframe(self): """Check if output is a DataFrame""" out_catch = io.StringIO() with redirect_stdout(out_catch): out = self.pd.characterize_primer( - self.pd.sequence, self.pd.mutation_type, self.pd.replacement, self.pd.mismatched_bases + sequence=self.pd.sequence, + mutation_type=MutationType(self.pd.mutation_type), + replacement=self.pd.replacement, + mismatched_bases=self.pd.mismatched_bases, ) self.assertTrue(isinstance(out, DataFrame)) diff --git a/primerdriver/checks.py b/primerdriver/checks.py index 50d3fb2..5362375 100644 --- a/primerdriver/checks.py +++ b/primerdriver/checks.py @@ -1,79 +1,90 @@ from json import load -from warnings import warn +from primerx.log import logger +from .exceptions import PrimerCheckError + + +@logger.catch class PrimerChecks: - def __init__(self, sequence): + def __init__(self, sequence: str, no_interaction: bool = False): self.sequence = sequence + self.no_interaction = no_interaction - def check_valid_base(self): + def check_valid_base(self) -> str: unique_bases = set(list(self.sequence.upper())) true_bases = {"A", "C", "T", "G"} invalid_bases = unique_bases.difference(true_bases) if len(invalid_bases) != 0: - warn("Sequence contains invalid bases. Automatically removing...", Warning) - for b in invalid_bases: - self.sequence = self.sequence.upper().replace(b, "") + if self.no_interaction: + logger.warning("Sequence contains invalid bases. Automatically removing...") + for b in invalid_bases: + self.sequence = self.sequence.upper().replace(b, "") + else: + raise PrimerCheckError(f"Sequence contains invalid bases: {', '.join(list(invalid_bases))}") return self.sequence - def check_valid_protein(self): - unique_prots = set(list(self.sequence.upper())) + def check_valid_protein(self) -> str: + unique_proteins = set(list(self.sequence.upper())) with open("primerdriver/AAcompressed.json", "r") as f: - true_prots = load(f) - invalid_prots = unique_prots.difference(true_prots.keys()) - if len(invalid_prots) != 0: - warn("Sequence contains invalid proteins. Automatically removing...", Warning) - for b in invalid_prots: - self.sequence = self.sequence.upper().replace(b, "") + true_proteins = load(f) + invalid_proteins = unique_proteins.difference(true_proteins.keys()) + if len(invalid_proteins) != 0: + if self.no_interaction: + logger.warning("Sequence contains invalid proteins. Automatically removing...") + for b in invalid_proteins: + self.sequence = self.sequence.upper().replace(b, "") + else: + raise PrimerCheckError(f"Sequence contains invalid proteins: {', '.join(list(invalid_proteins))}") return self.sequence - def check_sequence_length(self): + def check_sequence_length(self) -> None: if len(self.sequence) < 40: - warn("DNA sequence is too short", Warning) + error_message = "DNA sequence is too short" elif len(self.sequence) > 8000: - warn("DNA sequence is too long", Warning) + error_message = "DNA sequence is too long" + else: + return + + if self.no_interaction: + logger.warning(error_message) + else: + raise PrimerCheckError(error_message) - def check_gc_content(self): + def check_gc_content(self) -> None: seq = list(self.sequence) gc = (seq.count("C") + seq.count("G")) / len(seq) if gc < 0.40: - warn("GC content is less than 40%", Warning) + error_message = "GC content is less than 40%" + if self.no_interaction: + logger.warning(error_message) + else: + raise PrimerCheckError(error_message) elif gc > 0.60: - warn("GC content is greater than 60%", Warning) + error_message = "GC content is greater than 60%" + if self.no_interaction: + logger.warning(error_message) + else: + raise PrimerCheckError(error_message) class SequenceChecks: - def __init__(self, sequence): + def __init__(self, sequence: str | list[str]): self.sequence = sequence.upper() - def check_sequence_length(self, length_range): - if length_range[0] <= len(self.sequence) <= length_range[1]: - return True - else: - return False + def check_sequence_length(self, length_range: tuple[int, int]) -> bool: + return length_range[0] <= len(self.sequence) <= length_range[1] - def check_gc_content(self, gc_range): + def check_gc_content(self, gc_range: [int, int]) -> bool: seq = list(self.sequence) gc = (seq.count("C") + seq.count("G")) / len(seq) * 100 - if gc < gc_range[0] or gc > gc_range[1]: - return False - else: - return True + return not (gc < gc_range[0] or gc > gc_range[1]) - def check_Tm(self, Tm, Tm_range): - if Tm < Tm_range[0] or Tm > Tm_range[1]: - return False - else: - return True + def check_Tm(self, Tm, Tm_range) -> bool: + return not (Tm < Tm_range[0] or Tm > Tm_range[1]) - def check_close_Tm(self, fwd_Tm, rev_Tm): - if abs(fwd_Tm - rev_Tm) <= 2: - return True - else: - return False + def check_close_Tm(self, fwd_Tm, rev_Tm) -> bool: + return abs(fwd_Tm - rev_Tm) <= 2 - def check_ends_gc(self, terminate_gc): - if not terminate_gc or (self.sequence[0] in ["C", "G"] and self.sequence[-1] in ["C", "G"]): - return True - else: - return False + def check_ends_gc(self, terminate_gc) -> bool: + return not terminate_gc or (self.sequence[0] in ["C", "G"] and self.sequence[-1] in ["C", "G"]) diff --git a/primerdriver/exceptions.py b/primerdriver/exceptions.py new file mode 100644 index 0000000..835623d --- /dev/null +++ b/primerdriver/exceptions.py @@ -0,0 +1,2 @@ +class PrimerCheckError(ValueError): + pass diff --git a/primerdriver/input_handler.py b/primerdriver/input_handler.py index 0f791a4..ab8f335 100644 --- a/primerdriver/input_handler.py +++ b/primerdriver/input_handler.py @@ -1,7 +1,8 @@ -from .primer_design import * -from .version import __version__ from Bio import SeqIO +from .checks import PrimerChecks +from .version import __version__ + version = str(__version__) diff --git a/primerdriver/output_handler.py b/primerdriver/output_handler.py index 5261afa..61bbf6a 100644 --- a/primerdriver/output_handler.py +++ b/primerdriver/output_handler.py @@ -1,13 +1,15 @@ -from loguru import logger -from pandas import concat from datetime import datetime +from os import PathLike + from Bio import SeqIO -from Bio.Seq import Seq from Bio.Alphabet import IUPAC +from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord +from loguru import logger +from pandas import DataFrame, concat -def interactive_saver(df): +def interactive_saver(df: DataFrame) -> None: save = input("\nSave? [y/n] ") if save.upper() == "Y": while True: @@ -47,15 +49,13 @@ def interactive_saver(df): logger.error("Unsupported filetype. Supported filetypes are: .csv, .html, .fasta, .json") -def single_command_saver(res, df, savename): +def single_command_saver(df: DataFrame, savename: str | PathLike): if savename.endswith(".csv"): df = concat([*df]) df.to_csv(savename) - return 0 elif savename.endswith(".html"): df = concat([*df]) df.to_html(savename) - return 0 elif savename.endswith(".fasta"): seq_list = [] for i, seq in enumerate(df): @@ -79,5 +79,4 @@ def single_command_saver(res, df, savename): df = concat([*df]) df.to_json(savename, indent=4) else: - logger.error("Unsupported filetype. Supported filetypes are: .csv, .html, .fasta, .json") - return 1 + raise ValueError("Unsupported filetype. Supported filetypes are: .csv, .html, .fasta, .json") diff --git a/primerdriver/primer_design.py b/primerdriver/primer_design.py index f76498f..d724de6 100644 --- a/primerdriver/primer_design.py +++ b/primerdriver/primer_design.py @@ -1,15 +1,39 @@ -from loguru import logger -from json import loads +from enum import Enum +from json import load, loads +from typing import Any + +from numpy import array from pandas import DataFrame from tabulate import tabulate -from numpy import array -from .checks import * + +from primerx.log import logger + +from .checks import SequenceChecks + + +class OperationMode(Enum): + CHARACTERIZATION = "CHAR" + DNA = "DNA" + PROTEIN = "PRO" + + +class MutationType(Enum): + SUBSTITUTION = "S" + INSERTION = "I" + DELETION = "D" + + +class PrimerMode(Enum): + COMPLEMENTARY = "complementary" + OVERLAPPING = "overlapping" class PrimerDesign: + df: DataFrame + def __init__( self, - mode, + mode: str, sequence, mutation_type, mismatched_bases=None, @@ -17,103 +41,122 @@ def __init__( replacement=None, position=None, savename=None, - settings="primerdriver/settings.json", + config_file="primerdriver/settings.json", print_buffer=20, **kwargs, ): - if isinstance(settings, str): - if settings.endswith("json"): - with open(settings, "r") as f: - settings = load(f) + if isinstance(config_file, str): + if config_file.endswith("json"): + with open(config_file, "r") as f: + config_file = load(f) else: - settings = loads(settings) - self.settings = settings - self.mode = mode.upper() - self.sequence = sequence.upper() - self.mutation_type = mutation_type[0].upper() - self.mismatched_bases = int(mismatched_bases) if mismatched_bases is not None else None - self.replacement = replacement.upper() if replacement is not None else None - self.position = int(position) if position is not None else None - self.target = target.upper() if target is not None else None - self.Tm_range = (settings["Tm_range_min"], settings["Tm_range_max"]) - self.length_range = (settings["length_min"], settings["length_max"]) - self.gc_range = (settings["gc_range_min"], settings["gc_range_max"]) - self.flank5_range = (settings["flank5_range_min"], settings["flank5_range_max"]) - self.flank3_range = (settings["flank3_range_min"], settings["flank3_range_max"]) - self.forward_overlap5 = settings["forward_overlap5"] - self.forward_overlap3 = settings["forward_overlap3"] - self.terminate_gc = bool(settings["terminate_gc"]) - self.center_mutation = bool(settings["center_mutation"]) - self.primer_mode = settings["primer_mode"] - self.print_buffer = print_buffer - self.expression_name = settings["expression_system"] + config_file = loads(config_file) + self.settings: dict[str, Any] = config_file + self.mode = OperationMode(mode.upper()) + self.sequence: str = sequence.upper() + self.mutation_type = MutationType(mutation_type[0].upper()) + self.mismatched_bases: int | None = int(mismatched_bases) if mismatched_bases is not None else None + self.replacement: str | None = replacement.upper() if replacement is not None else None + self.position: int | None = int(position) if position is not None else None + self.target: str | None = target.upper() if target is not None else None + self.Tm_range: tuple[float, float] = (self.settings["Tm_range_min"], self.settings["Tm_range_max"]) + self.length_range: tuple[int, int] = (self.settings["length_min"], self.settings["length_max"]) + self.gc_range: tuple[float, float] = (self.settings["gc_range_min"], self.settings["gc_range_max"]) + self.flank5_range: tuple[int, int] = (self.settings["flank5_range_min"], self.settings["flank5_range_max"]) + self.flank3_range: tuple[int, int] = (self.settings["flank3_range_min"], self.settings["flank3_range_max"]) + self.forward_overlap5: int = self.settings["forward_overlap5"] + self.forward_overlap3: int = self.settings["forward_overlap3"] + self.terminate_gc = bool(self.settings["terminate_gc"]) + self.center_mutation = bool(self.settings["center_mutation"]) + self.primer_mode = PrimerMode(self.settings["primer_mode"]) + self.print_buffer: int = print_buffer + self.expression_name: str = self.settings["expression_system"] self.savename = savename with open("primerdriver/lut.json", "r", encoding="utf-8") as f: - self.lut = load(f) + self.lut: dict[str, Any] = load(f) with open(f"primerdriver/expression system/{self.expression_name}.json", "r") as f: - self.expression_system = load(f) + self.expression_system: dict[str, str] = load(f) - def calculate_gc_content(self, seq): + @staticmethod + def calculate_gc_content(seq: str | list[str]) -> float: return (seq.count("G") + seq.count("C")) / len(seq) - def calculate_mismatch(self, seq, mismatched_bases): + @staticmethod + def calculate_mismatch(seq: str | list[str], mismatched_bases: int) -> float: return mismatched_bases / len(seq) - def get_reverse_complement(self, seq): + def get_reverse_complement(self, seq: str | list[str]) -> list[str]: seq = list(seq) return [self.lut["complement"][b] for b in seq][::-1] - def is_gc_end(self, sequence): + @staticmethod + def is_gc_end(sequence: str | list[str]) -> bool: sequence = "".join(sequence) return (sequence.startswith("G") or sequence.startswith("C")) and ( sequence.endswith("G") or sequence.endswith("C") ) - def calculate_Tm(self, seq, mutation_type, replacement, gc_content, mismatch): + @staticmethod + def calculate_melting_temperature( + seq: str | list[str], + mutation_type: MutationType, + replacement: str | list[str], + gc_content: float, + mismatch: float, + ) -> float: gc_content = int(gc_content * 100) mismatch = int(mismatch * 100) - if mutation_type == "S": - N = len(seq) - return 81.5 + 0.41 * gc_content - 675 / N - mismatch + if mutation_type == MutationType.SUBSTITUTION: + sequence_length = len(seq) + return 81.5 + 0.41 * gc_content - 675 / sequence_length - mismatch else: - if mutation_type == "I": - N = len(seq) - elif mutation_type == "D": - N = len(seq) + if mutation_type == MutationType.INSERTION: + sequence_length = len(seq) + elif mutation_type == MutationType.DELETION: + sequence_length = len(seq) else: - N = len(seq) - len(replacement) - return 81.5 + 0.41 * gc_content - 675 / N + sequence_length = len(seq) - len(replacement) + return 81.5 + 0.41 * gc_content - 675 / sequence_length - def characterize_primer(self, sequence, mutation_type, replacement, mismatched_bases, index=None, reverse=None): + def characterize_primer( + self, + sequence: str | list[str], + mutation_type: MutationType, + replacement: str | list[str] | None, + mismatched_bases: int, + index: int = None, + reverse: list[str] = None, + ) -> DataFrame: mol_weight = self.lut["mol_weight"] - complement_dict = self.lut["complement"] seq = list(sequence) - if self.primer_mode == "complementary" or self.mode == "CHAR": + if self.primer_mode == PrimerMode.COMPLEMENTARY or self.mode == OperationMode.CHARACTERIZATION: rev = "".join(self.get_reverse_complement(sequence)) else: rev = reverse - forwards = {} - forwards["sequence"] = sequence - forwards["length"] = len(seq) - forwards["gc_content"] = self.calculate_gc_content(seq) - forwards["mismatch"] = self.calculate_mismatch(seq, mismatched_bases) - forwards["Tm"] = self.calculate_Tm( + forwards = { + "sequence": sequence, + "length": len(seq), + "gc_content": self.calculate_gc_content(seq), + "mismatch": self.calculate_mismatch(seq, mismatched_bases), + "gc_end": self.is_gc_end(seq), + "mol_weight": sum(float(mol_weight[b]) for b in seq), + } + forwards["Tm"] = self.calculate_melting_temperature( seq, mutation_type, replacement, forwards["gc_content"], forwards["mismatch"] ) - forwards["gc_end"] = self.is_gc_end(seq) - forwards["mol_weight"] = sum(float(mol_weight[b]) for b in seq) - reverses = {} - reverses["sequence"] = rev - reverses["length"] = len(rev) - reverses["gc_content"] = self.calculate_gc_content(rev) - reverses["mismatch"] = self.calculate_mismatch(rev, mismatched_bases) - reverses["Tm"] = self.calculate_Tm( + reverses = { + "sequence": rev, + "length": len(rev), + "gc_content": self.calculate_gc_content(rev), + "mismatch": self.calculate_mismatch(rev, mismatched_bases), + "gc_end": self.is_gc_end(rev), + "mol_weight": sum(float(mol_weight[b]) for b in rev), + } + reverses["Tm"] = self.calculate_melting_temperature( seq, mutation_type, replacement, reverses["gc_content"], reverses["mismatch"] ) - reverses["gc_end"] = self.is_gc_end(rev) - reverses["mol_weight"] = sum(float(mol_weight[b]) for b in rev) col = [ "Forward", @@ -147,7 +190,7 @@ def characterize_primer(self, sequence, mutation_type, replacement, mismatched_b forwards["gc_end"], reverses["gc_end"], ] - if index == None: + if index is None: index = 1 if index - 1 < self.print_buffer: print("\n", tabulate(array([col, dat]).T, headers=[f"Primer {index}"], tablefmt="orgtbl"), sep="") @@ -158,11 +201,19 @@ def characterize_primer(self, sequence, mutation_type, replacement, mismatched_b self.df = df return df - def substitution(self, sequence, mutation_type, target, replacement, start_position, mismatched_bases): - if self.primer_mode == "complementary": + def substitution( + self, + sequence: str | list[str], + mutation_type: MutationType, + target: str | list[str] | None, + replacement: str | list[str], + start_position: int, + mismatched_bases: int, + ) -> DataFrame | None: + if self.primer_mode == PrimerMode.COMPLEMENTARY: valid_primers = [] seq = list(sequence) - seqlen = len(replacement) + sequence_length = len(replacement) seq[start_position - 1] = replacement for f5 in range(*self.flank5_range): for f3 in range(*self.flank3_range): @@ -170,56 +221,62 @@ def substitution(self, sequence, mutation_type, target, replacement, start_posit continue candidate1 = seq[start_position - 1 - f5 : start_position - 1] candidate3 = list(replacement) - candidate2 = seq[start_position + seqlen - 1 : start_position + seqlen + f3] + candidate2 = seq[start_position + sequence_length - 1 : start_position + sequence_length + f3] candidate = candidate1 + candidate3 + candidate2 candidate = "".join(candidate) if len(candidate) == 0: continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + melting_temperature = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) + valid_temp = sc.check_Tm(melting_temperature, self.Tm_range) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length: valid_primers.append(candidate) else: valid_primers = {} - forseq = list(sequence) - revseq = list(sequence)[::-1] - seqlen = len(replacement) - forseq[start_position - 1] = replacement + forward_sequence = list(sequence) + sequence_length = len(replacement) + forward_sequence[start_position - 1] = replacement for f5 in range(*self.flank5_range): for f3 in range(*self.flank3_range): if abs(f5 - f3) > 1 and self.center_mutation: continue - candidate1 = forseq[start_position - 1 - f5 : start_position - 1] + candidate1 = forward_sequence[start_position - 1 - f5 : start_position - 1] candidate3 = list(replacement) - candidate2 = forseq[start_position + seqlen - 1 : start_position + seqlen + f3] + candidate2 = forward_sequence[ + start_position + sequence_length - 1 : start_position + sequence_length + f3 + ] candidate = candidate1 + candidate3 + candidate2 candidate = "".join(candidate) if len(candidate) == 0: continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + melting_temperature = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) + valid_temp = sc.check_Tm(melting_temperature, self.Tm_range) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length: valid_primers[candidate] = [] for primers in valid_primers: - sequence = sequence[: start_position - 1] + replacement + sequence[start_position - 1 + seqlen :] + sequence = ( + sequence[: start_position - 1] + replacement + sequence[start_position - 1 + sequence_length :] + ) start = sequence.find(primers) end = start + len(primers) - 1 - prilen = len(primers) while ( start < self.position - self.forward_overlap5 - and end > self.position + seqlen + self.forward_overlap3 + and end > self.position + sequence_length + self.forward_overlap3 ): start -= 1 end -= 1 @@ -230,12 +287,14 @@ def substitution(self, sequence, mutation_type, target, replacement, start_posit continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - fwd_Tm = Tm - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + forward_melting_temp = melting_temperature + melting_temperature = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) - valid_trange = sc.check_close_Tm(fwd_Tm, Tm) + valid_temp = sc.check_Tm(melting_temperature, self.Tm_range) + valid_trange = sc.check_close_Tm(forward_melting_temp, melting_temperature) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length and valid_trange: @@ -250,7 +309,7 @@ def substitution(self, sequence, mutation_type, target, replacement, start_posit print(f"\nGenerated forward primers: {len(valid_primers)}") if self.mode == "PRO": print(f"Using expression system: {self.expression_name}") - if self.primer_mode == "complementary": + if self.primer_mode == PrimerMode.COMPLEMENTARY: for i, p in enumerate(valid_primers): df.append(self.characterize_primer(p, mutation_type, replacement, mismatched_bases, i + 1)) else: @@ -261,74 +320,89 @@ def substitution(self, sequence, mutation_type, target, replacement, start_posit count += 1 return df - def deletion(self, sequence, mutation_type, target, replacement, start_position, mismatched_bases): - if self.primer_mode == "complementary": + def deletion( + self, + sequence: str | list[str], + mutation_type: MutationType, + target: str | list[str] | None, + replacement: str | list[str], + start_position: int, + mismatched_bases: int, + ) -> DataFrame | None: + if self.primer_mode == PrimerMode.COMPLEMENTARY: valid_primers = [] - seqlen = len(self.target) + sequence_length = len(self.target) seq = list(sequence) for f5 in range(*self.flank5_range): for f3 in range(*self.flank3_range): if abs(f5 - f3) > 1 and self.center_mutation: continue - if self.mode == "DNA": + if self.mode == OperationMode.DNA: candidate1 = seq[start_position - 1 - f5 : start_position - 1] - candidate2 = seq[start_position + seqlen - 1 : start_position + seqlen + f3] - elif self.mode == "PRO": + candidate2 = seq[start_position + sequence_length - 1 : start_position + sequence_length + f3] + elif self.mode == OperationMode.PROTEIN: candidate1 = seq[start_position - 1 - f5 : start_position - 1] - candidate2 = seq[start_position + seqlen * 3 - 1 : start_position + seqlen + f3] + candidate2 = seq[ + start_position + sequence_length * 3 - 1 : start_position + sequence_length + f3 + ] candidate = candidate1 + candidate2 candidate = "".join(candidate) if len(candidate) == 0: continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + melting_temperature = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) + valid_temp = sc.check_Tm(melting_temperature, self.Tm_range) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length: valid_primers.append(candidate) else: valid_primers = {} - seqlen = len(self.target) + sequence_length = len(self.target) seq = list(sequence) for f5 in range(*self.flank5_range): for f3 in range(*self.flank3_range): if abs(f5 - f3) > 1 and self.center_mutation: continue - if self.mode == "DNA": + if self.mode == OperationMode.DNA: candidate1 = seq[start_position - 1 - f5 : start_position - 1] - candidate2 = seq[start_position + seqlen - 1 : start_position + seqlen + f3] - elif self.mode == "PRO": + candidate2 = seq[start_position + sequence_length - 1 : start_position + sequence_length + f3] + else: candidate1 = seq[start_position - 1 - f5 : start_position - 1] - candidate2 = seq[start_position + seqlen * 3 - 1 : start_position + seqlen + f3] + candidate2 = seq[ + start_position + sequence_length * 3 - 1 : start_position + sequence_length + f3 + ] candidate = candidate1 + candidate2 candidate = "".join(candidate) if len(candidate) == 0: continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + melting_temperature = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) + valid_temp = sc.check_Tm(melting_temperature, self.Tm_range) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length: valid_primers[candidate] = [] - if self.mode == "DNA": - sequence = sequence[: start_position - 1] + sequence[start_position + seqlen - 1 :] - elif self.mode == "PRO": - sequence = sequence[: start_position - 1] + sequence[start_position + seqlen * 3 - 1 :] + if self.mode == OperationMode.DNA: + sequence = sequence[: start_position - 1] + sequence[start_position + sequence_length - 1 :] + elif self.mode == OperationMode.PROTEIN: + sequence = sequence[: start_position - 1] + sequence[start_position + sequence_length * 3 - 1 :] for primers in valid_primers: start = sequence.find(primers) end = start + len(primers) - 1 - prilen = len(primers) while ( start < self.position - self.forward_overlap5 - and end > self.position + seqlen + self.forward_overlap3 + and end > self.position + sequence_length + self.forward_overlap3 ): start -= 1 end -= 1 @@ -339,12 +413,14 @@ def deletion(self, sequence, mutation_type, target, replacement, start_position, continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - fwd_Tm = Tm - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + forward_melting_temp = melting_temperature + melting_temperature = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) - valid_trange = sc.check_close_Tm(fwd_Tm, Tm) + valid_temp = sc.check_Tm(melting_temperature, self.Tm_range) + valid_trange = sc.check_close_Tm(forward_melting_temp, melting_temperature) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length and valid_trange: @@ -369,29 +445,38 @@ def deletion(self, sequence, mutation_type, target, replacement, start_position, count += 1 return df - def insertion(self, sequence, mutation_type, target, replacement, start_position, mismatched_bases): - if self.primer_mode == "complementary": + def insertion( + self, + sequence: str | list[str], + mutation_type: MutationType, + target: str | list[str] | None, + replacement: str | list[str], + start_position: int, + mismatched_bases: int, + ) -> DataFrame | None: + if self.primer_mode == PrimerMode.COMPLEMENTARY: valid_primers = [] seq = list(sequence) - seqlen = len(replacement) + sequence_length = len(replacement) seq[start_position - 1] = replacement + seq[start_position - 1] for f5 in range(*self.flank5_range): for f3 in range(*self.flank3_range): if abs(f5 - f3) > 1 and self.center_mutation: continue candidate1 = seq[start_position - 1 - f5 : start_position - 1] - candidate3 = list(replacement) - candidate2 = seq[start_position - 1 : start_position + seqlen + f3] + candidate2 = seq[start_position - 1 : start_position + sequence_length + f3] candidate = candidate1 + candidate2 candidate = "".join(candidate) if len(candidate) == 0: continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + melting_temp = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) + valid_temp = sc.check_Tm(melting_temp, self.Tm_range) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length: @@ -399,25 +484,26 @@ def insertion(self, sequence, mutation_type, target, replacement, start_position else: valid_primers = dict() seq = list(sequence) - seqlen = len(replacement) + sequence_length = len(replacement) seq[start_position - 1] = replacement + seq[start_position - 1] for f5 in range(*self.flank5_range): for f3 in range(*self.flank3_range): if abs(f5 - f3) > 1 and self.center_mutation: continue candidate1 = seq[start_position - 1 - f5 : start_position - 1] - candidate3 = list(replacement) - candidate2 = seq[start_position - 1 : start_position + seqlen + f3] + candidate2 = seq[start_position - 1 : start_position + sequence_length + f3] candidate = candidate1 + candidate2 candidate = "".join(candidate) if len(candidate) == 0: continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + melting_temp = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) + valid_temp = sc.check_Tm(melting_temp, self.Tm_range) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length: @@ -426,10 +512,9 @@ def insertion(self, sequence, mutation_type, target, replacement, start_position for primers in valid_primers: start = sequence.find(primers) end = start + len(primers) - 1 - prilen = len(primers) while ( start < self.position - self.forward_overlap5 - and end > self.position + seqlen + self.forward_overlap3 + and end > self.position + sequence_length + self.forward_overlap3 ): start -= 1 end -= 1 @@ -440,12 +525,14 @@ def insertion(self, sequence, mutation_type, target, replacement, start_position continue gc_content = self.calculate_gc_content(candidate) mismatch = self.calculate_mismatch(candidate, mismatched_bases) - fwd_Tm = Tm - Tm = self.calculate_Tm(candidate, mutation_type, replacement, gc_content, mismatch) + fwd_Tm = melting_temp + melting_temp = self.calculate_melting_temperature( + candidate, mutation_type, replacement, gc_content, mismatch + ) sc = SequenceChecks(candidate) valid_gc = sc.check_gc_content(self.gc_range) - valid_temp = sc.check_Tm(Tm, self.Tm_range) - valid_trange = sc.check_close_Tm(fwd_Tm, Tm) + valid_temp = sc.check_Tm(melting_temp, self.Tm_range) + valid_trange = sc.check_close_Tm(fwd_Tm, melting_temp) valid_ends = sc.check_ends_gc(self.terminate_gc) valid_length = sc.check_sequence_length(self.length_range) if valid_gc and valid_temp and valid_ends and valid_length and valid_trange: @@ -458,7 +545,7 @@ def insertion(self, sequence, mutation_type, target, replacement, start_position else: df = [] print(f"\nGenerated forward primers: {len(valid_primers)}") - if self.primer_mode == "complementary": + if self.primer_mode == PrimerMode.COMPLEMENTARY: for i, p in enumerate(valid_primers): df.append(self.characterize_primer(p, mutation_type, replacement, mismatched_bases, i + 1)) else: @@ -470,38 +557,28 @@ def insertion(self, sequence, mutation_type, target, replacement, start_position return df def dna_based(self): - if self.mutation_type in ["S", "SUB"]: - if self.mismatched_bases is None: - self.mismatched_bases = len(self.replacement) - result = self.substitution( - self.sequence, self.mutation_type, self.target, self.replacement, self.position, self.mismatched_bases - ) - elif self.mutation_type in ["D", "DEL"]: + if self.mutation_type == MutationType.DELETION: if self.mismatched_bases is None: self.mismatched_bases = len(self.target) result = self.deletion( self.sequence, self.mutation_type, self.target, self.replacement, self.position, self.mismatched_bases ) - elif self.mutation_type in ["I", "INS"]: + elif self.mutation_type == MutationType.INSERTION: if self.mismatched_bases is None: self.mismatched_bases = len(self.replacement) result = self.insertion( self.sequence, self.mutation_type, self.target, self.replacement, self.position, self.mismatched_bases ) - return result - - def protein_based(self): - if self.mutation_type in ["S", "SUB"]: + else: if self.mismatched_bases is None: self.mismatched_bases = len(self.replacement) - rna = "".join([self.expression_system[b] for b in self.sequence]) - dna = rna.replace("U", "T") - target = "".join(self.expression_system[self.target]).replace("U", "T") - replacement = "".join(self.expression_system[self.replacement]).replace("U", "T") result = self.substitution( - dna, self.mutation_type, target, replacement, self.position * 3 - 2, self.mismatched_bases + self.sequence, self.mutation_type, self.target, self.replacement, self.position, self.mismatched_bases ) - elif self.mutation_type in ["D", "DEL"]: + return result + + def protein_based(self): + if self.mutation_type == MutationType.DELETION: if self.mismatched_bases is None: self.mismatched_bases = len(self.target) rna = "".join([self.expression_system[b] for b in self.sequence]) @@ -509,7 +586,7 @@ def protein_based(self): result = self.deletion( dna, self.mutation_type, self.target, self.replacement, self.position * 3 - 2, self.mismatched_bases ) - elif self.mutation_type in ["I", "INS"]: + elif self.mutation_type == MutationType.INSERTION: if self.mismatched_bases is None: self.mismatched_bases = len(self.replacement) rna = "".join([self.expression_system[b] for b in self.sequence]) @@ -518,13 +595,23 @@ def protein_based(self): result = self.insertion( dna, self.mutation_type, self.target, replacement, self.position * 3 - 2, self.mismatched_bases ) + else: + if self.mismatched_bases is None: + self.mismatched_bases = len(self.replacement) + rna = "".join([self.expression_system[b] for b in self.sequence]) + dna = rna.replace("U", "T") + target = "".join(self.expression_system[self.target]).replace("U", "T") + replacement = "".join(self.expression_system[self.replacement]).replace("U", "T") + result = self.substitution( + dna, self.mutation_type, target, replacement, self.position * 3 - 2, self.mismatched_bases + ) return result def main(self): - if self.mode == "CHAR": - df = self.characterize_primer(self.sequence, self.mutation_type, self.replacement, self.mismatched_bases) - elif self.mode == "DNA": + if self.mode == OperationMode.DNA: df = self.dna_based() - elif self.mode == "PRO": + elif self.mode == OperationMode.PROTEIN: df = self.protein_based() + else: + df = self.characterize_primer(self.sequence, self.mutation_type, self.replacement, self.mismatched_bases) self.df = df diff --git a/primerdriver/version.py b/primerdriver/version.py index 396a1ef..7a818ff 100644 --- a/primerdriver/version.py +++ b/primerdriver/version.py @@ -1,6 +1,5 @@ from semver import VersionInfo - __version__ = VersionInfo( major=1, minor=2, diff --git a/primerx/app.py b/primerx/app.py new file mode 100644 index 0000000..1fd5f30 --- /dev/null +++ b/primerx/app.py @@ -0,0 +1,85 @@ +import json +import os +from http import HTTPStatus as status + +from flask import Flask, Response, jsonify, request, send_from_directory +from pandas import concat + +from primerdriver import __version__ +from primerdriver.checks import PrimerChecks +from primerdriver.exceptions import PrimerCheckError +from primerdriver.primer_design import PrimerDesign + +from .cache import cache +from .config import BASE_DIR, PYTHON_ENV, SHORT_SHA +from .log import logger +from .tasks import on_ready + +app = Flask(__name__, static_url_path="", static_folder=BASE_DIR / "web" / "app") +cache.init_app(app) + +on_ready() + + +@app.route("/api/version") +def api_version(): + return jsonify( + { + "program_version": __version__, + "web_version": f"web {SHORT_SHA if SHORT_SHA else __version__}", + } + ) + + +@app.route("/api/expressionsys") +def api_expression_systems(): + try: + expression = json.loads(cache.get("expression_systems")) + return jsonify({"data": expression}) + except json.JSONDecodeError as e: + logger.error(str(e)) + return Response(status=status.INTERNAL_SERVER_ERROR) + + +@app.route("/api", methods=["POST"]) +def api(): + data = request.json + checks = PrimerChecks(data["sequence"]) + if data["mode"] == "PRO": + try: + data["sequence"] = checks.check_valid_protein() + except PrimerCheckError as e: + logger.error(str(e)) + return Response(str(e), status=status.BAD_REQUEST) + else: + try: + data["sequence"] = checks.check_valid_base() + except PrimerCheckError as e: + logger.error(str(e)) + return Response(str(e), status=status.BAD_REQUEST) + res = PrimerDesign(**data) + res.main() + if data["mode"] != "CHAR": + try: + df = concat([*res.df]).T + out = df.to_dict() + except TypeError: + out = {"data": "No valid primers found"} + else: + df = res.df + out = df.to_dict() + return jsonify(out) + + +if PYTHON_ENV != "development": + + @app.route("/", defaults={"path": ""}) + @app.route("/", + "Numeriano Amer E. Gutierrez =1.0.0"] +build-backend = "poetry.core.masonry.api" + [tool.black] line-length = 120 +target-version = ["py37", "py38", "py39", "py310"] + +[tool.isort] +profile = "black" \ No newline at end of file diff --git a/requirements.dev.txt b/requirements.dev.txt deleted file mode 100644 index 94c9c85..0000000 --- a/requirements.dev.txt +++ /dev/null @@ -1,10 +0,0 @@ -black -pyinstaller -Sphinx==3.5.1 -sphinxcontrib-applehelp==1.0.2 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==1.0.3 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.4 --r requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index c3c7fc6..0000000 --- a/requirements.txt +++ /dev/null @@ -1,35 +0,0 @@ -alabaster==0.7.12 -asgiref==3.4.1 -Babel==2.9.1 -biopython==1.76 -certifi==2020.12.5 -chardet==4.0.0 -colorama==0.4.4 -dj-database-url==0.5.0 -Django<4.0 -django-cors-headers==3.8.0 -djangorestframework==3.12.4 -docutils==0.16 -gunicorn==20.1.0 -idna==2.10 -imagesize==1.2.0 -Jinja2==2.11.3 -loguru -MarkupSafe==1.1.1 -numpy==1.20.1 -packaging==20.9 -pandas==1.2.3 -psycopg2==2.8.6 -Pygments==2.8.0 -pyparsing==2.4.7 -python-dateutil==2.8.1 -python-dotenv==0.15.0 -pytz==2021.1 -requests==2.25.1 -semver==2.13.0 -six==1.15.0 -snowballstemmer==2.1.0 -sqlparse==0.4.2 -tabulate==0.8.9 -urllib3==1.26.8 -whitenoise==5.2.0 diff --git a/sdm/admin.py b/sdm/admin.py deleted file mode 100644 index 8c38f3f..0000000 --- a/sdm/admin.py +++ /dev/null @@ -1,3 +0,0 @@ -from django.contrib import admin - -# Register your models here. diff --git a/sdm/apps.py b/sdm/apps.py deleted file mode 100644 index 7541d0b..0000000 --- a/sdm/apps.py +++ /dev/null @@ -1,5 +0,0 @@ -from django.apps import AppConfig - - -class SdmConfig(AppConfig): - name = "sdm" diff --git a/sdm/migrations/__init__.py b/sdm/migrations/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/sdm/models.py b/sdm/models.py deleted file mode 100644 index 137941f..0000000 --- a/sdm/models.py +++ /dev/null @@ -1 +0,0 @@ -from django.db import models diff --git a/sdm/tests.py b/sdm/tests.py deleted file mode 100644 index 019c183..0000000 --- a/sdm/tests.py +++ /dev/null @@ -1,118 +0,0 @@ -from django.conf import settings -from django.contrib.staticfiles.testing import StaticLiveServerTestCase -from selenium.webdriver.firefox.webdriver import WebDriver -from selenium.webdriver.firefox.options import Options -from selenium.webdriver.support.ui import Select -from percy import percySnapshot - - -PERCY_BS_WIDTHS = [576, 768, 992, 1200] - - -class WebTestCase(StaticLiveServerTestCase): - @classmethod - def setUpClass(cls): - super().setUpClass() - if settings.ON_CI: - options = Options() - options.headless = True - cls.selenium = WebDriver(options=options) - else: - cls.selenium = WebDriver() - cls.selenium.implicitly_wait(10) - - @classmethod - def tearDownClass(cls): - cls.selenium.quit() - super().tearDownClass() - - def test_landing_view(self): - self.selenium.get(self.live_server_url) - self.selenium.execute_script("window.scrollTo(0, 100)") - percySnapshot(browser=self.selenium, name="homepage", widths=PERCY_BS_WIDTHS) - - def test_characterize_view(self): - self.selenium.get(f"{self.live_server_url}/characterize") - percySnapshot(browser=self.selenium, name="characterize", widths=PERCY_BS_WIDTHS) - - def test_dna_view(self): - self.selenium.get(f"{self.live_server_url}/dna") - percySnapshot(browser=self.selenium, name="dna", widths=PERCY_BS_WIDTHS) - - def test_protein_view(self): - self.selenium.get(f"{self.live_server_url}/protein") - percySnapshot(browser=self.selenium, name="protein", widths=PERCY_BS_WIDTHS) - - def test_characterize_submit_disabled_on_characterize_landing(self): - self.selenium.get(f"{self.live_server_url}/characterize") - submit_button = self.selenium.find_element_by_id("submit") - submit_disabled = submit_button.get_attribute("disabled") - self.assertEqual(submit_disabled, "true") - - def test_characterize_submit_disabled_on_type_sequence(self): - self.selenium.get(f"{self.live_server_url}/characterize") - textarea = self.selenium.find_element_by_id("sequence") - textarea.send_keys("GATTACA") - submit_button = self.selenium.find_element_by_id("submit") - submit_disabled = submit_button.get_attribute("disabled") - self.assertEqual(submit_disabled, "true") - - def test_characterize_submit_disabled_on_set_mismatch(self): - self.selenium.get(f"{self.live_server_url}/characterize") - textarea = self.selenium.find_element_by_id("sequence") - textarea.send_keys("GATTACA") - mismatch = self.selenium.find_element_by_id("mismatched_bases") - mismatch.send_keys("1") - submit_button = self.selenium.find_element_by_id("submit") - submit_disabled = submit_button.get_attribute("disabled") - self.assertEqual(submit_disabled, "true") - - def test_characterize_submit_enabled_on_set_mutation(self): - self.selenium.get(f"{self.live_server_url}/characterize") - textarea = self.selenium.find_element_by_id("sequence") - textarea.send_keys("GATTACA") - mismatch = self.selenium.find_element_by_id("mismatched_bases") - mismatch.send_keys("1") - mutation = Select(self.selenium.find_element_by_id("mutation_type")) - mutation.select_by_visible_text("Substitution") - submit_button = self.selenium.find_element_by_id("submit") - submit_disabled = submit_button.get_attribute("disabled") - self.assertEqual(submit_disabled, None) - - def test_characterize_submit_disabled_on_form_reset(self): - self.selenium.get(f"{self.live_server_url}/characterize") - textarea = self.selenium.find_element_by_id("sequence") - textarea.send_keys("GATTACA") - mismatch = self.selenium.find_element_by_id("mismatched_bases") - mismatch.send_keys("1") - mutation = Select(self.selenium.find_element_by_id("mutation_type")) - mutation.select_by_visible_text("Substitution") - reset_button = self.selenium.find_element_by_id("reset") - reset_button.click() - submit_button = self.selenium.find_element_by_id("submit") - submit_disabled = submit_button.get_attribute("disabled") - self.assertEqual(submit_disabled, "true") - - def test_characterize_press_back(self): - self.selenium.get(self.live_server_url) - goto_char = self.selenium.find_element_by_id("characterize") - goto_char.click() - back_button = self.selenium.find_element_by_id("back") - back_button.click() - submit_buttons = self.selenium.find_elements_by_id("submit") - self.assertEqual(len(submit_buttons), 0) - - def test_characterize_submit(self): - self.selenium.get(self.live_server_url) - goto_char = self.selenium.find_element_by_id("characterize") - goto_char.click() - textarea = self.selenium.find_element_by_id("sequence") - textarea.send_keys("CGATCGTACGGACGCAGCTCGTAGCTACGATCGATCGATCGATCGTACGTACGTACGATCGTACGATCGATCGTACG") - mismatch = self.selenium.find_element_by_id("mismatched_bases") - mismatch.send_keys("1") - mutation = Select(self.selenium.find_element_by_id("mutation_type")) - mutation.select_by_visible_text("Substitution") - submit = self.selenium.find_element_by_id("submit") - submit.click() - table_rows = self.selenium.find_elements_by_tag_name("td") - self.assertEqual(len(table_rows), 14) diff --git a/sdm/urls.py b/sdm/urls.py deleted file mode 100644 index df2cfc9..0000000 --- a/sdm/urls.py +++ /dev/null @@ -1,9 +0,0 @@ -from django.urls import path -from . import views - - -urlpatterns = [ - path("", views.PrimerDriverAPIView.as_view(), name="api"), - path("version", views.VersionView.as_view(), name="version"), - path("expressionsys", views.ExpressionSystemsView.as_view(), name="expressions"), -] diff --git a/sdm/views.py b/sdm/views.py deleted file mode 100644 index 1e2b57b..0000000 --- a/sdm/views.py +++ /dev/null @@ -1,65 +0,0 @@ -import os -from pandas import concat -from rest_framework import status -from rest_framework.views import APIView -from rest_framework.response import Response -from rest_framework.permissions import AllowAny -from django.conf import settings -from primerdriver.primer_design import PrimerDesign -from primerdriver.checks import PrimerChecks -from primerdriver.version import __version__ - -BASE_DIR = settings.BASE_DIR - - -class PrimerDriverAPIView(APIView): - permission_classes = [AllowAny] - - def post(self, request): - data = request.data - checks = PrimerChecks(data["sequence"]) - if data["mode"] == "PRO": - data["sequence"] = checks.check_valid_protein() - else: - data["sequence"] = checks.check_valid_base() - res = PrimerDesign(**data) - res.main() - if data["mode"] != "CHAR": - try: - df = concat([*res.df]).T - out = df.to_dict() - except TypeError: - out = {"data": "No valid primers found"} - else: - df = res.df - out = df.to_dict() - return Response(data=out, status=status.HTTP_200_OK) - - -class VersionView(APIView): - permission_classes = [AllowAny] - - def get(self, request): - _short_sha = os.environ.get("SHORT_SHA") - return Response( - data={ - "program_version": str(__version__), - "web_version": f"web {_short_sha if _short_sha else str(__version__)}", - } - ) - - -class ExpressionSystemsView(APIView): - permission_classes = [AllowAny] - - def get(self, request): - return Response( - { - "data": sorted( - [ - "".join(f.split(".")[:-1]).strip() - for f in os.listdir(BASE_DIR / "primerdriver" / "expression system") - ] - ) - } - ) diff --git a/setup.py b/setup.py index 53a93e7..2a0ae5f 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,4 @@ from primerdriver.__main__ import main - if __name__ == "__main__": main() diff --git a/web/app/Dockerfile b/web/app/Dockerfile index bccbf0b..9092871 100644 --- a/web/app/Dockerfile +++ b/web/app/Dockerfile @@ -2,4 +2,4 @@ FROM node:16-alpine as dev WORKDIR /web/app -ENTRYPOINT yarn install && yarn start +ENTRYPOINT ["/bin/sh", "-c", "yarn && yarn start"] diff --git a/web/app/package.json b/web/app/package.json index fa71acc..2529af4 100644 --- a/web/app/package.json +++ b/web/app/package.json @@ -2,7 +2,7 @@ "name": "primerdriver", "author": "Kenneth V. Domingo ", "license": "GPL-3.0", - "version": "1.1.1", + "version": "1.2.0", "private": true, "dependencies": { "@testing-library/jest-dom": "^5.11.9", @@ -15,22 +15,18 @@ "mdbreact": "^5.0.1", "react": "^17.0.2", "react-dom": "^17.0.2", - "react-router-dom": "^5.3.0", - "react-scripts": "4.0.3", - "web-vitals": "^1.1.0" + "react-ga": "^3.3.1", + "react-router-dom": "^6.3.0", + "react-scripts": "^5.0.1", + "web-vitals": "^2.1.0" }, "devDependencies": { - "prettier": "^2.4.0", + "@trivago/prettier-plugin-sort-imports": "^3.3.0", + "prettier": "^2.7.1", "prop-types": "^15.7.2" }, - "resolutions": { - "react": "17.0.2", - "react-dom": "17.0.2", - "react-error-overlay": "6.0.9", - "react-router-dom": "5.3.0" - }, "scripts": { - "start": "react-scripts start", + "start": "node ./setup.js && react-scripts start", "build": "react-scripts build", "test": "react-scripts test", "eject": "react-scripts eject" @@ -56,6 +52,15 @@ "prettier": { "arrowParens": "avoid", "bracketSpacing": true, + "importOrder": [ + "react", + "react-dom", + "^react(.*)$", + "", + "^[./]" + ], + "importOrderSeparation": false, + "importOrderSortSpecifiers": true, "jsxSingleQuote": false, "printWidth": 120, "quoteProps": "consistent", diff --git a/web/app/setup.js b/web/app/setup.js new file mode 100644 index 0000000..cffa37d --- /dev/null +++ b/web/app/setup.js @@ -0,0 +1,19 @@ +const fs = require("fs"); +const path = require("path"); + +if (process.env.NODE_ENV === "development") { + const webPackConfigFile = path.resolve("./node_modules/react-scripts/config/webpack.config.js"); + let webPackConfigFileText = fs.readFileSync(webPackConfigFile, "utf8"); + + if (!webPackConfigFileText.includes("watchOptions")) { + if (webPackConfigFileText.includes("performance: false,")) { + webPackConfigFileText = webPackConfigFileText.replace( + "performance: false,", + "performance: false,\n\t\twatchOptions: { aggregateTimeout: 200, poll: 1000, ignored: '**/node_modules', },", + ); + fs.writeFileSync(webPackConfigFile, webPackConfigFileText, "utf8"); + } else { + throw new Error(`Failed to inject watchOptions`); + } + } +} diff --git a/web/app/src/App.css b/web/app/src/App.css index 6849650..21e77a8 100644 --- a/web/app/src/App.css +++ b/web/app/src/App.css @@ -4,19 +4,19 @@ body { @media (min-width: 576px) { html { - font-size: 0.9rem + font-size: 0.9rem; } } @media (min-width: 768px) { html { - font-size: 0.95rem + font-size: 0.95rem; } } @media (min-width: 992px) { html { - font-size: 1rem + font-size: 1rem; } } @@ -30,11 +30,13 @@ body { top: 0; } -.fade-appear, .fade-enter { +.fade-appear, +.fade-enter { opacity: 0; } -.fade-appear-active, .fade-enter-active { +.fade-appear-active, +.fade-enter-active { opacity: 1; transition: opacity 300ms ease-in-out; } @@ -52,11 +54,13 @@ body { opacity: 0; } -.slide-enter, .slide-appear { +.slide-enter, +.slide-appear { transform: translate(100%); } -.slide-enter-active, .slide-appear-active { +.slide-enter-active, +.slide-appear-active { transform: translate(0%); transition: transform 300ms ease-in-out; } diff --git a/web/app/src/utils/Endpoints.js b/web/app/src/api/index.js similarity index 81% rename from web/app/src/utils/Endpoints.js rename to web/app/src/api/index.js index bd4738e..808f329 100644 --- a/web/app/src/utils/Endpoints.js +++ b/web/app/src/api/index.js @@ -1,13 +1,13 @@ import axios from "axios"; -const baseURL = "/api/"; +const baseURL = "/api"; const axiosInstance = axios.create({ baseURL }); const api = { data: { primerDriver(body) { - return axiosInstance.post("/", body); + return axiosInstance.post("", body); }, version() { return axiosInstance.get("/version"); diff --git a/web/app/src/components/Landing.js b/web/app/src/components/Landing.js index 665a01f..c6214cd 100644 --- a/web/app/src/components/Landing.js +++ b/web/app/src/components/Landing.js @@ -1,7 +1,7 @@ -import { useEffect, useState } from "react"; import { Image } from "cloudinary-react"; import { MDBContainer as Container } from "mdbreact"; -import api from "../utils/Endpoints"; +import { useEffect, useState } from "react"; +import api from "../api"; function Landing() { const [programVersion, setProgramVersion] = useState(""); diff --git a/web/app/src/components/Station.js b/web/app/src/components/Station.js index 9060d70..e1cc89b 100644 --- a/web/app/src/components/Station.js +++ b/web/app/src/components/Station.js @@ -1,13 +1,14 @@ -import { Suspense, useState } from "react"; -import { BrowserRouter as Router, Route, Switch } from "react-router-dom"; import { MDBContainer as Container, MDBJumbotron as Jumbotron } from "mdbreact"; -import Loading from "./shared/LoadingScreen"; -import Menu from "./menu/Menu"; +import { Suspense, useState } from "react"; +import { Route, BrowserRouter as Router, Routes } from "react-router-dom"; +import ErrorBoundary from "../utils/ErrorBoundary"; +import GAUtil from "../utils/GAUtil"; import Characterize from "./menu/Characterize"; import Dna from "./menu/DnaView"; +import Menu from "./menu/Menu"; import Protein from "./menu/ProteinView"; import Results from "./menu/Result"; -import ErrorBoundary from "../utils/ErrorBoundary"; +import Loading from "./shared/LoadingScreen"; const styles = { appContainer: { @@ -35,21 +36,22 @@ function Station() { style={styles.appContainer} > + }> - - - } /> - } /> - } /> + + } /> + } /> + } /> + } /> ( + element={ - )} + } /> - + diff --git a/web/app/src/components/form/AdvancedSettings.js b/web/app/src/components/form/AdvancedSettings.js index 13590af..05623c4 100644 --- a/web/app/src/components/form/AdvancedSettings.js +++ b/web/app/src/components/form/AdvancedSettings.js @@ -1,13 +1,13 @@ -import { useState } from "react"; -import PropTypes from "prop-types"; import { MDBCard as Card, - MDBCardHeader as CardHeader, MDBCardBody as CardBody, - MDBRow as Row, + MDBCardHeader as CardHeader, MDBCol as Col, MDBCollapse as Collapse, + MDBRow as Row, } from "mdbreact"; +import { useState } from "react"; +import PropTypes from "prop-types"; function AdvancedSettings(props) { const [isOpen, setIsOpen] = useState(false); diff --git a/web/app/src/components/form/DnaSequenceInput.js b/web/app/src/components/form/DnaSequenceInput.js index 6182853..6ffb9ba 100644 --- a/web/app/src/components/form/DnaSequenceInput.js +++ b/web/app/src/components/form/DnaSequenceInput.js @@ -1,5 +1,5 @@ +import { MDBCol as Col, MDBIcon as Icon, MDBRow as Row, MDBTooltip as Tooltip } from "mdbreact"; import PropTypes from "prop-types"; -import { MDBIcon as Icon, MDBTooltip as Tooltip, MDBRow as Row, MDBCol as Col } from "mdbreact"; function DnaSequenceInput(props) { return ( diff --git a/web/app/src/components/form/Form.js b/web/app/src/components/form/Form.js index b575aa1..5b3b1a1 100644 --- a/web/app/src/components/form/Form.js +++ b/web/app/src/components/form/Form.js @@ -1,6 +1,6 @@ -import PropTypes from "prop-types"; +import { MDBContainer as Container, MDBIcon as Icon, MDBTypography as Typography } from "mdbreact"; import { Link } from "react-router-dom"; -import { MDBContainer as Container, MDBTypography as Typography, MDBIcon as Icon } from "mdbreact"; +import PropTypes from "prop-types"; function Form(props) { return ( diff --git a/web/app/src/components/form/MutationSelector.js b/web/app/src/components/form/MutationSelector.js index 731e5e3..7820e29 100644 --- a/web/app/src/components/form/MutationSelector.js +++ b/web/app/src/components/form/MutationSelector.js @@ -1,5 +1,5 @@ +import { MDBCol as Col, MDBRow as Row } from "mdbreact"; import PropTypes from "prop-types"; -import { MDBRow as Row, MDBCol as Col } from "mdbreact"; function MutationSelector(props) { const columns = props.mutation_type === "sub" ? 3 : 2; diff --git a/web/app/src/components/form/ProteinSequenceInput.js b/web/app/src/components/form/ProteinSequenceInput.js index 93b79ed..389e4ec 100644 --- a/web/app/src/components/form/ProteinSequenceInput.js +++ b/web/app/src/components/form/ProteinSequenceInput.js @@ -1,5 +1,5 @@ +import { MDBCol as Col, MDBIcon as Icon, MDBRow as Row, MDBTooltip as Tooltip } from "mdbreact"; import PropTypes from "prop-types"; -import { MDBIcon as Icon, MDBTooltip as Tooltip, MDBRow as Row, MDBCol as Col } from "mdbreact"; function ProteinSequenceInput(props) { return ( diff --git a/web/app/src/components/menu/Characterize.js b/web/app/src/components/menu/Characterize.js index 71f90cb..cbba4f1 100644 --- a/web/app/src/components/menu/Characterize.js +++ b/web/app/src/components/menu/Characterize.js @@ -1,11 +1,11 @@ +import { MDBCol as Col, MDBRow as Row } from "mdbreact"; import { useEffect, useState } from "react"; -import { useHistory } from "react-router-dom"; +import { useNavigate } from "react-router-dom"; import PropTypes from "prop-types"; -import { MDBRow as Row, MDBCol as Col } from "mdbreact"; -import LoadingScreen from "../shared/LoadingScreen"; +import api from "../../api"; import { usePrimerDriverContext } from "../../contexts/PrimerDriverContext"; -import { Form, DnaSequenceInput, NumberMismatch, MutationType } from "../form"; -import api from "../../utils/Endpoints"; +import { DnaSequenceInput, Form, MutationType, NumberMismatch } from "../form"; +import LoadingScreen from "../shared/LoadingScreen"; function Characterize(props) { const [formData, setFormData] = useState({}); @@ -16,7 +16,7 @@ function Characterize(props) { const [sequenceLength, setSequenceLength] = useState(0); const [isValid, setIsValid] = useState(false); const [loading, setLoading] = useState(false); - const history = useHistory(); + const navigate = useNavigate(); const { PDDispatch } = usePrimerDriverContext(); const mode = "CHAR"; @@ -63,7 +63,7 @@ function Characterize(props) { loaded: true, }, }); - history.push("/results"); + navigate("/results"); }); } diff --git a/web/app/src/components/menu/DnaView.js b/web/app/src/components/menu/DnaView.js index 4bc878c..7373b26 100644 --- a/web/app/src/components/menu/DnaView.js +++ b/web/app/src/components/menu/DnaView.js @@ -1,10 +1,12 @@ import { useEffect, useState } from "react"; +import { useNavigate } from "react-router-dom"; import PropTypes from "prop-types"; -import { useHistory } from "react-router-dom"; +import api from "../../api"; import { usePrimerDriverContext } from "../../contexts/PrimerDriverContext"; -import { Form, DnaSequenceInput, MutationType, MutationSelector, AdvancedSettings } from "../form"; +import { AdvancedSettings, DnaSequenceInput, Form, MutationSelector, MutationType } from "../form"; import LoadingScreen from "../shared/LoadingScreen"; -import api from "../../utils/Endpoints"; + +const BASES = ["A", "C", "G", "T"]; function DnaView(props) { const [formData, setFormData] = useState({}); @@ -29,7 +31,7 @@ function DnaView(props) { const [primerMode, setPrimerMode] = useState("complementary"); const [expressionSystem, setExpressionSystem] = useState("Homo sapiens"); const { PDDispatch } = usePrimerDriverContext(); - const history = useHistory(); + const navigate = useNavigate(); const mode = "DNA"; useEffect(() => { @@ -40,12 +42,11 @@ function DnaView(props) { }, [PDDispatch]); function validateSequence(sequence) { - sequence = sequence.toUpperCase().split(""); - let filteredSequence = []; - sequence.forEach(char => { - if (["A", "G", "T", "C"].includes(char)) filteredSequence.push(char); - }); - return filteredSequence.join(""); + return sequence + .toUpperCase() + .split("") + .filter(char => BASES.includes(char)) + .join(""); } function handleChangeSequence(e) { @@ -87,7 +88,7 @@ function DnaView(props) { loaded: true, }, }); - history.push("/results"); + navigate("/results"); }); } diff --git a/web/app/src/components/menu/Menu.js b/web/app/src/components/menu/Menu.js index 3c710be..9620fc2 100644 --- a/web/app/src/components/menu/Menu.js +++ b/web/app/src/components/menu/Menu.js @@ -1,8 +1,8 @@ +import { Image } from "cloudinary-react"; +import { MDBCard as Card, MDBCardBody as CardBody, MDBCol as Col, MDBRow as Row } from "mdbreact"; import { useEffect } from "react"; import { Link } from "react-router-dom"; import PropTypes from "prop-types"; -import { Image } from "cloudinary-react"; -import { MDBRow as Row, MDBCol as Col, MDBCard as Card, MDBCardBody as CardBody } from "mdbreact"; import { usePrimerDriverContext } from "../../contexts/PrimerDriverContext"; const menu_data = [ diff --git a/web/app/src/components/menu/ProteinView.js b/web/app/src/components/menu/ProteinView.js index 4092769..5828b12 100644 --- a/web/app/src/components/menu/ProteinView.js +++ b/web/app/src/components/menu/ProteinView.js @@ -1,10 +1,33 @@ import { useEffect, useState } from "react"; -import { useHistory } from "react-router-dom"; +import { useNavigate } from "react-router-dom"; +import PropTypes from "prop-types"; +import api from "../../api"; import { usePrimerDriverContext } from "../../contexts/PrimerDriverContext"; +import { AdvancedSettings, Form, MutationSelector, MutationType, ProteinSequenceInput } from "../form"; import LoadingScreen from "../shared/LoadingScreen"; -import { Form, ProteinSequenceInput, MutationSelector, MutationType, AdvancedSettings } from "../form"; -import api from "../../utils/Endpoints"; -import PropTypes from "prop-types"; + +const AMINO_ACIDS = [ + "A", + "R", + "N", + "D", + "C", + "Q", + "E", + "G", + "H", + "I", + "L", + "K", + "M", + "F", + "P", + "S", + "T", + "W", + "Y", + "V", +]; function ProteinView(props) { const [formData, setFormData] = useState({}); @@ -30,7 +53,7 @@ function ProteinView(props) { const [expressionSystem, setExpressionSystem] = useState("Homo sapiens"); const [expressionList, setExpressionList] = useState([]); const { PDDispatch } = usePrimerDriverContext(); - const history = useHistory(); + const navigate = useNavigate(); const mode = "PRO"; useEffect(() => { @@ -46,36 +69,11 @@ function ProteinView(props) { }, [PDDispatch]); function validateSequence(sequence) { - sequence = sequence.toUpperCase().split(""); - let aminoAcids = [ - "A", - "R", - "N", - "D", - "B", - "C", - "E", - "Q", - "Z", - "G", - "H", - "I", - "L", - "K", - "M", - "F", - "P", - "S", - "T", - "W", - "Y", - "V", - ]; - let filteredSequence = []; - sequence.forEach(char => { - if (aminoAcids.includes(char)) filteredSequence.push(char); - }); - return filteredSequence.join(""); + return sequence + .toUpperCase() + .split("") + .filter(char => AMINO_ACIDS.includes(char)) + .join(""); } function handleChangeSequence(e) { @@ -117,7 +115,7 @@ function ProteinView(props) { loaded: true, }, }); - history.push("/results"); + navigate("/results"); }); } diff --git a/web/app/src/components/menu/Result.js b/web/app/src/components/menu/Result.js index 90530dc..cb9ed0e 100644 --- a/web/app/src/components/menu/Result.js +++ b/web/app/src/components/menu/Result.js @@ -1,12 +1,12 @@ -import { Fragment, useEffect, useState } from "react"; -import { Link, Redirect } from "react-router-dom"; import { + MDBIcon as Icon, MDBTable as Table, - MDBTableHead as TableHead, MDBTableBody as TableBody, - MDBIcon as Icon, + MDBTableHead as TableHead, MDBTypography as Typography, } from "mdbreact"; +import { Fragment, useEffect, useState } from "react"; +import { Link, useNavigate } from "react-router-dom"; import { usePrimerDriverContext } from "../../contexts/PrimerDriverContext"; const styles = { @@ -19,11 +19,16 @@ const styles = { }; function Result() { + const navigate = useNavigate(); const [mode, setMode] = useState(""); const [results, setResults] = useState({}); const [viewLimit, setViewLimit] = useState(10); const { PDState, PDDispatch } = usePrimerDriverContext(); + useEffect(() => { + if (!PDState.loadedResultsFromModule) navigate("/"); + }, [PDState.loadedResultsFromModule]); + useEffect(() => { return () => { PDDispatch({ @@ -63,91 +68,87 @@ function Result() { ); } - if (!PDState.loadedResultsFromModule) { - return ; - } else { - if (typeof results === "object") { - if (mode === "CHAR") + if (typeof results === "object") { + if (mode === "CHAR") + return ( +
+
+ + + {Object.keys(results).map((key, i) => ( + + + + + ))} + +
{key}{results[key]["1"]}
+
+ ); + else { + if (Object.keys(results).length >= 1) { + return ( +
+
+ + {Object.keys(results).length} result{Object.keys(results).length !== 1 && "s"} + + {Object.keys(results).map( + (item, i) => + i < viewLimit && ( + + + + + + + + + {Object.keys(results[(i + 1).toString()]).map((key, j) => ( + + + + + ))} + +
+ {`Primer ${i + 1}`}
{key}{results[(i + 1).toString()][key]}
+ {i + 1 === viewLimit && i + 1 < Object.keys(results).length && ( +
+ +
+ )} + + ), + )} +
+ ); + } else { return (
- - - {Object.keys(results).map((key, i) => ( - - - - - ))} - -
{key}{results[key]["1"]}
+ + {results.data} +
); - else { - if (Object.keys(results).length >= 1) { - return ( -
-
- - {Object.keys(results).length} result{Object.keys(results).length !== 1 && "s"} - - {Object.keys(results).map( - (item, i) => - i < viewLimit && ( - - - - - - - - - {Object.keys(results[(i + 1).toString()]).map((key, j) => ( - - - - - ))} - -
- {`Primer ${i + 1}`}
{key}{results[(i + 1).toString()][key]}
- {i + 1 === viewLimit && i + 1 < Object.keys(results).length && ( -
- -
- )} - - ), - )} -
- ); - } else { - return ( -
-
- - {results.data} - -
- ); - } } - } else { - return ( -
-
-

- Oops! Something went wrong on the server. Please try again later, or{" "} - - report an issue - - . -

-
- ); } + } else { + return ( +
+
+

+ Oops! Something went wrong on the server. Please try again later, or{" "} + + report an issue + + . +

+
+ ); } } diff --git a/web/app/src/contexts/PrimerDriverContext.js b/web/app/src/contexts/PrimerDriverContext.js index bc359d2..1d7307d 100644 --- a/web/app/src/contexts/PrimerDriverContext.js +++ b/web/app/src/contexts/PrimerDriverContext.js @@ -1,4 +1,4 @@ -import { createContext, useReducer, useContext } from "react"; +import { createContext, useContext, useReducer } from "react"; let PrimerDriverContext = createContext(); diff --git a/web/app/src/index.css b/web/app/src/index.css index bdb32d4..b3043f8 100644 --- a/web/app/src/index.css +++ b/web/app/src/index.css @@ -1,13 +1,11 @@ body { margin: 0; - font-family: -apple-system, BlinkMacSystemFont, 'Rubik', 'Segoe UI', 'Roboto', 'Oxygen', - 'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans', 'Helvetica Neue', - sans-serif; + font-family: -apple-system, BlinkMacSystemFont, "Rubik", "Segoe UI", "Roboto", "Oxygen", "Ubuntu", "Cantarell", + "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } code { - font-family: source-code-pro, Menlo, Monaco, Consolas, 'Courier New', - monospace; + font-family: source-code-pro, Menlo, Monaco, Consolas, "Courier New", monospace; } diff --git a/web/app/src/reportWebVitals.js b/web/app/src/reportWebVitals.js index 5253d3a..97d92e2 100644 --- a/web/app/src/reportWebVitals.js +++ b/web/app/src/reportWebVitals.js @@ -1,6 +1,6 @@ const reportWebVitals = onPerfEntry => { if (onPerfEntry && onPerfEntry instanceof Function) { - import('web-vitals').then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => { + import("web-vitals").then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => { getCLS(onPerfEntry); getFID(onPerfEntry); getFCP(onPerfEntry); diff --git a/web/app/src/setupTests.js b/web/app/src/setupTests.js index 8f2609b..1dd407a 100644 --- a/web/app/src/setupTests.js +++ b/web/app/src/setupTests.js @@ -2,4 +2,4 @@ // allows you to do things like: // expect(element).toHaveTextContent(/react/i) // learn more: https://github.com/testing-library/jest-dom -import '@testing-library/jest-dom'; +import "@testing-library/jest-dom"; diff --git a/web/app/src/utils/ErrorBoundary.js b/web/app/src/utils/ErrorBoundary.js index a068358..74a471a 100644 --- a/web/app/src/utils/ErrorBoundary.js +++ b/web/app/src/utils/ErrorBoundary.js @@ -1,5 +1,5 @@ -import { Component } from "react"; import { MDBTypography as Typography } from "mdbreact"; +import { Component } from "react"; class ErrorBoundary extends Component { state = { diff --git a/web/app/src/utils/GAUtil.js b/web/app/src/utils/GAUtil.js new file mode 100644 index 0000000..518695b --- /dev/null +++ b/web/app/src/utils/GAUtil.js @@ -0,0 +1,25 @@ +import { useEffect } from "react"; +import ReactGA from "react-ga"; +import { useLocation } from "react-router-dom"; + +const PROD = (process.env.NODE_ENV ?? "production") === "production"; + +function GAUtil() { + const location = useLocation(); + + useEffect(() => { + if (PROD) { + ReactGA.initialize("UA-162676656-3"); + } + }, []); + + useEffect(() => { + if (PROD) { + ReactGA.pageview(`${location.pathname}${location.search}`); + } + }, [location.pathname, location.search]); + + return null; +} + +export default GAUtil; diff --git a/web/app/yarn.lock b/web/app/yarn.lock index 340cd60..e965b39 100644 --- a/web/app/yarn.lock +++ b/web/app/yarn.lock @@ -2,84 +2,125 @@ # yarn lockfile v1 -"@babel/code-frame@7.10.4": - version "7.10.4" - resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.10.4.tgz#168da1a36e90da68ae8d49c0f1b48c7c6249213a" - integrity sha512-vG6SvB6oYEhvgisZNFRmRCUkLz11c7rp+tbNTynGqc6mS1d5ATd/sGyV6W0KZZnXRKMTzZDRgQT3Ou9jhpAfUg== +"@ampproject/remapping@^2.1.0": + version "2.2.0" + resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.0.tgz#56c133824780de3174aed5ab6834f3026790154d" + 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"@babel/code-frame@^7.16.7", "@babel/code-frame@^7.5.5": +"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.10.4", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.16.0", "@babel/code-frame@^7.16.7", "@babel/code-frame@^7.8.3": version "7.16.7" resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.16.7.tgz#44416b6bd7624b998f5b1af5d470856c40138789" integrity sha512-iAXqUn8IIeBTNd72xsFlgaXHkMBMt6y4HJp1tIaK465CWLT/fG1aqB7ykr95gHHmlBdGbFeWWfyB4NJJ0nmeIg== dependencies: "@babel/highlight" "^7.16.7" -"@babel/compat-data@^7.13.11", "@babel/compat-data@^7.16.4", "@babel/compat-data@^7.16.8": - version "7.16.8" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.16.8.tgz#31560f9f29fdf1868de8cb55049538a1b9732a60" - integrity sha512-m7OkX0IdKLKPpBlJtF561YJal5y/jyI5fNfWbPxh2D/nbzzGI4qRyrD8xO2jB24u7l+5I2a43scCG2IrfjC50Q== +"@babel/code-frame@^7.18.6": + version "7.18.6" + resolved 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"https://registry.yarnpkg.com/css-prefers-color-scheme/-/css-prefers-color-scheme-6.0.3.tgz#ca8a22e5992c10a5b9d315155e7caee625903349" + integrity sha512-4BqMbZksRkJQx2zAjrokiGMd07RqOa2IxIrrN10lyBe9xhn9DEvjUK79J6jkeiv9D9hQFXKb6g1jwU62jziJZA== css-select-base-adapter@^0.1.1: version "0.1.1" @@ -3812,13 +3693,13 @@ css-select@^2.0.0: nth-check "^1.0.2" css-select@^4.1.3: - version "4.2.1" - resolved "https://registry.yarnpkg.com/css-select/-/css-select-4.2.1.tgz#9e665d6ae4c7f9d65dbe69d0316e3221fb274cdd" - integrity sha512-/aUslKhzkTNCQUB2qTX84lVmfia9NyjP3WpDGtj/WxhwBzWBYUV3DgUpurHTme8UTPcPlAD1DJ+b0nN/t50zDQ== + version "4.3.0" + resolved "https://registry.yarnpkg.com/css-select/-/css-select-4.3.0.tgz#db7129b2846662fd8628cfc496abb2b59e41529b" + integrity sha512-wPpOYtnsVontu2mODhA19JrqWxNsfdatRKd64kmpRbQgh1KtItko5sTnEpPdpSaJszTOhEMlF/RPz28qj4HqhQ== dependencies: boolbase "^1.0.0" - css-what "^5.1.0" - domhandler "^4.3.0" + css-what "^6.0.1" + domhandler "^4.3.1" domutils "^2.8.0" nth-check "^2.0.1" @@ -3830,7 +3711,7 @@ css-tree@1.0.0-alpha.37: mdn-data "2.0.4" source-map "^0.6.1" -css-tree@^1.1.2: +css-tree@^1.1.2, css-tree@^1.1.3: version "1.1.3" resolved "https://registry.yarnpkg.com/css-tree/-/css-tree-1.1.3.tgz#eb4870fb6fd7707327ec95c2ff2ab09b5e8db91d" integrity sha512-tRpdppF7TRazZrjJ6v3stzv93qxRcSsFmW6cX0Zm2NVKpxE1WV1HblnghVv9TreireHkqI/VDEsfolRF1p6y7Q== @@ -3850,26 +3731,16 @@ css-what@^3.2.1: resolved "https://registry.yarnpkg.com/css-what/-/css-what-3.4.2.tgz#ea7026fcb01777edbde52124e21f327e7ae950e4" integrity sha512-ACUm3L0/jiZTqfzRM3Hi9Q8eZqd6IK37mMWPLz9PJxkLWllYeRf+EHUSHYEtFop2Eqytaq1FizFVh7XfBnXCDQ== -css-what@^5.1.0: - version "5.1.0" - resolved "https://registry.yarnpkg.com/css-what/-/css-what-5.1.0.tgz#3f7b707aadf633baf62c2ceb8579b545bb40f7fe" - integrity sha512-arSMRWIIFY0hV8pIxZMEfmMI47Wj3R/aWpZDDxWYCPEiOMv6tfOrnpDtgxBYPEQD4V0Y/958+1TdC3iWTFcUPw== +css-what@^6.0.1: + version "6.1.0" + resolved 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"^5.3.0" + postcss-convert-values "^5.1.1" + postcss-discard-comments "^5.1.1" + postcss-discard-duplicates "^5.1.0" + postcss-discard-empty "^5.1.1" + postcss-discard-overridden "^5.1.0" + postcss-merge-longhand "^5.1.5" + postcss-merge-rules "^5.1.1" + postcss-minify-font-values "^5.1.0" + postcss-minify-gradients "^5.1.1" + postcss-minify-params "^5.1.3" + postcss-minify-selectors "^5.2.0" + postcss-normalize-charset "^5.1.0" + postcss-normalize-display-values "^5.1.0" + postcss-normalize-positions "^5.1.0" + postcss-normalize-repeat-style "^5.1.0" + postcss-normalize-string "^5.1.0" + postcss-normalize-timing-functions "^5.1.0" + postcss-normalize-unicode "^5.1.0" + postcss-normalize-url "^5.1.0" + postcss-normalize-whitespace "^5.1.1" + postcss-ordered-values "^5.1.1" + postcss-reduce-initial "^5.1.0" + postcss-reduce-transforms "^5.1.0" + postcss-svgo "^5.1.0" + postcss-unique-selectors "^5.1.1" + +cssnano-utils@^3.1.0: + version "3.1.0" + resolved 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"https://registry.yarnpkg.com/csso/-/csso-4.2.0.tgz#ea3a561346e8dc9f546d6febedd50187cf389529" integrity sha512-wvlcdIbf6pwKEk7vHj8/Bkc0B4ylXZruLvOgs9doS5eOsOpuodOV2zJChSpkp+pRpYQLQMeF04nr3Z68Sta9jA== @@ -3987,27 +3834,14 @@ cssstyle@^2.3.0: cssom "~0.3.6" csstype@^2.0.0, csstype@^2.5.2: - version "2.6.19" - resolved "https://registry.yarnpkg.com/csstype/-/csstype-2.6.19.tgz#feeb5aae89020bb389e1f63669a5ed490e391caa" - integrity sha512-ZVxXaNy28/k3kJg0Fou5MiYpp88j7H9hLZp8PDC3jV0WFjfH5E9xHb56L0W59cPbKbcHXeP4qyT8PrHp8t6LcQ== + version "2.6.20" + resolved "https://registry.yarnpkg.com/csstype/-/csstype-2.6.20.tgz#9229c65ea0b260cf4d3d997cb06288e36a8d6dda" + integrity sha512-/WwNkdXfckNgw6S5R125rrW8ez139lBHWouiBvX8dfMFtcn6V81REDqnH7+CRpRipfYlyU1CmOnOxrmGcFOjeA== csstype@^3.0.2: - version "3.0.10" - resolved "https://registry.yarnpkg.com/csstype/-/csstype-3.0.10.tgz#2ad3a7bed70f35b965707c092e5f30b327c290e5" - integrity 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big.js "^5.2.2" - emojis-list "^3.0.0" - json5 "^2.1.2" +loader-runner@^4.2.0: + version "4.3.0" + resolved "https://registry.yarnpkg.com/loader-runner/-/loader-runner-4.3.0.tgz#c1b4a163b99f614830353b16755e7149ac2314e1" + integrity sha512-3R/1M+yS3j5ou80Me59j7F9IMs4PXs3VqRrm0TU3AbKPxlmpoY1TNscJV/oGJXo8qCatFGTfDbY6W6ipGOYXfg== -loader-utils@^1.1.0, loader-utils@^1.2.3, loader-utils@^1.4.0: +loader-utils@^1.2.3: version "1.4.0" resolved "https://registry.yarnpkg.com/loader-utils/-/loader-utils-1.4.0.tgz#c579b5e34cb34b1a74edc6c1fb36bfa371d5a613" integrity sha512-qH0WSMBtn/oHuwjy/NucEgbx5dbxxnxup9s4PVXJUDHZBQY+s0NWA9rJf53RBnQZxfch7euUui7hpoAPvALZdA== @@ -7214,6 +6428,11 @@ loader-utils@^2.0.0: emojis-list "^3.0.0" json5 "^2.1.2" +loader-utils@^3.2.0: + version "3.2.0" + resolved "https://registry.yarnpkg.com/loader-utils/-/loader-utils-3.2.0.tgz#bcecc51a7898bee7473d4bc6b845b23af8304d4f" + integrity 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lodash.uniq@^4.5.0: version "4.5.0" resolved "https://registry.yarnpkg.com/lodash.uniq/-/lodash.uniq-4.5.0.tgz#d0225373aeb652adc1bc82e4945339a842754773" integrity sha1-0CJTc662Uq3BvILklFM5qEJ1R3M= -"lodash@>=3.5 <5", lodash@^4.17.11, lodash@^4.17.14, lodash@^4.17.15, lodash@^4.17.19, lodash@^4.17.20, lodash@^4.17.21, lodash@^4.17.4, lodash@^4.17.5, lodash@^4.7.0: +lodash@4.17.21, lodash@^4.17.15, lodash@^4.17.20, lodash@^4.17.21, lodash@^4.17.4, lodash@^4.7.0: version "4.17.21" resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.21.tgz#679591c564c3bffaae8454cf0b3df370c3d6911c" integrity sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg== -loglevel@^1.6.8: - version "1.8.0" - resolved "https://registry.yarnpkg.com/loglevel/-/loglevel-1.8.0.tgz#e7ec73a57e1e7b419cb6c6ac06bf050b67356114" - integrity sha512-G6A/nJLRgWOuuwdNuA6koovfEV1YpqqAG4pRUlFaz3jj2QNZ8M4vBqnVA+HBTmU/AMNUtlOsMmSpF6NyOjztbA== - loose-envify@^1.0.0, loose-envify@^1.1.0, loose-envify@^1.2.0, loose-envify@^1.3.1, loose-envify@^1.4.0: version "1.4.0" resolved "https://registry.yarnpkg.com/loose-envify/-/loose-envify-1.4.0.tgz#71ee51fa7be4caec1a63839f7e682d8132d30caf" @@ -7316,13 +6517,6 @@ lower-case@^2.0.2: dependencies: tslib "^2.0.3" -lru-cache@^5.1.1: - version "5.1.1" - resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-5.1.1.tgz#1da27e6710271947695daf6848e847f01d84b920" - integrity sha512-KpNARQA3Iwv+jTA0utUVVbrh+Jlrr1Fv0e56GGzAFOXN7dk/FviaDW8LHmK52DlcH4WP2n6gI8vN1aesBFgo9w== - dependencies: - yallist "^3.0.2" - lru-cache@^6.0.0: version "6.0.0" resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-6.0.0.tgz#6d6fe6570ebd96aaf90fcad1dafa3b2566db3a94" @@ -7336,21 +6530,13 @@ lz-string@^1.4.4: integrity sha1-wNjq82BZ9wV5bh40SBHPTEmNOiY= magic-string@^0.25.0, magic-string@^0.25.7: - version "0.25.7" - resolved "https://registry.yarnpkg.com/magic-string/-/magic-string-0.25.7.tgz#3f497d6fd34c669c6798dcb821f2ef31f5445051" - integrity 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- integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw== - -parallel-transform@^1.1.0: - version "1.2.0" - resolved "https://registry.yarnpkg.com/parallel-transform/-/parallel-transform-1.2.0.tgz#9049ca37d6cb2182c3b1d2c720be94d14a5814fc" - integrity sha512-P2vSmIu38uIlvdcU7fDkyrxj33gTUy/ABO5ZUbGowxNCopBq/OoD42bP4UmMrJoPyk4Uqf0mu3mtWBhHCZD8yg== - dependencies: - cyclist "^1.0.1" - inherits "^2.0.3" - readable-stream "^2.1.5" - -param-case@^3.0.3: +param-case@^3.0.4: version "3.0.4" resolved "https://registry.yarnpkg.com/param-case/-/param-case-3.0.4.tgz#7d17fe4aa12bde34d4a77d91acfb6219caad01c5" integrity sha512-RXlj7zCYokReqWpOPH9oYivUzLYZ5vAPIfEmCTNViosC78F8F0H9y7T7gG2M39ymgutxF5gcFEsyZQSph9Bp3A== @@ -8226,26 +7074,7 @@ parent-module@^1.0.0: dependencies: callsites "^3.0.0" -parse-asn1@^5.0.0, parse-asn1@^5.1.5: - version "5.1.6" - resolved 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postcss@^7.0.6: +postcss@^7.0.35: version "7.0.39" resolved "https://registry.yarnpkg.com/postcss/-/postcss-7.0.39.tgz#9624375d965630e2e1f2c02a935c82a59cb48309" integrity sha512-yioayjNbHn6z1/Bywyb2Y4s3yvDAeXGOyxqD+LnVOinq6Mdmd++SW2wUNVzavyyHxd6+DxzWGIuosg6P1Rj8uA== @@ -9107,14 +7720,14 @@ postcss@^7, postcss@^7.0.0, postcss@^7.0.1, postcss@^7.0.14, postcss@^7.0.17, po picocolors "^0.2.1" source-map "^0.6.1" -postcss@^8.1.0: - version "8.4.5" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.5.tgz#bae665764dfd4c6fcc24dc0fdf7e7aa00cc77f95" - integrity sha512-jBDboWM8qpaqwkMwItqTQTiFikhs/67OYVvblFFTM7MrZjt6yMKd6r2kgXizEbTTljacm4NldIlZnhbjr84QYg== +postcss@^8.3.5, postcss@^8.4.12, postcss@^8.4.4, postcss@^8.4.7: + version "8.4.14" + resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.14.tgz#ee9274d5622b4858c1007a74d76e42e56fd21caf" + integrity sha512-E398TUmfAYFPBSdzgeieK2Y1+1cpdxJx8yXbK/m57nRhKSmk1GB2tO4lbLBtlkfPQTDKfe4Xqv1ASWPpayPEig== dependencies: - nanoid 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renderkid "^3.0.0" -pretty-format@^26.6.0, pretty-format@^26.6.2: +pretty-format@^26.6.2: version "26.6.2" resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-26.6.2.tgz#e35c2705f14cb7fe2fe94fa078345b444120fc93" integrity sha512-7AeGuCYNGmycyQbCqd/3PWH4eOoX/OiCa0uphp57NVTeAGdJGaAliecxwBDHYQCIvrW7aDBZCYeNTP/WX69mkg== @@ -9159,35 +7767,30 @@ pretty-format@^26.6.0, pretty-format@^26.6.2: ansi-styles "^4.0.0" react-is "^17.0.1" -pretty-format@^27.0.0, pretty-format@^27.4.6: - version "27.4.6" - resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-27.4.6.tgz#1b784d2f53c68db31797b2348fa39b49e31846b7" - integrity sha512-NblstegA1y/RJW2VyML+3LlpFjzx62cUrtBIKIWDXEDkjNeleA7Od7nrzcs/VLQvAeV4CgSYhrN39DRN88Qi/g== +pretty-format@^27.0.0, pretty-format@^27.5.1: + version "27.5.1" + resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-27.5.1.tgz#2181879fdea51a7a5851fb39d920faa63f01d88e" + integrity 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strip-ansi "^6.0.1" - -tapable@^1.0.0, tapable@^1.1.3: +tailwindcss@^3.0.2: + version "3.0.24" + resolved "https://registry.yarnpkg.com/tailwindcss/-/tailwindcss-3.0.24.tgz#22e31e801a44a78a1d9a81ecc52e13b69d85704d" + integrity sha512-H3uMmZNWzG6aqmg9q07ZIRNIawoiEcNFKDfL+YzOPuPsXuDXxJxB9icqzLgdzKNwjG3SAro2h9SYav8ewXNgig== + dependencies: + arg "^5.0.1" + chokidar "^3.5.3" + color-name "^1.1.4" + detective "^5.2.0" + didyoumean "^1.2.2" + dlv "^1.1.3" + fast-glob "^3.2.11" + glob-parent "^6.0.2" + is-glob "^4.0.3" + lilconfig "^2.0.5" + normalize-path "^3.0.0" + object-hash "^3.0.0" + picocolors "^1.0.0" + postcss "^8.4.12" + postcss-js "^4.0.0" + postcss-load-config "^3.1.4" + postcss-nested "5.0.6" + postcss-selector-parser "^6.0.10" + postcss-value-parser "^4.2.0" + quick-lru "^5.1.1" + resolve "^1.22.0" + +tapable@^1.0.0: version "1.1.3" resolved "https://registry.yarnpkg.com/tapable/-/tapable-1.1.3.tgz#a1fccc06b58db61fd7a45da2da44f5f3a3e67ba2" integrity 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