From de5f764c0c01df999a8ff21a2b7fea53539d1d84 Mon Sep 17 00:00:00 2001 From: Shane Jaroch Date: Sun, 10 Jul 2022 18:11:51 -0400 Subject: [PATCH 1/1] initial commit --- .banditrc | 3 + .editorconfig | 36 ++ .envrc | 2 + .github/workflows/test.yml | 33 + .gitignore | 128 ++++ .gitmodules | 3 + .pylintrc | 10 + .yamllint.yml | 44 ++ LICENSE | 674 ++++++++++++++++++++ MANIFEST.in | 14 + Makefile | 155 +++++ README.rst | 171 +++++ ntclient/CHANGELOG.md | 67 ++ ntclient/LICENSE | 674 ++++++++++++++++++++ ntclient/__init__.py | 105 +++ ntclient/__main__.py | 149 +++++ ntclient/argparser/__init__.py | 176 +++++ ntclient/argparser/funcs.py | 99 +++ ntclient/argparser/types.py | 17 + ntclient/core/__init__.py | 0 ntclient/core/nnest.py | 19 + ntclient/core/nnr2.py | 9 + ntclient/core/nutprogbar.py | 38 ++ ntclient/ntsqlite | 1 + ntclient/persistence/__init__.py | 37 ++ ntclient/persistence/sql/__init__.py | 70 ++ ntclient/persistence/sql/nt/__init__.py | 41 ++ ntclient/persistence/sql/nt/funcs.py | 93 +++ ntclient/persistence/sql/usda/__init__.py | 101 +++ ntclient/persistence/sql/usda/funcs.py | 158 +++++ ntclient/services/__init__.py | 65 ++ ntclient/services/analyze.py | 354 ++++++++++ ntclient/services/biometrics.py | 53 ++ ntclient/services/recipe.py | 129 ++++ ntclient/services/usda.py | 244 +++++++ ntclient/utils/__init__.py | 96 +++ ntclient/utils/exceptions.py | 20 + nutra | 15 + requirements-lint.txt | 8 + requirements-optional.txt | 1 + requirements.txt | 4 + scripts/nutra | 12 + scripts/nutra.py | 12 + setup.cfg | 45 ++ setup.py | 75 +++ tests/__init__.py | 0 tests/__main__.py | 38 ++ tests/requirements-win_xp-ubu1604.txt | 3 + tests/requirements.txt | 2 + tests/resources/day/dog-simple.csv | 14 + tests/resources/day/dog.csv | 20 + tests/resources/day/human-test.csv | 23 + tests/resources/day/original-dog-simple.csv | 10 + tests/resources/prefs.json | 3 + tests/resources/rda/dog-18lbs.csv | 83 +++ tests/test_cli.py | 286 +++++++++ 56 files changed, 4742 insertions(+) create mode 100644 .banditrc create mode 100644 .editorconfig create mode 100644 .envrc create mode 100644 .github/workflows/test.yml create mode 100644 .gitignore create mode 100644 .gitmodules create mode 100644 .pylintrc create mode 100644 .yamllint.yml create mode 100644 LICENSE create mode 100644 MANIFEST.in create mode 100644 Makefile create mode 100644 README.rst create mode 100644 ntclient/CHANGELOG.md create mode 100644 ntclient/LICENSE create mode 100755 ntclient/__init__.py create mode 100644 ntclient/__main__.py create mode 100644 ntclient/argparser/__init__.py create mode 100644 ntclient/argparser/funcs.py create mode 100644 ntclient/argparser/types.py create mode 100644 ntclient/core/__init__.py create mode 100755 ntclient/core/nnest.py create mode 100755 ntclient/core/nnr2.py create mode 100644 ntclient/core/nutprogbar.py create mode 160000 ntclient/ntsqlite create mode 100644 ntclient/persistence/__init__.py create mode 100644 ntclient/persistence/sql/__init__.py create mode 100644 ntclient/persistence/sql/nt/__init__.py create mode 100644 ntclient/persistence/sql/nt/funcs.py create mode 100644 ntclient/persistence/sql/usda/__init__.py create mode 100644 ntclient/persistence/sql/usda/funcs.py create mode 100644 ntclient/services/__init__.py create mode 100755 ntclient/services/analyze.py create mode 100644 ntclient/services/biometrics.py create mode 100644 ntclient/services/recipe.py create mode 100644 ntclient/services/usda.py create mode 100644 ntclient/utils/__init__.py create mode 100644 ntclient/utils/exceptions.py create mode 100755 nutra create mode 100644 requirements-lint.txt create mode 100644 requirements-optional.txt create mode 100644 requirements.txt create mode 100755 scripts/nutra create mode 100755 scripts/nutra.py create mode 100644 setup.cfg create mode 100644 setup.py create mode 100644 tests/__init__.py create mode 100644 tests/__main__.py create mode 100644 tests/requirements-win_xp-ubu1604.txt create mode 100644 tests/requirements.txt create mode 100644 tests/resources/day/dog-simple.csv create mode 100644 tests/resources/day/dog.csv create mode 100644 tests/resources/day/human-test.csv create mode 100644 tests/resources/day/original-dog-simple.csv create mode 100644 tests/resources/prefs.json create mode 100644 tests/resources/rda/dog-18lbs.csv create mode 100644 tests/test_cli.py diff --git a/.banditrc b/.banditrc new file mode 100644 index 0000000..f5fba94 --- /dev/null +++ b/.banditrc @@ -0,0 +1,3 @@ +assert_used: # B101 + skips: ["*/test_*.py"] + diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..d9f1e38 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,36 @@ +root = true + +[*] +indent_style = space +indent_size = 4 +end_of_line = lf +charset = utf-8 +trim_trailing_whitespace = true + +max_line_length = 100 + + +[{nutra,*.py}] +max_line_length = 88 + + +[*.{yaml,yml}] +indent_size = 2 + + +[Makefile] +indent_style = tab +max_line_length = 120 + + +[*.md] +max_line_length = 90 +trim_trailing_whitespace = false + + +[*.rst] +max_line_length = 79 + + +[{COMMIT_EDITMSG,MERGE_MSG,SQUASH_MSG,git-rebase-todo}] +max_line_length = 72 diff --git a/.envrc b/.envrc new file mode 100644 index 0000000..1c21d04 --- /dev/null +++ b/.envrc @@ -0,0 +1,2 @@ +source .venv/bin/activate +unset PS1 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..4091385 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,33 @@ +--- +name: CI +"on": + push: {} + +jobs: + test: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + with: + submodules: recursive + + - name: Reload Cache / pip + uses: actions/cache@v3 + with: + path: ~/.cache/pip + key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} + restore-keys: | + ${{ runner.os }}-pip- + + - name: Install requirements + # NOTE: container lacks OS dist for testresources/launchpadlib + run: | + pip install testresources==2.0.1 + make _deps + + - name: Lint + run: make _lint + + - name: Test + run: make _test diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..c99d0b3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,128 @@ +# macOS/backup files +.~* +._* +.DS_Store +*.swp + +# Our files +.vscode/ +.idea/ +__sha__.py +*.sqlite + +#################### +## Python Ignores ## +#################### + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ +.pytest_cache/ +Pipfile* + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..37de861 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "ntclient/ntsqlite"] + path = ntclient/ntsqlite + url = https://github.com/nutratech/nt-sqlite.git diff --git a/.pylintrc b/.pylintrc new file mode 100644 index 0000000..e7345a8 --- /dev/null +++ b/.pylintrc @@ -0,0 +1,10 @@ +[MASTER] + +fail-under=9.5 + + +[MESSAGES CONTROL] + +disable= + fixme, + consider-using-f-string, diff --git a/.yamllint.yml b/.yamllint.yml new file mode 100644 index 0000000..757ef82 --- /dev/null +++ b/.yamllint.yml @@ -0,0 +1,44 @@ +--- +rules: + braces: + min-spaces-inside: 0 + max-spaces-inside: 1 + brackets: + min-spaces-inside: 0 + max-spaces-inside: 0 + colons: + max-spaces-before: 0 + max-spaces-after: 1 + commas: + max-spaces-before: 0 + min-spaces-after: 1 + max-spaces-after: 1 + comments: + level: warning + require-starting-space: yes + min-spaces-from-content: 1 + comments-indentation: + level: warning + document-end: disable + document-start: + level: warning + present: yes + empty-lines: + max: 2 + max-start: 0 + max-end: 0 + hyphens: + max-spaces-after: 1 + indentation: + spaces: 2 + indent-sequences: yes + check-multi-line-strings: no + key-duplicates: {} + line-length: + level: warning + max: 80 + allow-non-breakable-words: yes + new-line-at-end-of-file: { level: error } + new-lines: + type: unix + trailing-spaces: {} diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..da653db --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,14 @@ +include requirements.txt +include requirements-*.txt + +include ntclient/LICENSE +include ntclient/CHANGELOG.md + +include ntclient/ntsqlite/LICENSE +include ntclient/ntsqlite/README.rst +include ntclient/ntsqlite/CHANGELOG.md +graft ntclient/ntsqlite/sql/ + +global-exclude *.sqlite3 + +global-exclude __pycache__/* diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..f414d91 --- /dev/null +++ b/Makefile @@ -0,0 +1,155 @@ +SHELL=/bin/bash + +.DEFAULT_GOAL := _help + +# NOTE: must put a character and two pound "\t##" to show up in this list. Keep it brief! IGNORE_ME +.PHONY: _help +_help: + @grep -h "##" $(MAKEFILE_LIST) | grep -v IGNORE_ME | sed -e 's/##//' | column -t -s $$'\t' + + + +# --------------------------------------- +# init & venv +# --------------------------------------- +.PHONY: init +init: ## Set up a Python virtual environment + git submodule update --init + if [ ! -d .venv ]; then \ + /usr/bin/python3 -m venv .venv; \ + fi + - direnv allow + @echo -e "\r\nNOTE: activate venv, and run 'make deps'\r\n" + @echo -e "HINT: run 'source .venv/bin/activate'" + + +PYTHON ?= $(shell which python) +PWD ?= $(shell pwd) +.PHONY: _venv +_venv: + # Test to enforce venv usage across important make targets + [ "$(PYTHON)" = "$(PWD)/.venv/bin/python" ] || [ "$(PYTHON)" = "$(PWD)/.venv/Scripts/python" ] + + +# --------------------------------------- +# Install requirements +# --------------------------------------- + +PIP := python -m pip +REQ_OPT := requirements-optional.txt +REQ_LINT := requirements-lint.txt +REQ_TEST := tests/requirements.txt +REQ_OLD := tests/requirements-win_xp-ubu1604.txt +.PHONY: _deps +_deps: + $(PIP) install wheel + $(PIP) install -r requirements.txt + - $(PIP) install -r $(REQ_OPT) + - $(PIP) install -r $(REQ_LINT) + - $(PIP) install -r $(REQ_TEST) || (echo "\r\nTEST REQs failed... try old version" && $(PIP) install -r $(REQ_OLD)) + +.PHONY: deps +deps: _venv _deps ## Install requirements + + +# --------------------------------------- +# Format, lint, test +# --------------------------------------- + +.PHONY: format +format: + isort $(LINT_LOCS) + autopep8 --recursive --in-place --max-line-length 88 $(LINT_LOCS) + black $(LINT_LOCS) + + +LINT_LOCS := ntclient/ tests/ scripts/ nutra setup.py +YAML_LOCS := ntclient/ntsqlite/.*.yml .github/workflows/ .*.yml +# NOTE: yamllint ntclient/ntsqlite/.travis.yml ? (submodule) +# NOTE: doc8 ntclient/ntsqlite/README.rst ? (submodule) +.PHONY: _lint +_lint: + # check formatting: Python + pycodestyle --max-line-length=99 --statistics $(LINT_LOCS) + autopep8 --recursive --diff --max-line-length 88 --exit-code $(LINT_LOCS) + isort --diff --check $(LINT_LOCS) + black --check $(LINT_LOCS) + # lint RST (last param is search term, NOT ignore) + doc8 --quiet *.rst ntclient/ntsqlite/*.rst + # lint YAML + yamllint $(YAML_LOCS) + # lint Python + bandit -q -c .banditrc -r $(LINT_LOCS) + mypy $(LINT_LOCS) + flake8 $(LINT_LOCS) + pylint $(LINT_LOCS) + +.PHONY: lint +lint: _venv _lint ## Lint code and documentation + + +TEST_HOME := tests/ +MIN_COV := 80 +.PHONY: _test +_test: + coverage run -m pytest -v -s -p no:cacheprovider -o log_cli=true $(TEST_HOME) + coverage report + +.PHONY: test +test: _venv _test ## Run CLI unittests + + +# --------------------------------------- +# SQLite submodule: nt-sqlite +# --------------------------------------- + +# TODO: why does this still work? Is this what `ntserv.ntdb.sql` should do? + +.PHONY: ntsqlite/build +ntsqlite/build: + python ntclient/ntsqlite/sql/__init__.py + +# TODO: nt-sqlite/test + + +# --------------------------------------- +# Python build stuff +# --------------------------------------- + +.PHONY: _build +_build: + python setup.py --quiet sdist + +.PHONY: build +build: _venv _build clean ## Create sdist binary *.tar.gz + +.PHONY: _install +_install: + python -m pip install wheel + python -m pip install . + python -m pip show nutra + - python -c 'import shutil; print(shutil.which("nutra"));' + nutra -v + +.PHONY: install +install: _venv _install ## pip install nutra + +.PHONY: _uninstall +_uninstall: + python -m pip uninstall -y nutra + +.PHONY: uninstall +uninstall: _venv _uninstall ## pip uninstall nutra + + +# --------------------------------------- +# Clean +# --------------------------------------- + +.PHONY: clean +clean: ## Clean up __pycache__ and leftover bits + rm -f .coverage ntclient/ntsqlite/sql/nt.sqlite3 + rm -rf build/ + rm -rf nutra.egg-info/ + rm -rf .pytest_cache/ .mypy_cache/ + find ntclient/ tests/ -name __pycache__ -o -name .coverage -o -name .pytest_cache | xargs rm -rf diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..47f0390 --- /dev/null +++ b/README.rst @@ -0,0 +1,171 @@ +************** + nutratracker +************** + +.. image:: https://badgen.net/pypi/v/nutra + :target: https://pypi.org/project/nutra/ + :alt: Latest version unknown| +.. image:: https://github.com/nutratech/cli/actions/workflows/test.yml/badge.svg + :target: https://github.com/nutratech/cli/actions/workflows/test.yml + :alt: Build status unknown| +.. image:: https://pepy.tech/badge/nutra/month + :target: https://pepy.tech/project/nutra + :alt: Monthly downloads unknown| +.. image:: https://img.shields.io/pypi/pyversions/nutra.svg + :alt: Python3 (3.4 - 3.10)| +.. image:: https://badgen.net/badge/code%20style/black/000 + :target: https://github.com/ambv/black + :alt: Code style: black| +.. image:: https://badgen.net/pypi/license/nutra + :target: https://www.gnu.org/licenses/gpl-3.0.en.html + :alt: License GPL-3 + +Extensible command-line tools for nutrient analysis. + +*Requires:* + +- Python 3.4.0 or later (lzma, ssl & sqlite3 modules) [Win XP / Ubuntu 16.04] +- Packages: see ``setup.py``, ``requirements.txt``, and ``config`` folder +- Internet connection, to download food database & package dependencies + +See nt database: https://github.com/nutratech/nt-sqlite + +See usda database: https://github.com/nutratech/usda-sqlite + +Notes +===== + +On Windows you should check the box during the Python installer +to include ``Scripts`` directory in your ``$PATH``. This can be done +manually after installation too. + +Linux may need to install ``python-dev`` package to build +``python-Levenshtein``. + +Windows users may not be able to install ``python-Levenshtein``. + +Mac and Linux developers will do well to install ``direnv``. + +Main program works 100%, but test and lint may not on older operating +systems (Ubuntu 16.04, Windows XP). + +Install PyPi release (from pip) +=============================== + +.. code-block:: bash + + pip install nutra + +(**Specify:** flag ``-U`` to upgrade, or ``--pre`` for development releases) + +Using the source code directly +============================== +Clone down, initialize ``nt-sqlite`` submodule, and install requirements: + +.. code-block:: bash + + git clone https://github.com/nutratech/cli.git + cd cli + make init + # source .venv/bin/activate # uncomment if NOT using direnv + make deps + + ./nutra -h + +Initialize the DBs (nt and usda). + +.. code-block:: bash + + # source .venv/bin/activate # uncomment if NOT using direnv + ./nutra init + + # Or install and run as package script + make install + nutra init + +If installed (or inside ``cli``) folder, the program can also run +with ``python -m ntclient`` + +Building the PyPi release +######################### + +.. code-block:: bash + + # source .venv/bin/activate # uncomment if NOT using direnv + make build # python3 setup.py --quiet sdist + twine upload dist/nutra-X.X.X.tar.gz + +Linting & Tests +=============== + +Install the dependencies (``make deps``) and then: + +.. code-block:: bash + + # source .venv/bin/activate # uncomment if NOT using direnv + make format lint test + +Argcomplete (tab completion on Linux/macOS) +=========================================== + +After installing nutra, argcomplete package should also be installed, + +Simply run the following out of a ``bash`` shell: + +.. code-block:: bash + + activate-global-python-argcomplete + +Then you can press tab to fill in or complete subcommands +and to list argument flags. + +**NOTE:** This is a work in progress, we are adding more autocomplete +functions. + +Currently Supported Data +======================== + +**USDA Stock database** + +- Standard reference database (SR28) `[7794 foods]` + + +**Relative USDA Extensions** + +- Flavonoid, Isoflavonoids, and Proanthocyanidins `[1352 foods]` + +Usage +===== + +Requires internet connection to download initial datasets. +Run ``nutra init`` for this step. + +Run the ``nutra`` script to output usage. + +Usage: ``nutra [options] `` + + +Commands +######## + +:: + + usage: nutra [-h] [-v] [-d] [--no-pager] + {init,nt,search,sort,anl,day,recipe,bio} ... + + optional arguments: + -h, --help show this help message and exit + -v, --version show program's version number and exit + -d, --debug enable detailed error messages + --no-pager disable paging (print full output) + + nutra subcommands: + {init,nt,search,sort,anl,day,recipe,bio} + init setup profiles, USDA and NT database + nt list out nutrients and their info + search search foods by name, list overview info + sort sort foods by nutrient ID + anl analyze food(s) + day analyze a DAY.csv file, RDAs optional + recipe list and analyze recipes + bio view, add, remove biometric logs diff --git a/ntclient/CHANGELOG.md b/ntclient/CHANGELOG.md new file mode 100644 index 0000000..c690c1d --- /dev/null +++ b/ntclient/CHANGELOG.md @@ -0,0 +1,67 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [Unreleased] + +### Added + +- Download cache & checksum verification +- Basic functionality of `import` and `export` subcommands +- `[DEVELOPMENT]` Added `Makefile` with easy commands for `init`, `lint`, `test`, etc + +## [0.2.2] - 2022-04-08 + +### Added + +- Limit search & sort results to top `n` results (e.g. top 10 or top 100) +- Enhanced terminal sizing (buffer termination) +- Pydoc PAGING flag via `--no-pager` command line arg (with `set_flags()` method) +- Check for appropriate `ntsqlite` database version +- `[DEVELOPMENT]` Special `file_or_dir_path` and `file_path` custom type validators + for argparse +- `[DEVELOPMENT]` Added special requirements files for + (`test`, `lint`, `optional` [Levenshtein], and `win_xp-test` [Python 3.4]) +- `[DEVELOPMENT]` Added `CHANGELOG.md` file + +### Changed + +- Print `exit_code` in DEBUG mode (`--debug` flag/arg) +- Moved `subparsers` module in `ntclient.argparser` to `__init__` +- Moved tests out of `ntclient/` and into `tests/` folder + +## [0.2.1] - 2021-05-30 + +### Added + +- Python 3.4.3 support (Windows XP and Ubuntu 16.04) +- Debug flag (`--debug | -d`) for all commands + +### Changed + +- Overall structure with main file and argparse methods +- Use soft pip requirements `~=` instead of `==` +- `DEFAULT` and `OVER` colors + +### Removed + +- guid columns from `ntsqlite` submodule + +## [0.2.0] - 2021-05-21 + +### Added + +- SQLite support for `usda` and `nt` schemas (removed API calls to remote server) +- Preliminary support for `recipe` and `bio` subcommands +- On-boarding process with `init` subcommand +- Support for `argcomplete` on `bash` (Linux/macOS) +- Tests + +## [0.0.38] - 2020-08-01 + +### Added + +- Support for analysis of day CSV files diff --git a/ntclient/LICENSE b/ntclient/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/ntclient/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/ntclient/__init__.py b/ntclient/__init__.py new file mode 100755 index 0000000..b2cb6cc --- /dev/null +++ b/ntclient/__init__.py @@ -0,0 +1,105 @@ +# -*- coding: utf-8 -*- +""" +Created on Fri Jan 31 16:01:31 2020 + +@author: shane + +This file is part of nutra, a nutrient analysis program. + https://github.com/nutratech/cli + https://pypi.org/project/nutra/ + +nutra is an extensible nutrient analysis and composition application. +Copyright (C) 2018-2022 Shane Jaroch + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +""" + +import argparse +import os +import platform +import shutil +import sys + +from ntclient.ntsqlite.sql import NT_DB_NAME + +# Package info +__title__ = "nutra" +__version__ = "0.2.3.dev0" +__author__ = "Shane Jaroch" +__email__ = "nutratracker@gmail.com" +__license__ = "GPL v3" +__copyright__ = "Copyright 2018-2022 Shane Jaroch" +__url__ = "https://github.com/nutratech/cli" + +# Sqlite target versions +__db_target_nt__ = "0.0.4" +__db_target_usda__ = "0.0.8" + +# Global variables +ROOT_DIR = os.path.abspath(os.path.dirname(__file__)) +NUTRA_DIR = os.path.join(os.path.expanduser("~"), ".nutra") +USDA_DB_NAME = "usda.sqlite" +# NT_DB_NAME = "nt.sqlite" # defined in ntclient.ntsqlite.sql +DEBUG = False +PAGING = True + +NTSQLITE_BUILDPATH = os.path.join(ROOT_DIR, "ntsqlite", "sql", NT_DB_NAME) +NTSQLITE_DESTINATION = os.path.join(NUTRA_DIR, NT_DB_NAME) + +# Check Python version +PY_MIN_VER = (3, 4, 0) +PY_SYS_VER = sys.version_info[0:3] +PY_MIN_STR = ".".join(str(x) for x in PY_MIN_VER) +PY_SYS_STR = ".".join(str(x) for x in PY_SYS_VER) +if PY_SYS_VER < PY_MIN_VER: + print("ERROR: nutra requires Python %s or later to run" % PY_MIN_STR) + print("HINT: You're running Python %s" % PY_SYS_STR) + sys.exit(1) + +# Buffer truncation +BUFFER_WD = shutil.get_terminal_size()[0] +BUFFER_HT = shutil.get_terminal_size()[1] + +DEFAULT_RESULT_LIMIT = BUFFER_HT - 4 + +DEFAULT_DAY_H_BUFFER = BUFFER_WD - 4 if BUFFER_WD > 12 else 8 + +DECREMENT = 1 if platform.system() == "Windows" else 0 +DEFAULT_SORT_H_BUFFER = ( + BUFFER_WD - (38 + DECREMENT) if BUFFER_WD > 50 else (12 - DECREMENT) +) +DEFAULT_SEARCH_H_BUFFER = ( + BUFFER_WD - (50 + DECREMENT) if BUFFER_WD > 70 else (20 - DECREMENT) +) + + +def set_flags(args: argparse.Namespace) -> None: + """ + Sets + DEBUG flag + PAGING flag + from main (after arg parse). Accessible throughout package + """ + global DEBUG, PAGING # pylint: disable=global-statement + DEBUG = args.debug + PAGING = not args.no_paging + + if DEBUG: + print("Console size: %sh x %sw" % (BUFFER_HT, BUFFER_WD)) + + +# TODO: +# nested nutrient tree, like: http://www.whfoods.com/genpage.php?tname=nutrientprofile&dbid=132 +# attempt to record errors in failed try/catch block (bottom of __main__.py) +# make use of argcomplete.warn(msg) ? diff --git a/ntclient/__main__.py b/ntclient/__main__.py new file mode 100644 index 0000000..e500e9c --- /dev/null +++ b/ntclient/__main__.py @@ -0,0 +1,149 @@ +# -*- coding: utf-8 -*- +""" +Created on Fri Jan 31 16:02:19 2020 + +@author: shane + +This file is part of nutra, a nutrient analysis program. + https://github.com/nutratech/cli + https://pypi.org/project/nutra/ + +nutra is an extensible nutrient analysis and composition application. +Copyright (C) 2018-2022 Shane Jaroch + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +""" +import argparse +import sys +import time +from typing import Sequence +from urllib.error import HTTPError, URLError + +import argcomplete +from colorama import init as colorama_init + +from ntclient import ( + __db_target_nt__, + __db_target_usda__, + __title__, + __version__, + set_flags, +) +from ntclient.argparser import build_subcommands +from ntclient.persistence import persistence_init +from ntclient.utils.exceptions import SqlException + +colorama_init() + + +def build_argparser() -> argparse.ArgumentParser: + """Adds all subparsers and parsing logic""" + + arg_parser = argparse.ArgumentParser(prog=__title__) + arg_parser.add_argument( + "-v", + "--version", + action="version", + version="{0} cli version {1} ".format(__title__, __version__) + + "[DB usda v{0}, nt v{1}]".format(__db_target_usda__, __db_target_nt__), + ) + + arg_parser.add_argument( + "-d", "--debug", action="store_true", help="enable detailed error messages" + ) + arg_parser.add_argument( + "--no-pager", + dest="no_paging", + action="store_true", + help="disable paging (print full output)", + ) + + # Subparsers + subparsers = arg_parser.add_subparsers(title="%s subcommands" % __title__) + build_subcommands(subparsers) + + return arg_parser + + +def main(args: Sequence[str] = None) -> int: + """Main method for CLI""" + + start_time = time.time() + arg_parser = build_argparser() + argcomplete.autocomplete(arg_parser) + + def parse_args() -> argparse.Namespace: + """Returns parsed args""" + if args is None: + return arg_parser.parse_args() + return arg_parser.parse_args(args=args) + + def func(parser: argparse.Namespace) -> tuple: + """Executes a function for a given argument call to the parser""" + if hasattr(parser, "func"): + # More than an empty command, so initialize the storage folder + persistence_init() + + args_dict = dict(vars(parser)) + for expected_arg in ["func", "debug", "no_paging"]: + args_dict.pop(expected_arg) + + # Run function + if args_dict: + return parser.func(args=parser) + return parser.func() + + # Otherwise print help + arg_parser.print_help() + return 1, None + + # Build the parser, set flags + _parser = parse_args() + set_flags(_parser) + from ntclient import DEBUG # pylint: disable=import-outside-toplevel + + # TODO: bug reporting? + # Try to run the function + exit_code = None + try: + exit_code, *_results = func(_parser) + return exit_code + except SqlException as sql_exception: + print("Issue with an sqlite database: " + repr(sql_exception)) + if DEBUG: + raise + except HTTPError as http_error: + err_msg = "{0}: {1}".format(http_error.code, repr(http_error)) + print("Server response error, try again: " + err_msg) + if DEBUG: + raise + except URLError as url_error: + print("Connection error, check your internet: " + repr(url_error.reason)) + if DEBUG: + raise + except Exception as exception: # pylint: disable=broad-except + print("There was an unforeseen error: " + repr(exception)) + if DEBUG: + raise + finally: + if DEBUG: + exc_time = time.time() - start_time + print("\nExecuted in: %s ms" % round(exc_time * 1000, 1)) + print("Exit code: %s" % exit_code) + + return exit_code + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/ntclient/argparser/__init__.py b/ntclient/argparser/__init__.py new file mode 100644 index 0000000..1e62671 --- /dev/null +++ b/ntclient/argparser/__init__.py @@ -0,0 +1,176 @@ +"""Main module for things related to argparse""" + +from ntclient.argparser import funcs as parser_funcs +from ntclient.argparser import types + + +def build_subcommands(subparsers) -> None: + """Attaches subcommands to main parser""" + build_init_subcommand(subparsers) + build_nt_subcommand(subparsers) + build_search_subcommand(subparsers) + build_sort_subcommand(subparsers) + build_analyze_subcommand(subparsers) + build_day_subcommand(subparsers) + build_recipe_subcommand(subparsers) + build_biometric_subcommand(subparsers) + + +################################################################################ +# Methods to build subparsers, and attach back to main arg_parser +################################################################################ +def build_init_subcommand(subparsers) -> None: + """Self running init command""" + init_parser = subparsers.add_parser( + "init", help="setup profiles, USDA and NT database" + ) + init_parser.add_argument( + "-y", + dest="yes", + action="store_true", + help="automatically agree to (potentially slow) USDA download", + ) + init_parser.set_defaults(func=parser_funcs.init) + + +def build_nt_subcommand(subparsers) -> None: + """Lists out nutrients details with computed totals and averages""" + nutrient_parser = subparsers.add_parser( + "nt", help="list out nutrients and their info" + ) + nutrient_parser.set_defaults(func=parser_funcs.nutrients) + + +def build_search_subcommand(subparsers) -> None: + """Search: terms [terms ... ]""" + search_parser = subparsers.add_parser( + "search", help="search foods by name, list overview info" + ) + search_parser.add_argument( + "terms", + nargs="+", + help='search query, e.g. "grass fed beef" or "ultraviolet mushrooms"', + ) + search_parser.add_argument( + "-t", + dest="top", + metavar="N", + type=int, + help="show top N results (defaults to console height)", + ) + search_parser.add_argument( + "-g", + dest="fdgrp_id", + type=int, + help="filter by a specific food group ID", + ) + search_parser.set_defaults(func=parser_funcs.search) + + +def build_sort_subcommand(subparsers) -> None: + """Sort foods ranked by nutr_id, per 100g or 200kcal""" + sort_parser = subparsers.add_parser("sort", help="sort foods by nutrient ID") + sort_parser.add_argument( + "-c", + dest="kcal", + action="store_true", + help="sort by value per 200 kcal, instead of per 100 g", + ) + sort_parser.add_argument( + "-t", + dest="top", + metavar="N", + type=int, + help="show top N results (defaults to console height)", + ) + sort_parser.add_argument("nutr_id", type=int) + sort_parser.set_defaults(func=parser_funcs.sort) + + +def build_analyze_subcommand(subparsers) -> None: + """Analyzes (foods only for now)""" + analyze_parser = subparsers.add_parser("anl", help="analyze food(s)") + analyze_parser.add_argument( + "-g", + dest="grams", + type=float, + help="scale to custom number of grams (default is 100g)", + ) + analyze_parser.add_argument("food_id", type=int, nargs="+") + analyze_parser.set_defaults(func=parser_funcs.analyze) + + +def build_day_subcommand(subparsers) -> None: + """Analyzes a DAY.csv, uses new colored progress bar spec""" + day_parser = subparsers.add_parser( + "day", help="analyze a DAY.csv file, RDAs optional" + ) + day_parser.add_argument( + "food_log", + metavar="food_log.csv", + nargs="+", + type=types.file_or_dir_path, + help="path to CSV file of food log", + ) + day_parser.add_argument( + "-r", + dest="rda", + metavar="rda.csv", + type=types.file_path, + help="provide a custom RDA file in csv format", + ) + day_parser.set_defaults(func=parser_funcs.day) + + +def build_recipe_subcommand(subparsers) -> None: + """View, add, edit, delete recipes""" + recipe_parser = subparsers.add_parser("recipe", help="list and analyze recipes") + recipe_subparsers = recipe_parser.add_subparsers(title="recipe subcommands") + + recipe_anl_parser = recipe_subparsers.add_parser( + "anl", help="view and analyze for recipe" + ) + recipe_anl_parser.add_argument( + "recipe_id", type=int, help="view (and analyze) recipe by ID" + ) + recipe_anl_parser.set_defaults(func=parser_funcs.recipe) + + recipe_import_parser = recipe_subparsers.add_parser("import", help="add a recipe") + recipe_import_parser.add_argument( + "path", + type=types.file_or_dir_path, + help="path to recipe.csv (or folder with multiple CSV files)", + ) + recipe_import_parser.set_defaults(func=parser_funcs.recipe_import) + + # TODO: edit.. support renaming, and overwriting/re-importing food_amts (from CSV) + + recipe_delete_parser = recipe_subparsers.add_parser( + "delete", help="delete a recipe(s) by ID or range" + ) + recipe_delete_parser.add_argument("recipe_id", type=int, help="delete recipe by ID") + recipe_delete_parser.set_defaults(func=parser_funcs.recipe_delete) + + recipe_parser.set_defaults(func=parser_funcs.recipes) + + +def build_biometric_subcommand(subparsers) -> None: + """View biometrics, and view, add, edit, delete log entries""" + bio_parser = subparsers.add_parser("bio", help="view, add, remove biometric logs") + bio_subparsers = bio_parser.add_subparsers(title="biometric subcommands") + + bio_log_parser = bio_subparsers.add_parser("log", help="manage biometric logs") + bio_log_subparsers = bio_log_parser.add_subparsers( + title="biometric log subcommands" + ) + bio_log_parser.set_defaults(func=parser_funcs.bio_log) + + bio_log_add_parser = bio_log_subparsers.add_parser( + "add", help="add a biometric log" + ) + bio_log_add_parser.add_argument( + "biometric_val", help="id,value pairs, e.g. 22,59 23,110 24,65 ", nargs="+" + ) + bio_log_add_parser.set_defaults(func=parser_funcs.bio_log_add) + + bio_parser.set_defaults(func=parser_funcs.bio) diff --git a/ntclient/argparser/funcs.py b/ntclient/argparser/funcs.py new file mode 100644 index 0000000..d1a8605 --- /dev/null +++ b/ntclient/argparser/funcs.py @@ -0,0 +1,99 @@ +"""Current home to subparsers and service-level logic""" +import os + +from ntclient import services + + +def init(args): + """Wrapper init method for persistence stuff""" + return services.init(yes=args.yes) + + +################################################################################ +# Nutrients, search and sort +################################################################################ +def nutrients(): + """List nutrients""" + return services.usda.list_nutrients() + + +def search(args): + """Searches all dbs, foods, recipes, recents and favorites.""" + if args.top: + return services.usda.search( + words=args.terms, fdgrp_id=args.fdgrp_id, limit=args.top + ) + return services.usda.search(words=args.terms, fdgrp_id=args.fdgrp_id) + + +def sort(args): + """Sorts based on nutrient id""" + if args.top: + return services.usda.sort_foods(args.nutr_id, by_kcal=args.kcal, limit=args.top) + return services.usda.sort_foods(args.nutr_id, by_kcal=args.kcal) + + +################################################################################ +# Analysis and Day scoring +################################################################################ +def analyze(args): + """Analyze a food""" + food_ids = args.food_id + grams = args.grams + + return services.analyze.foods_analyze(food_ids, grams) + + +def day(args): + """Analyze a day's worth of meals""" + day_csv_paths = args.food_log + day_csv_paths = [os.path.expanduser(x) for x in day_csv_paths] + rda_csv_path = os.path.expanduser(args.rda) if args.rda else None + + return services.analyze.day_analyze(day_csv_paths, rda_csv_path=rda_csv_path) + + +################################################################################ +# Biometrics +################################################################################ +def bio(): + """List biometrics""" + return services.biometrics.biometrics() + + +def bio_log(): + """List biometric logs""" + return services.biometrics.biometric_logs() + + +def bio_log_add(args): + """Add a biometric log entry""" + bio_vals = { + int(x.split(",")[0]): float(x.split(",")[1]) for x in args.biometric_val + } + + return services.biometrics.biometric_add(bio_vals) + + +################################################################################ +# Recipes +################################################################################ +def recipes(): + """Return recipes""" + return services.recipe.recipes_overview() + + +def recipe(args): + """Return recipe view (analysis)""" + return services.recipe.recipe_overview(args.recipe_id) + + +def recipe_import(args): + """Add a recipe""" + # TODO: custom serving sizes, not always in grams? + return services.recipe.recipe_import(args.path) + + +def recipe_delete(args): + """Delete a recipe""" + return services.recipe.recipe_delete(args.recipe_id) diff --git a/ntclient/argparser/types.py b/ntclient/argparser/types.py new file mode 100644 index 0000000..1943cf7 --- /dev/null +++ b/ntclient/argparser/types.py @@ -0,0 +1,17 @@ +"""Custom types for argparse validation""" +import argparse +import os + + +def file_path(string): + """Returns file if it exists, else raises argparse error""" + if os.path.isfile(string): + return string + raise argparse.ArgumentTypeError('FileNotFoundError: "%s"' % string) + + +def file_or_dir_path(string): + """Returns path if it exists, else raises argparse error""" + if os.path.exists(string): + return string + raise argparse.ArgumentTypeError('FileNotFoundError: "%s"' % string) diff --git a/ntclient/core/__init__.py b/ntclient/core/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/ntclient/core/nnest.py b/ntclient/core/nnest.py new file mode 100755 index 0000000..c22d7c7 --- /dev/null +++ b/ntclient/core/nnest.py @@ -0,0 +1,19 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Sat Aug 29 19:43:55 2020 + +@author: shane +""" + +nnest = { + "basics": ["Protein", "Carbs", "Fats", "Fiber", "Calories"], + "macro_details": {"Carbs": {}, "Fat": {}}, + "micro_nutrients": { + "Vitamins": {"Water-Soluble": {}, "Fat-Soluble": {}}, + "Minerals": [], + }, + "fatty_acids": {}, + "amino_acids": set(), + "other_components": {}, +} diff --git a/ntclient/core/nnr2.py b/ntclient/core/nnr2.py new file mode 100755 index 0000000..dd94458 --- /dev/null +++ b/ntclient/core/nnr2.py @@ -0,0 +1,9 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Fri Jul 31 21:23:51 2020 + +@author: shane +""" + +# NOTE: based on diff --git a/ntclient/core/nutprogbar.py b/ntclient/core/nutprogbar.py new file mode 100644 index 0000000..38aa10d --- /dev/null +++ b/ntclient/core/nutprogbar.py @@ -0,0 +1,38 @@ +"""Temporary [wip] module for more visual (& colorful) RDA output""" + + +def nutprogbar(food_amts, food_analyses, nutrients): + """Returns progress bars, colorized, for foods analyses""" + + def tally(): + for nut in nut_percs: + # TODO: get RDA values from nt DB, tree node nested organization + print(nut) + + food_analyses = { + x[0]: {y[1]: y[2] for y in food_analyses if y[0] == x[0]} for x in food_analyses + } + + # print(food_ids) + # print(food_analyses) + + nut_amts = {} + + for food_id, grams in food_amts.items(): + # r = grams / 100.0 + analysis = food_analyses[food_id] + for nutrient_id, amt in analysis.items(): + if nutrient_id not in nut_amts: + nut_amts[nutrient_id] = amt + else: + nut_amts[nutrient_id] += amt + + nut_percs = {} + + for nutrient_id, amt in nut_amts.items(): + # TODO: if not rda, show raw amounts? + if isinstance(nutrients[nutrient_id][1], float): + nut_percs[nutrient_id] = round(amt / nutrients[nutrient_id][1], 3) + + tally() + return nut_percs diff --git a/ntclient/ntsqlite b/ntclient/ntsqlite new file mode 160000 index 0000000..a245574 --- /dev/null +++ b/ntclient/ntsqlite @@ -0,0 +1 @@ +Subproject commit a2455748d628963df01afeecd2b058b2cdd8344a diff --git a/ntclient/persistence/__init__.py b/ntclient/persistence/__init__.py new file mode 100644 index 0000000..014dcc3 --- /dev/null +++ b/ntclient/persistence/__init__.py @@ -0,0 +1,37 @@ +# -*- coding: utf-8 -*- +""" +Created on Sat Mar 23 13:09:07 2019 + +@author: shane +""" + +import json +import os + +from ntclient import NUTRA_DIR + +# TODO: init, handle when it doesn't exist yet +# TODO: prompt to create profile if copying default `prefs.json` with PROFILE_ID: -1 (non-existent) +PREFS_FILE = os.path.join(NUTRA_DIR, "prefs.json") +PREFS = {} +PROFILE_ID = None + + +def persistence_init() -> None: + """Loads the preferences file and relevant bits""" + global PREFS, PROFILE_ID # pylint: disable=global-statement + from ntclient import DEBUG # pylint: disable=import-outside-toplevel + + if os.path.isfile(PREFS_FILE): + with open(PREFS_FILE, encoding="utf-8") as file_path: + PREFS = json.load(file_path) + else: + if DEBUG: + print("WARN: ~/.nutra/prefs.json doesn't exist, using defaults") + PREFS = {} + + PROFILE_ID = PREFS.get("current_user") + if DEBUG and not PROFILE_ID: + print( + "WARN: ~/.nutra/prefs.json doesn't contain valid PROFILE_ID, proceeding in bare mode" + ) diff --git a/ntclient/persistence/sql/__init__.py b/ntclient/persistence/sql/__init__.py new file mode 100644 index 0000000..58d6f4e --- /dev/null +++ b/ntclient/persistence/sql/__init__.py @@ -0,0 +1,70 @@ +"""Main SQL persistence module, need to rethink circular imports and shared code""" +import sqlite3 +from typing import Union + +# FIXME: maybe just use separate methods for calls with vs. without headers +# avoid the mypy headaches, and the liberal comments # type: ignore + + +def sql_entries(sql_result: sqlite3.Cursor, headers=False) -> Union[list, tuple]: + """Formats and returns a `sql_result()` for console digestion and output""" + # TODO: return object: metadata, command, status, errors, etc? + rows = sql_result.fetchall() + + if headers: + headers = [x[0] for x in sql_result.description] + return headers, rows + + return rows + + +def version(con: sqlite3.Connection) -> str: + """Gets the latest entry from version table""" + + cur = con.cursor() + result = cur.execute("SELECT * FROM version;").fetchall() + close_con_and_cur(con, cur, commit=False) + return result[-1][1] + + +def close_con_and_cur( + con: sqlite3.Connection, cur: sqlite3.Cursor, commit=True +) -> None: + """Cleans up, commits, and closes after an SQL command is run""" + + cur.close() + if commit: + con.commit() + con.close() + + +def _sql( + con: sqlite3.Connection, + query: str, + db_name: str, + values: Union[tuple, list] = None, + headers=False, +) -> Union[list, tuple]: + from ntclient import DEBUG # pylint: disable=import-outside-toplevel + + cur = con.cursor() + + if DEBUG: + print("%s.sqlite3: %s" % (db_name, query)) + if values: + # TODO: better debug logging, more "control-findable", distinguish from most prints() + print(values) + + # TODO: separate `entry` & `entries` entity for single vs. bulk insert? + if values: + if isinstance(values, list): + rows = cur.executemany(query, values) + else: # tuple + rows = cur.execute(query, values) + else: + rows = cur.execute(query) + + # TODO: print " SELECTED", or other info BASED ON command SELECT/INSERT/DELETE/UPDATE + result = sql_entries(rows, headers=headers) + close_con_and_cur(con, cur) + return result diff --git a/ntclient/persistence/sql/nt/__init__.py b/ntclient/persistence/sql/nt/__init__.py new file mode 100644 index 0000000..8dee265 --- /dev/null +++ b/ntclient/persistence/sql/nt/__init__.py @@ -0,0 +1,41 @@ +"""Nutratracker DB specific sqlite module""" +import os +import sqlite3 + +from ntclient import NT_DB_NAME, NUTRA_DIR, __db_target_nt__ +from ntclient.persistence.sql import _sql, version +from ntclient.utils.exceptions import SqlConnectError, SqlInvalidVersionError + + +def nt_sqlite_connect(version_check=True): + """Connects to the nt.sqlite3 file, or throws an exception""" + db_path = os.path.join(NUTRA_DIR, NT_DB_NAME) + if os.path.isfile(db_path): + con = sqlite3.connect(db_path) + con.row_factory = sqlite3.Row + + # Verify version + if version_check and nt_ver() != __db_target_nt__: + raise SqlInvalidVersionError( + "ERROR: nt target [{0}] mismatch actual [{1}] ".format( + __db_target_nt__, nt_ver() + ) + + "upgrades not supported, please remove '~/.nutra/nt.sqlite3'" + "and re-run 'nutra init'" + ) + return con + + # Else it's not on disk + raise SqlConnectError("ERROR: nt database doesn't exist, please run `nutra init`") + + +def nt_ver(): + """Gets version string for nt.sqlite3 database""" + con = nt_sqlite_connect(version_check=False) + return version(con) + + +def sql(query, values=None, headers=False): + """Executes a SQL command to nt.sqlite3""" + con = nt_sqlite_connect() + return _sql(con, query, db_name="nt", values=values, headers=headers) diff --git a/ntclient/persistence/sql/nt/funcs.py b/ntclient/persistence/sql/nt/funcs.py new file mode 100644 index 0000000..2ee2d70 --- /dev/null +++ b/ntclient/persistence/sql/nt/funcs.py @@ -0,0 +1,93 @@ +"""nt.sqlite3 functions module""" +from ntclient.persistence import PROFILE_ID +from ntclient.persistence.sql.nt import nt_sqlite_connect, sql + + +def sql_nt_next_index(table=None): + """Used for previewing inserts""" + query = "SELECT MAX(id) FROM %s;" % table # nosec: B608 + return int(sql(query)[0]["MAX(id)"]) + + +################################################################################ +# Recipe functions +################################################################################ +def sql_recipe(recipe_id): + """Selects columns for recipe_id""" + query = "SELECT * FROM recipes WHERE id=?;" + return sql(query, values=(recipe_id,)) + + +def sql_recipes(): + """Show recipes with selected details""" + query = """ +SELECT + id, + tagname, + name, + COUNT(recipe_id) AS n_foods, + SUM(grams) AS grams, + created +FROM + recipes + LEFT JOIN recipe_dat ON recipe_id = id +GROUP BY + id; +""" + return sql(query, headers=True) + + +def sql_analyze_recipe(recipe_id): + """Output (nutrient) analysis columns for a given recipe_id""" + query = """ +SELECT + id, + name, + food_id, + grams +FROM + recipes + INNER JOIN recipe_dat ON recipe_id = id + AND id = ?; +""" + return sql(query, values=(recipe_id,)) + + +def sql_recipe_add(): + """TODO: method for adding recipe""" + query = """ +""" + return sql(query) + + +################################################################################ +# Biometric functions +################################################################################ +def sql_biometrics(): + """Selects biometrics""" + query = "SELECT * FROM biometrics;" + return sql(query, headers=True) + + +def sql_biometric_logs(profile_id): + """Selects biometric logs""" + query = "SELECT * FROM biometric_log WHERE profile_id=?" + return sql(query, values=(profile_id,), headers=True) + + +def sql_biometric_add(bio_vals): + """Insert biometric log item""" + con = nt_sqlite_connect() + cur = con.cursor() + + # TODO: finish up + query1 = "INSERT INTO biometric_log(profile_id, tags, notes) VALUES (?, ?, ?)" + sql(query1, (PROFILE_ID, "", "")) + log_id = cur.lastrowid + print(log_id) + query2 = "INSERT INTO bio_log_entry(log_id, biometric_id, value) VALUES (?, ?, ?)" + records = [ + (log_id, biometric_id, value) for biometric_id, value in bio_vals.items() + ] + cur.executemany(query2, records) + return log_id diff --git a/ntclient/persistence/sql/usda/__init__.py b/ntclient/persistence/sql/usda/__init__.py new file mode 100644 index 0000000..a2f27aa --- /dev/null +++ b/ntclient/persistence/sql/usda/__init__.py @@ -0,0 +1,101 @@ +"""USDA DB specific sqlite module""" +import os +import sqlite3 +import tarfile +import urllib.request +from typing import Union + +from ntclient import NUTRA_DIR, USDA_DB_NAME, __db_target_usda__ +from ntclient.persistence.sql import _sql, version +from ntclient.utils.exceptions import SqlConnectError, SqlInvalidVersionError + + +def usda_init(yes=False) -> None: + """On-boarding function. Downloads tarball and unpacks usda.sqlite3 file""" + + def input_agree() -> str: + return input("\nAgree to USDA download, may take minutes? [Y/n] ") + + def download_extract_usda() -> None: + """Download USDA tarball from BitBucket and extract to storage folder""" + + if yes or input_agree().lower() == "y": + # TODO: save with version in filename? Don't re-download tarball, just extract? + save_path = os.path.join(NUTRA_DIR, "%s.tar.xz" % USDA_DB_NAME) + + # Download usda.sqlite3.tar.xz + print("curl -L %s -o %s.tar.xz" % (url, USDA_DB_NAME)) + urllib.request.urlretrieve(url, save_path) # nosec: B310 + + # Extract the archive + with tarfile.open(save_path, mode="r:xz") as usda_sqlite_file: + print("\ntar xvf %s.tar.xz" % USDA_DB_NAME) + usda_sqlite_file.extractall(NUTRA_DIR) + + print("==> done downloading %s" % USDA_DB_NAME) + + # TODO: handle resource moved on Bitbucket or version mismatch due to manual overwrite? + url = ( + "https://bitbucket.org/dasheenster/nutra-utils/downloads/{0}-{1}.tar.xz".format( + USDA_DB_NAME, __db_target_usda__ + ) + ) + + if USDA_DB_NAME not in os.listdir(NUTRA_DIR): + print("INFO: usda.sqlite3 doesn't exist, is this a fresh install?") + download_extract_usda() + elif usda_ver() != __db_target_usda__: + print( + "INFO: usda.sqlite3 target [{0}] doesn't match actual [{1}], ".format( + __db_target_usda__, usda_ver() + ) + + "static resource (no user data lost).. downloading and extracting correct version" + ) + download_extract_usda() + + if usda_ver() != __db_target_usda__: + raise SqlInvalidVersionError( + "ERROR: usda target [{0}] failed to match actual [{1}], ".format( + __db_target_usda__, usda_ver() + ) + + "please contact support or try again" + ) + + +def usda_sqlite_connect(version_check=True) -> sqlite3.Connection: + """Connects to the usda.sqlite3 file, or throws an exception""" + + # TODO: support as customizable env var ? + db_path = os.path.join(NUTRA_DIR, USDA_DB_NAME) + if os.path.isfile(db_path): + con = sqlite3.connect(db_path) + # con.row_factory = sqlite3.Row # see: https://chrisostrouchov.com/post/python_sqlite/ + + # Verify version + if version_check and usda_ver() != __db_target_usda__: + raise SqlInvalidVersionError( + "ERROR: usda target [{0}] mismatch actual [{1}], ".format( + __db_target_usda__, usda_ver() + ) + + "remove '~/.nutra/usda.sqlite3' and run 'nutra init'" + ) + return con + + # Else it's not on disk + raise SqlConnectError("ERROR: usda database doesn't exist, please run `nutra init`") + + +def usda_ver() -> str: + """Gets version string for usda.sqlite3 database""" + + con = usda_sqlite_connect(version_check=False) + return version(con) + + +def sql(query, values=None, headers=False, version_check=True) -> Union[list, tuple]: + """Executes a SQL command to usda.sqlite3""" + + con = usda_sqlite_connect(version_check=version_check) + + # TODO: support argument: _sql(..., params=params, ...) + return _sql(con, query, db_name="usda", values=values, headers=headers) diff --git a/ntclient/persistence/sql/usda/funcs.py b/ntclient/persistence/sql/usda/funcs.py new file mode 100644 index 0000000..ff21588 --- /dev/null +++ b/ntclient/persistence/sql/usda/funcs.py @@ -0,0 +1,158 @@ +"""usda.sqlite functions module""" +from ntclient.persistence.sql.usda import sql +from ntclient.utils import NUTR_ID_KCAL + + +################################################################################ +# Basic functions +################################################################################ +def sql_fdgrp(): + """Shows food groups""" + + query = "SELECT * FROM fdgrp;" + result = sql(query) + return {x[0]: x for x in result} + + +def sql_food_details(food_ids=None) -> list: + """Readable human details for foods""" + + if food_ids is None: + query = "SELECT * FROM food_des;" + else: + # TODO: does sqlite3 driver support this? cursor.executemany() ? + query = "SELECT * FROM food_des WHERE id IN (%s);" + food_ids = ",".join(str(x) for x in set(food_ids)) + query = query % food_ids + + return sql(query) # type: ignore + + +def sql_nutrients_overview() -> dict: + """Shows nutrients overview""" + + query = "SELECT * FROM nutrients_overview;" + result = sql(query) + return {x[0]: x for x in result} + + +def sql_nutrients_details() -> tuple: + """Shows nutrients 'details'""" + + query = "SELECT * FROM nutrients_overview;" + return sql(query, headers=True) # type: ignore + + +def sql_servings(food_ids) -> list: + """Food servings""" + # TODO: apply connective logic from `sort_foods()` IS ('None') ? + query = """ +SELECT + serv.food_id, + serv.msre_id, + serv_desc.msre_desc, + serv.grams +FROM + serving serv + LEFT JOIN serv_desc ON serv.msre_id = serv_desc.id +WHERE + serv.food_id IN (%s); +""" + food_ids = ",".join(str(x) for x in set(food_ids)) + return sql(query % food_ids) # type: ignore + + +def sql_analyze_foods(food_ids) -> list: + """Nutrient analysis for foods""" + query = """ +SELECT + id, + nutr_id, + nutr_val +FROM + food_des + INNER JOIN nut_data ON food_des.id = nut_data.food_id +WHERE + food_des.id IN (%s); +""" + # TODO: parameterized queries + food_ids = ",".join(str(x) for x in set(food_ids)) + return sql(query % food_ids) # type: ignore + + +################################################################################ +# Sort +################################################################################ +def sql_sort_helper1(nutrient_id) -> list: + """Selects relevant bits from nut_data for sorting""" + + query = """ +SELECT + food_id, + nutr_id, + nutr_val +FROM + nut_data +WHERE + nutr_id = %s + OR nutr_id = %s +ORDER BY + food_id; +""" + + return sql(query % (NUTR_ID_KCAL, nutrient_id)) # type: ignore + + +def sql_sort_foods(nutr_id) -> list: + """Sort foods by nutr_id per 100 g""" + + query = """ +SELECT + nut_data.food_id, + fdgrp_id, + nut_data.nutr_val, + kcal.nutr_val AS kcal, + long_desc +FROM + nut_data + INNER JOIN food_des food ON food.id = nut_data.food_id + INNER JOIN nutr_def ndef ON ndef.id = nut_data.nutr_id + INNER JOIN fdgrp ON fdgrp.id = fdgrp_id + LEFT JOIN nut_data kcal ON food.id = kcal.food_id + AND kcal.nutr_id = 208 +WHERE + nut_data.nutr_id = %s +ORDER BY + nut_data.nutr_val DESC; +""" + + return sql(query % nutr_id) # type: ignore + + +def sql_sort_foods_by_kcal(nutr_id) -> list: + """Sort foods by nutr_id per 200 kcal""" + + # TODO: use parameterized queries + query = """ +SELECT + nut_data.food_id, + fdgrp_id, + ROUND((nut_data.nutr_val * 200 / kcal.nutr_val), 2) AS nutr_val, + kcal.nutr_val AS kcal, + long_desc +FROM + nut_data + INNER JOIN food_des food ON food.id = nut_data.food_id + INNER JOIN nutr_def ndef ON ndef.id = nut_data.nutr_id + INNER JOIN fdgrp ON fdgrp.id = fdgrp_id + -- filter out NULL kcal + INNER JOIN nut_data kcal ON food.id = kcal.food_id + AND kcal.nutr_id = 208 + AND kcal.nutr_val > 0 +WHERE + nut_data.nutr_id = %s +ORDER BY + (nut_data.nutr_val / kcal.nutr_val) DESC; +""" + + return sql(query % nutr_id) # type: ignore diff --git a/ntclient/services/__init__.py b/ntclient/services/__init__.py new file mode 100644 index 0000000..e889809 --- /dev/null +++ b/ntclient/services/__init__.py @@ -0,0 +1,65 @@ +"""Services module, currently only home to SQL/persistence init method""" +import os + +from ntclient import ( + NTSQLITE_BUILDPATH, + NTSQLITE_DESTINATION, + NUTRA_DIR, + __db_target_nt__, +) +from ntclient.ntsqlite.sql import build_ntsqlite +from ntclient.persistence.sql.nt import nt_ver +from ntclient.persistence.sql.usda import usda_init +from ntclient.services import analyze, biometrics, recipe, usda +from ntclient.utils.exceptions import SqlInvalidVersionError + + +def init(yes=False): + """ + TODO: Check for: + 1. .nutra folder + 2. usda + 3a. nt + 3b. default profile? + 4. prefs.json + """ + print("Nutra directory ", end="") + if not os.path.isdir(NUTRA_DIR): + os.makedirs(NUTRA_DIR, 0o755) + print("..DONE!") + + # TODO: print off checks, return False if failed + print("USDA db ", end="") + usda_init(yes=yes) + print("..DONE!") + + print("Nutra db ", end="") + build_ntsqlite() + # TODO: don't overwrite, + # verbose toggle for download, + # option to upgrade + if os.path.isfile(NTSQLITE_DESTINATION): + if nt_ver() != __db_target_nt__: + # TODO: hard requirement? raise error? + print( + "WARN: upgrades/downgrades not supported " + + "(actual: {0} vs. target: {1}), ".format(nt_ver(), __db_target_nt__) + + "please remove `~/.nutra/nt.sqlite3` file or ignore this warning" + ) + print("..DONE!") + os.remove(NTSQLITE_BUILDPATH) # clean up + else: + # TODO: is this logic (and these error messages) the best? + # what if .isdir() == True ? Fails with stacktrace? + os.rename(NTSQLITE_BUILDPATH, NTSQLITE_DESTINATION) + if not nt_ver() == __db_target_nt__: + raise SqlInvalidVersionError( + "ERROR: nt target [{0}] mismatch actual [{1}], ".format( + __db_target_nt__, nt_ver() + ) + + ", please contact support or try again" + ) + print("..DONE!") + + print("\nAll checks have passed!") + return 0, True diff --git a/ntclient/services/analyze.py b/ntclient/services/analyze.py new file mode 100755 index 0000000..656bfb9 --- /dev/null +++ b/ntclient/services/analyze.py @@ -0,0 +1,354 @@ +# -*- coding: utf-8 -*- +""" +Created on Sun Nov 11 23:57:03 2018 + +@author: shane +""" + +import csv +from collections import OrderedDict + +from colorama import Fore, Style +from tabulate import tabulate + +from ntclient import BUFFER_WD +from ntclient.persistence.sql.usda.funcs import ( + sql_analyze_foods, + sql_food_details, + sql_nutrients_overview, + sql_servings, +) +from ntclient.utils import ( + COLOR_CRIT, + COLOR_DEFAULT, + COLOR_OVER, + COLOR_WARN, + NUTR_ID_CARBS, + NUTR_ID_FAT_TOT, + NUTR_ID_FIBER, + NUTR_ID_KCAL, + NUTR_ID_PROTEIN, + THRESH_CRIT, + THRESH_OVER, + THRESH_WARN, +) + + +################################################################################ +# Foods +################################################################################ +def foods_analyze(food_ids, grams=None): + """ + Analyze a list of food_ids against stock RDA values + TODO: from ntclient.utils.nutprogbar import nutprogbar + TODO: support -t (tabular/non-visual) output flag + """ + + ################################################################################ + # Get analysis + ################################################################################ + raw_analyses = sql_analyze_foods(food_ids) + analyses = {} + for analysis in raw_analyses: + food_id = analysis[0] + if grams is not None: + anl = (analysis[1], round(analysis[2] * grams / 100, 2)) + else: + anl = (analysis[1], analysis[2]) + if food_id not in analyses: + analyses[food_id] = [anl] + else: + analyses[food_id].append(anl) + + serving = sql_servings(food_ids) + food_des = sql_food_details(food_ids) + food_des = {x[0]: x for x in food_des} + nutrients = sql_nutrients_overview() + rdas = {x[0]: x[1] for x in nutrients.values()} + + ################################################################################ + # Food-by-food analysis (w/ servings) + ################################################################################ + servings_rows = [] + nutrients_rows = [] + for food_id in analyses: + food_name = food_des[food_id][2] + print( + "\n======================================\n" + + "==> {0} ({1})\n".format(food_name, food_id) + + "======================================\n" + ) + print("\n=========================\nSERVINGS\n=========================\n") + + ################################################################################ + # Serving table + ################################################################################ + headers = ["msre_id", "msre_desc", "grams"] + serving_rows = [(x[1], x[2], x[3]) for x in serving if x[0] == food_id] + # Print table + servings_table = tabulate(serving_rows, headers=headers, tablefmt="presto") + print(servings_table) + servings_rows.append(serving_rows) + + refuse = next( + ((x[7], x[8]) for x in food_des.values() if x[0] == food_id and x[7]), None + ) + if refuse: + print("\n=========================\nREFUSE\n=========================\n") + print(refuse[0]) + print(" ({0}%, by mass)".format(refuse[1])) + + print("\n=========================\nNUTRITION\n=========================\n") + + ################################################################################ + # Nutrient table + ################################################################################ + headers = ["id", "nutrient", "rda", "amount", "units"] + nutrient_rows = [] + for nutrient_id, amount in analyses[food_id]: + # Skip zero values + if not amount: + continue + + nutr_desc = nutrients[nutrient_id][4] or nutrients[nutrient_id][3] + unit = nutrients[nutrient_id][2] + + # Insert RDA % into row + if rdas[nutrient_id]: + rda_perc = str(round(amount / rdas[nutrient_id] * 100, 1)) + "%" + else: + rda_perc = None + row = [nutrient_id, nutr_desc, rda_perc, round(amount, 2), unit] + + nutrient_rows.append(row) + + ################################################################################ + # Print table + ################################################################################ + table = tabulate(nutrient_rows, headers=headers, tablefmt="presto") + print(table) + nutrients_rows.append(nutrient_rows) + + return 0, nutrients_rows, servings_rows + + +################################################################################ +# Day +################################################################################ +def day_analyze(day_csv_paths, rda_csv_path=None): + """Analyze a day optionally with custom RDAs, + e.g. nutra day ~/.nutra/rocky.csv -r ~/.nutra/dog-rdas-18lbs.csv + TODO: Should be a subset of foods_analyze + """ + from ntclient import DEBUG # pylint: disable=import-outside-toplevel + + if rda_csv_path is not None: + with open(rda_csv_path, encoding="utf-8") as file_path: + rda_csv_input = csv.DictReader( + row for row in file_path if not row.startswith("#") + ) + rdas = list(rda_csv_input) + else: + rdas = [] + + logs = [] + food_ids = set() + for day_csv_path in day_csv_paths: + with open(day_csv_path, encoding="utf-8") as file_path: + rows = [row for row in file_path if not row.startswith("#")] + day_csv_input = csv.DictReader(rows) + log = list(day_csv_input) + for entry in log: + if entry["id"]: + food_ids.add(int(entry["id"])) + logs.append(log) + + # Inject user RDAs + nutrients = [list(x) for x in sql_nutrients_overview().values()] + for rda in rdas: + nutrient_id = int(rda["id"]) + _rda = float(rda["rda"]) + for nutrient in nutrients: + if nutrient[0] == nutrient_id: + nutrient[1] = _rda + if DEBUG: + substr = "{0} {1}".format(_rda, nutrient[2]).ljust(12) + print("INJECT RDA: {0} --> {1}".format(substr, nutrient[4])) + nutrients = {x[0]: x for x in nutrients} + + # Analyze foods + foods_analysis = {} + for food in sql_analyze_foods(food_ids): + food_id = food[0] + anl = food[1], food[2] + if food_id not in foods_analysis: + foods_analysis[food_id] = [anl] + else: + foods_analysis[food_id].append(anl) + + # Compute totals + nutrients_totals = [] + for log in logs: + nutrient_totals = OrderedDict() # dict()/{} is NOT ORDERED before 3.6/3.7 + for entry in log: + if entry["id"]: + food_id = int(entry["id"]) + grams = float(entry["grams"]) + for nutrient in foods_analysis[food_id]: + nutr_id = nutrient[0] + nutr_per_100g = nutrient[1] + nutr_val = grams / 100 * nutr_per_100g + if nutr_id not in nutrient_totals: + nutrient_totals[nutr_id] = nutr_val + else: + nutrient_totals[nutr_id] += nutr_val + nutrients_totals.append(nutrient_totals) + + ####### + # Print + buffer = BUFFER_WD - 4 if BUFFER_WD > 4 else BUFFER_WD + for analysis in nutrients_totals: + day_format(analysis, nutrients, buffer=buffer) + return 0, nutrients_totals + + +def day_format(analysis, nutrients, buffer=None): + """Formats day analysis for printing to console""" + + def print_header(header): + print(Fore.CYAN, end="") + print("~~~~~~~~~~~~~~~~~~~~~~~~~~~") + print("--> %s" % header) + print("~~~~~~~~~~~~~~~~~~~~~~~~~~~") + print(Style.RESET_ALL) + + def print_macro_bar(_fat, _net_carb, _pro, _kcals_max, _buffer=None): + _kcals = fat * 9 + net_carb * 4 + _pro * 4 + + p_fat = (_fat * 9) / _kcals + p_car = (_net_carb * 4) / _kcals + p_pro = (_pro * 4) / _kcals + + # TODO: handle rounding cases, tack on to, or trim off FROM LONGEST ? + mult = _kcals / _kcals_max + n_fat = round(p_fat * _buffer * mult) + n_car = round(p_car * _buffer * mult) + n_pro = round(p_pro * _buffer * mult) + + # Headers + f_buf = " " * (n_fat // 2) + "Fat" + " " * (n_fat - n_fat // 2 - 3) + c_buf = " " * (n_car // 2) + "Carbs" + " " * (n_car - n_car // 2 - 5) + p_buf = " " * (n_pro // 2) + "Pro" + " " * (n_pro - n_pro // 2 - 3) + print( + " " + + Fore.YELLOW + + f_buf + + Fore.BLUE + + c_buf + + Fore.RED + + p_buf + + Style.RESET_ALL + ) + + # Bars + print(" <", end="") + print(Fore.YELLOW + "=" * n_fat, end="") + print(Fore.BLUE + "=" * n_car, end="") + print(Fore.RED + "=" * n_pro, end="") + print(Style.RESET_ALL + ">") + + # Calorie footers + k_fat = str(round(fat * 9)) + k_car = str(round(net_carb * 4)) + k_pro = str(round(pro * 4)) + f_buf = " " * (n_fat // 2) + k_fat + " " * (n_fat - n_fat // 2 - len(k_fat)) + c_buf = " " * (n_car // 2) + k_car + " " * (n_car - n_car // 2 - len(k_car)) + p_buf = " " * (n_pro // 2) + k_pro + " " * (n_pro - n_pro // 2 - len(k_pro)) + print( + " " + + Fore.YELLOW + + f_buf + + Fore.BLUE + + c_buf + + Fore.RED + + p_buf + + Style.RESET_ALL + ) + + def print_nute_bar(_n_id, amount, _nutrients): + nutrient = _nutrients[_n_id] + rda = nutrient[1] + tag = nutrient[3] + unit = nutrient[2] + # anti = nutrient[5] + + if not rda: + return False, nutrient + attain = amount / rda + perc = round(100 * attain, 1) + + if attain >= THRESH_OVER: + color = COLOR_OVER + elif attain <= THRESH_CRIT: + color = COLOR_CRIT + elif attain <= THRESH_WARN: + color = COLOR_WARN + else: + color = COLOR_DEFAULT + + # Print + detail_amount = "{0}/{1} {2}".format(round(amount, 1), rda, unit).ljust(18) + detail_amount = "{0} -- {1}".format(detail_amount, tag) + left_index = 20 + left_pos = round(left_index * attain) if attain < 1 else left_index + print(" {0}<".format(color), end="") + print("=" * left_pos + " " * (left_index - left_pos) + ">", end="") + print(" {0}%\t[{1}]".format(perc, detail_amount), end="") + print(Style.RESET_ALL) + + return True, perc + + # Actual values + kcals = round(analysis[NUTR_ID_KCAL]) + pro = analysis[NUTR_ID_PROTEIN] + net_carb = analysis[NUTR_ID_CARBS] - analysis[NUTR_ID_FIBER] + fat = analysis[NUTR_ID_FAT_TOT] + kcals_449 = round(4 * pro + 4 * net_carb + 9 * fat) + + # Desired values + kcals_rda = round(nutrients[NUTR_ID_KCAL][1]) + pro_rda = nutrients[NUTR_ID_PROTEIN][1] + net_carb_rda = nutrients[NUTR_ID_CARBS][1] - nutrients[NUTR_ID_FIBER][1] + fat_rda = nutrients[NUTR_ID_FAT_TOT][1] + + # Print calories and macronutrient bars + print_header("Macronutrients") + kcals_max = max(kcals, kcals_rda) + rda_perc = round(kcals * 100 / kcals_rda, 1) + print( + "Actual: {0} kcal ({1}% RDA), {2} by 4-4-9".format( + kcals, rda_perc, kcals_449 + ) + ) + print_macro_bar(fat, net_carb, pro, kcals_max, _buffer=buffer) + print( + "\nDesired: {0} kcal ({1} kcal)".format( + kcals_rda, "%+d" % (kcals - kcals_rda) + ) + ) + print_macro_bar( + fat_rda, + net_carb_rda, + pro_rda, + kcals_max, + _buffer=buffer, + ) + + # Nutrition detail report + print_header("Nutrition detail report") + for n_id in analysis: + print_nute_bar(n_id, analysis[n_id], nutrients) + # TODO: below + print( + "work in progress...some minor fields with negligible data, they are not shown here" + ) diff --git a/ntclient/services/biometrics.py b/ntclient/services/biometrics.py new file mode 100644 index 0000000..9ac8de1 --- /dev/null +++ b/ntclient/services/biometrics.py @@ -0,0 +1,53 @@ +"""Biometrics SQL functions""" +from tabulate import tabulate + +from ntclient.persistence import PROFILE_ID +from ntclient.persistence.sql.nt.funcs import ( + sql_biometric_add, + sql_biometric_logs, + sql_biometrics, +) + + +def biometrics(): + """Shows biometrics""" + headers, rows = sql_biometrics() + table = tabulate(rows, headers=headers, tablefmt="presto") + print(table) + return 0, rows + + +def biometric_logs(): + """Shows biometric logs""" + headers, rows = sql_biometric_logs(PROFILE_ID) + + table = tabulate(rows, headers=headers, tablefmt="presto") + print(table) + return 0, rows + + +def biometric_add(bio_vals): + """Add a biometric type""" + print() + # print("New biometric log: " + name + "\n") + + bio_names = {x[0]: x for x in sql_biometrics()[1]} + + results = [] + for biometric_id, value in bio_vals.items(): + bio = bio_names[biometric_id] + results.append( + {"id": biometric_id, "name": bio[1], "value": value, "unit": bio[2]} + ) + + table = tabulate(results, headers="keys", tablefmt="presto") + print(table) + + # TODO: print current profile and date? + + confirm = input("\nConfirm add biometric? [Y/n] ") + + if confirm.lower() == "y": + sql_biometric_add(bio_vals) + print("not implemented ;]") + return 1, False diff --git a/ntclient/services/recipe.py b/ntclient/services/recipe.py new file mode 100644 index 0000000..8eb73e2 --- /dev/null +++ b/ntclient/services/recipe.py @@ -0,0 +1,129 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Wed Aug 12 15:14:00 2020 + +@author: shane +""" +import csv +import os + +from tabulate import tabulate + +from ntclient.core.nutprogbar import nutprogbar +from ntclient.persistence.sql.nt.funcs import ( + sql_analyze_recipe, + sql_nt_next_index, + sql_recipe, + sql_recipes, +) +from ntclient.persistence.sql.usda.funcs import ( + sql_analyze_foods, + sql_food_details, + sql_nutrients_overview, +) + + +def recipes_overview(): + """Shows overview for all recipes""" + recipes = sql_recipes()[1] + + results = [] + for recipe in recipes: + result = { + "id": recipe[0], + "name": recipe[2], + "tagname": recipe[1], + "n_foods": recipe[3], + "weight": recipe[4], + } + results.append(result) + + table = tabulate(results, headers="keys", tablefmt="presto") + print(table) + return 0, results + + +def recipe_overview(recipe_id): + """Shows single recipe overview""" + recipe = sql_analyze_recipe(recipe_id) + name = recipe[0][1] + print(name) + + food_ids = {x[2]: x[3] for x in recipe} + food_names = {x[0]: x[3] for x in sql_food_details(food_ids.keys())} + food_analyses = sql_analyze_foods(food_ids.keys()) + + table = tabulate( + [[food_names[food_id], grams] for food_id, grams in food_ids.items()], + headers=["food", "g"], + ) + print(table) + # tabulate nutrient RDA %s + nutrients = sql_nutrients_overview() + # rdas = {x[0]: x[1] for x in nutrients.values()} + progbars = nutprogbar(food_ids, food_analyses, nutrients) + print(progbars) + + return 0, recipe + + +def recipe_import(file_path): + """Import a recipe to SQL database""" + + def extract_id_from_filename(path): + filename = str(os.path.basename(path)) + if ( + "[" in filename + and "]" in filename + and filename.index("[") < filename.index("]") + ): + # TODO: try, raise: print/warn + return int(filename.split("[")[1].split("]")[0]) + return None + + if os.path.isfile(file_path): + # TODO: better logic than this + recipe_id = extract_id_from_filename(file_path) or sql_nt_next_index("recipes") + print(recipe_id) + with open(file_path, encoding="utf-8") as file: + reader = csv.DictReader(file) + # headers = next(reader) + rows = list(reader) + print(rows) + else: # os.path.isdir() + print("not implemented ;]") + return 1, False + + +def recipe_add(name, food_amts): + """Add a recipe to SQL database""" + print() + print("New recipe: " + name + "\n") + + food_names = {x[0]: x[2] for x in sql_food_details(food_amts.keys())} + + results = [] + for food_id, grams in food_amts.items(): + results.append([food_id, food_names[food_id], grams]) + + table = tabulate(results, headers=["id", "food_name", "grams"], tablefmt="presto") + print(table) + + confirm = input("\nCreate recipe? [Y/n] ") + + if confirm.lower() == "y": + print("not implemented ;]") + return 1, False + + +def recipe_delete(recipe_id): + """Deletes recipe by ID, along with any FK constraints""" + recipe = sql_recipe(recipe_id)[0] + + print(recipe[4]) + confirm = input("Do you wish to delete? [Y/n] ") + + if confirm.lower() == "y": + print("not implemented ;]") + return 1, False diff --git a/ntclient/services/usda.py b/ntclient/services/usda.py new file mode 100644 index 0000000..e4199ff --- /dev/null +++ b/ntclient/services/usda.py @@ -0,0 +1,244 @@ +# -*- coding: utf-8 -*- +""" +Created on Sat Oct 27 20:28:06 2018 + +@author: shane +""" + +import pydoc + +from tabulate import tabulate + +from ntclient import ( + DEFAULT_RESULT_LIMIT, + DEFAULT_SEARCH_H_BUFFER, + DEFAULT_SORT_H_BUFFER, +) +from ntclient.persistence.sql.usda.funcs import ( + sql_analyze_foods, + sql_food_details, + sql_nutrients_details, + sql_nutrients_overview, + sql_sort_helper1, +) +from ntclient.utils import NUTR_ID_KCAL, NUTR_IDS_AMINOS, NUTR_IDS_FLAVONES + + +def list_nutrients(): + """Lists out nutrients with basic details""" + from ntclient import PAGING # pylint: disable=import-outside-toplevel + + headers, nutrients = sql_nutrients_details() + # TODO: include in SQL table cache? + headers.append("avg_rda") + nutrients = [list(x) for x in nutrients] + for nutrient in nutrients: + rda = nutrient[1] + val = nutrient[6] + if rda: + nutrient.append(round(100 * val / rda, 1)) + else: + nutrient.append(None) + + table = tabulate(nutrients, headers=headers, tablefmt="simple") + if PAGING: + pydoc.pager(table) + else: + print(table) + + return 0, nutrients + + +################################################################################ +# Sort +################################################################################ +def sort_foods(nutrient_id, by_kcal, limit=DEFAULT_RESULT_LIMIT): + """Sort, by nutrient, either (amount / 100 g) or (amount / 200 kcal)""" + + # TODO: sub shrt_desc for long if available, and support config.FOOD_NAME_TRUNC + + def print_results(_results, _nutrient_id): + """Prints truncated list for sort""" + nutrients = sql_nutrients_overview() + nutrient = nutrients[_nutrient_id] + unit = nutrient[2] + + val_header = "grams" if by_kcal else "kcal" + headers = ["food", "fdgrp", "val (%s)" % unit, val_header, "long_desc"] + + table = tabulate(_results, headers=headers, tablefmt="simple") + print(table) + return _results + + # Gets values for nutrient_id and kcal=208 + nut_data = sql_sort_helper1(nutrient_id) + + # Assembles duplicate tuples into single dict entry + food_dat = {} + for food_id, nutr_id, nutr_val in nut_data: + entry = nutr_id, nutr_val + if food_id not in food_dat: + food_dat[food_id] = [entry] + else: + food_dat[food_id].append(entry) + + # Builds main results list + foods = [] + for food_id, _food in food_dat.items(): + kcal = None + nutr_val = 0.0 + for _nutr_id, _nutr_val in _food: + if _nutr_id == NUTR_ID_KCAL: + kcal = _nutr_val + else: + nutr_val = _nutr_val + food = [food_id, nutr_val, kcal] + foods.append(food) + if by_kcal is True: + foods = list(filter(lambda x: x[2], foods)) # removes kcal = 0 case + foods = list( + map( + lambda x: [x[0], round(x[1] * 200 / x[2], 2), round(200 / x[2] * 100)], + foods, + ) + ) + foods.sort(key=lambda x: x[1], reverse=True) + foods = foods[:limit] + food_ids = {x[0] for x in foods} + + # Gets fdgrp and long_desc + food_des = {x[0]: x for x in sql_food_details(food_ids)} + for food in foods: + food_id = food[0] + fdgrp = food_des[food_id][1] + long_desc = food_des[food_id][2] + food.insert(1, fdgrp) + food.append(long_desc[:DEFAULT_SORT_H_BUFFER]) + + print_results(foods, nutrient_id) + return 0, foods # , nutrient_id + + +################################################################################ +# Search +################################################################################ +def search(words, fdgrp_id=None, limit=DEFAULT_RESULT_LIMIT): + """Searches foods for input""" + + def tabulate_search(_results): + """Makes search results more readable""" + # Current terminal size + # TODO: display "nonzero/total" report nutrients, aminos, and flavones.. + # sometimes zero values are not useful + # TODO: macros, ANDI score, and other metrics on preview + + headers = [ + "food", + "fdgrp", + "kcal", + "food_name", + "Nutr", + "Amino", + "Flav", + ] + rows = [] + for i, result in enumerate(_results): + if i == limit: + break + _food_id = result["food_id"] + # TODO: dynamic buffer + # food_name = r["long_desc"][:45] + # food_name = r["long_desc"][:BUFFER_WD] + food_name = result["long_desc"][:DEFAULT_SEARCH_H_BUFFER] + # TODO: decide on food group description? + # fdgrp_desc = r["fdgrp_desc"] + fdgrp = result["fdgrp_id"] + + nutrients = result["nutrients"] + kcal = nutrients.get(NUTR_ID_KCAL) + len_aminos = len( + [nutrients[n_id] for n_id in nutrients if int(n_id) in NUTR_IDS_AMINOS] + ) + len_flavones = len( + [ + nutrients[n_id] + for n_id in nutrients + if int(n_id) in NUTR_IDS_FLAVONES + ] + ) + + row = [ + _food_id, + fdgrp, + kcal, + food_name, + len(nutrients), + len_aminos, + len_flavones, + ] + rows.append(row) + # avail_buffer = bufferwidth - len(food_id) - 15 + # if len(food_name) > avail_buffer: + # rows.append([food_id, food_name[:avail_buffer] + "..."]) + # else: + # rows.append([food_id, food_name]) + table = tabulate(rows, headers=headers, tablefmt="simple") + print(table) + return rows + + ### + # MAIN SEARCH METHOD + from fuzzywuzzy import fuzz # pylint: disable=import-outside-toplevel + + food_des = sql_food_details() + if fdgrp_id is not None: + food_des = list(filter(lambda x: x[1] == fdgrp_id, food_des)) + + query = " ".join(words) + scores = {f[0]: fuzz.token_set_ratio(query, f[2]) for f in food_des} + scores = sorted(scores.items(), key=lambda x: x[1], reverse=True)[:limit] + + food_ids = {x[0] for x in scores} + nut_data = sql_analyze_foods(food_ids) + + # Tally foods + foods_nutrients = {} + for food_id, nutr_id, nutr_val in nut_data: + if food_id not in foods_nutrients: + foods_nutrients[food_id] = {nutr_id: nutr_val} # init dict + else: + foods_nutrients[food_id][nutr_id] = nutr_val + + def search_results(_scores): + """Generates search results, consumable by tabulate""" + _results = [] + for score in _scores: + _food_id = score[0] + score = score[1] + + food = food_des[_food_id] + _fdgrp_id = food[1] + long_desc = food[2] + shrt_desc = food[3] + + nutrients = foods_nutrients[_food_id] + result = { + "food_id": _food_id, + "fdgrp_id": _fdgrp_id, + # TODO: get more details from another function, maybe enhance food_details() ? + # is that useful tho? + # "fdgrp_desc": cache.fdgrp[fdgrp_id]["fdgrp_desc"], + # "data_src": cache.data_src[data_src_id]["name"], + "long_desc": shrt_desc if shrt_desc else long_desc, + "score": score, + "nutrients": nutrients, + } + _results.append(result) + return _results + + # TODO: include C/F/P macro ratios as column? + food_des = {f[0]: f for f in food_des} + results = search_results(scores) + + tabulate_search(results) + return 0, results diff --git a/ntclient/utils/__init__.py b/ntclient/utils/__init__.py new file mode 100644 index 0000000..a6ef413 --- /dev/null +++ b/ntclient/utils/__init__.py @@ -0,0 +1,96 @@ +"""Constants and default settings""" +from colorama import Fore + +################################################################################ +# Colors and buffer settings +################################################################################ + +THRESH_WARN = 0.7 +COLOR_WARN = Fore.YELLOW + +THRESH_CRIT = 0.4 +COLOR_CRIT = Fore.RED + +THRESH_OVER = 1.9 +COLOR_OVER = Fore.MAGENTA # Fore.LIGHTMAGENTA_EX, Fore.LIGHTBLACK_EX + +COLOR_DEFAULT = Fore.LIGHTCYAN_EX # Fore.BLUE, Fore.LIGHTBLUE_EX + +################################################################################ +# Nutrient IDs +################################################################################ +NUTR_ID_KCAL = 208 + +NUTR_ID_PROTEIN = 203 + +NUTR_ID_CARBS = 205 +NUTR_ID_SUGAR = 269 +NUTR_ID_FIBER = 291 + +NUTR_ID_FAT_TOT = 204 +NUTR_ID_FAT_SAT = 606 +NUTR_ID_FAT_MONO = 645 +NUTR_ID_FAT_POLY = 646 + +NUTR_IDS_FLAVONES = [ + 710, + 711, + 712, + 713, + 714, + 715, + 716, + 734, + 735, + 736, + 737, + 738, + 731, + 740, + 741, + 742, + 743, + 745, + 749, + 750, + 751, + 752, + 753, + 755, + 756, + 758, + 759, + 762, + 770, + 773, + 785, + 786, + 788, + 789, + 791, + 792, + 793, + 794, +] + +NUTR_IDS_AMINOS = [ + 501, + 502, + 503, + 504, + 505, + 506, + 507, + 508, + 509, + 510, + 511, + 512, + 513, + 514, + 515, + 516, + 517, + 518, + 521, +] diff --git a/ntclient/utils/exceptions.py b/ntclient/utils/exceptions.py new file mode 100644 index 0000000..290618e --- /dev/null +++ b/ntclient/utils/exceptions.py @@ -0,0 +1,20 @@ +"""Custom exception classes, used for bubbling up more specific errors""" + + +class SqlException(Exception): + """Base class for Sql errors""" + + +class SqlConnectError(SqlException): + """Typically when it can't find the *.sqlite3 file(s) on disk""" + + +class SqlInvalidVersionError(SqlException): + """Raised when the expected version differs from actual, either for nt or usda DB""" + + +class SqlCrossDatabaseValidationError(SqlException): + """ + Raised when data-bindings (e.g. food_id) in one db (typically nt) + can't be found in another (typically usda) + """ diff --git a/nutra b/nutra new file mode 100755 index 0000000..ba0eb31 --- /dev/null +++ b/nutra @@ -0,0 +1,15 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# PYTHON_ARGCOMPLETE_OK +""" +Created on Fri Sep 28 22:25:38 2018 + +@author: gamesguru +""" + +import sys + +from ntclient.__main__ import main + +if __name__ == "__main__": + sys.exit(main(sys.argv[1:])) diff --git a/requirements-lint.txt b/requirements-lint.txt new file mode 100644 index 0000000..642306b --- /dev/null +++ b/requirements-lint.txt @@ -0,0 +1,8 @@ +autopep8~=1.6 +bandit~=1.7 +black~=22.3 +doc8~=0.11 +flake8~=4.0 +mypy~=0.960 +pylint~=2.13 +yamllint~=1.26 diff --git a/requirements-optional.txt b/requirements-optional.txt new file mode 100644 index 0000000..3e3e163 --- /dev/null +++ b/requirements-optional.txt @@ -0,0 +1 @@ +python-Levenshtein==0.12.2 diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..67ad948 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,4 @@ +argcomplete==2.0.0 +colorama==0.4.5 +fuzzywuzzy==0.18.0 +tabulate==0.8.10 diff --git a/scripts/nutra b/scripts/nutra new file mode 100755 index 0000000..a1b3619 --- /dev/null +++ b/scripts/nutra @@ -0,0 +1,12 @@ +#!/usr/bin/python3 +# -*- coding: utf-8 -*- +# PYTHON_ARGCOMPLETE_OK +"""Executable script, copied over by pip""" +import re +import sys + +from ntclient.__main__ import main + +if __name__ == "__main__": + sys.argv[0] = re.sub(r"(-script\.pyw|\.exe)?$", "", sys.argv[0]) + sys.exit(main()) diff --git a/scripts/nutra.py b/scripts/nutra.py new file mode 100755 index 0000000..a1b3619 --- /dev/null +++ b/scripts/nutra.py @@ -0,0 +1,12 @@ +#!/usr/bin/python3 +# -*- coding: utf-8 -*- +# PYTHON_ARGCOMPLETE_OK +"""Executable script, copied over by pip""" +import re +import sys + +from ntclient.__main__ import main + +if __name__ == "__main__": + sys.argv[0] = re.sub(r"(-script\.pyw|\.exe)?$", "", sys.argv[0]) + sys.exit(main()) diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..adf2686 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,45 @@ +[coverage:run] +source = ntclient + +[coverage:report] +fail_under = 80 + +show_missing = True +skip_empty = True +skip_covered = True + + +[pycodestyle] +max-line-length = 88 + + +[flake8] +per-file-ignores = + # Allow unused imports in __init__.py files + __init__.py:F401 + +max-line-length = 100 + +ignore = + E501, # line-length (currently handled by pycodestyle) + W503, # line break before binary operator + + +[isort] +line_length=88 +known_first_party=ntclient + +# See: https://copdips.com/2020/04/making-isort-compatible-with-black.html +multi_line_output=3 +include_trailing_comma=true + + +[mypy] +ignore_missing_imports = True +show_error_codes = True +disable_error_code = import +disallow_untyped_calls = True +disallow_untyped_decorators = True +strict_optional = False +warn_redundant_casts = True +warn_unused_ignores = True diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..fffe1b8 --- /dev/null +++ b/setup.py @@ -0,0 +1,75 @@ +# -*- coding: utf-8 -*- +""" +Created on Sat Oct 13 16:30:30 2018 + +@author: shane +""" + +import glob +import os +import platform + +from setuptools import find_packages, setup + +from ntclient import PY_MIN_STR, __author__, __email__, __title__, __version__ + +# cd to parent dir of setup.py +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +CLASSIFIERS = [ + "Environment :: Console", + "Intended Audience :: End Users/Desktop", + "Intended Audience :: Science/Research", + "Intended Audience :: Healthcare Industry", + "Intended Audience :: Education", + "Development Status :: 3 - Alpha", + "Natural Language :: English", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Framework :: Flake8", + "Framework :: Pytest", + "Operating System :: OS Independent", + "Operating System :: Microsoft :: Windows :: Windows XP", + "Operating System :: Microsoft :: Windows :: Windows 10", + "Operating System :: MacOS :: MacOS X", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: Implementation :: CPython", + "Programming Language :: Python :: Implementation :: PyPy", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.4", + "Programming Language :: Python :: 3.11", + "Programming Language :: SQL", + "Programming Language :: Unix Shell", +] + +with open("README.rst", encoding="utf-8") as file: + README = file.read() + +with open("requirements.txt", encoding="utf-8") as file: + REQUIREMENTS = file.read().split() + +if platform.system() != "Windows": + # python-Levenshtein builds natively on unix, requires vcvarsall.bat or vc++10 on Windows + with open("requirements-optional.txt", encoding="utf-8") as file: + optional_reqs = file.read().split() + REQUIREMENTS.extend(optional_reqs) + +setup( + name=__title__, + author=__author__, + author_email=__email__, + classifiers=CLASSIFIERS, + install_requires=REQUIREMENTS, + python_requires=">=%s" % PY_MIN_STR, + zip_safe=False, + packages=find_packages(exclude=["tests"]), + include_package_data=True, + platforms=["linux", "darwin", "win32"], + scripts=glob.glob("scripts/*"), + # entry_points={"console_scripts": ["nutra=ntclient.__main__:main"]}, + description="Home and office nutrient tracking software", + long_description=README, + long_description_content_type="text/x-rst", + url="https://github.com/nutratech/cli", + license="GPL v3", + version=__version__, +) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/__main__.py b/tests/__main__.py new file mode 100644 index 0000000..895d6d6 --- /dev/null +++ b/tests/__main__.py @@ -0,0 +1,38 @@ +""" +Allows contributors to run tests on their machine (and in GitHub actions / Travis CI) +""" +import os +import subprocess # nosec: B404 +import sys + +import coverage + + +def main() -> int: + """ + Main test method, callable with `python -m tests` + + 1. Calls a subprocess for `coverage run` + 2. Programmatically invokes coverage.report() + """ + + cmd = "coverage run -m pytest -v -s -p no:cacheprovider tests/" + print(cmd) + subprocess.call(cmd.split(), shell=False) # nosec: B603 + + print("\ncoverage report -m --skip-empty") + cov = coverage.Coverage() + cov.load() + cov.report(show_missing=True, skip_empty=True) + + # Try to clean up + try: + os.remove(".coverage") + except (FileNotFoundError, PermissionError) as error: + print("WARN: failed to remove `.coverage`, %s" % repr(error)) + + return 0 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/tests/requirements-win_xp-ubu1604.txt b/tests/requirements-win_xp-ubu1604.txt new file mode 100644 index 0000000..39fde64 --- /dev/null +++ b/tests/requirements-win_xp-ubu1604.txt @@ -0,0 +1,3 @@ +# Don't update these, they are the last supported versions on winXP, Ubuntu 16.04 & Python 3.4 +coverage==5.5 +pytest==3.2.5 diff --git a/tests/requirements.txt b/tests/requirements.txt new file mode 100644 index 0000000..311678e --- /dev/null +++ b/tests/requirements.txt @@ -0,0 +1,2 @@ +coverage~=6.0 +pytest~=7.0 diff --git a/tests/resources/day/dog-simple.csv b/tests/resources/day/dog-simple.csv new file mode 100644 index 0000000..e91283b --- /dev/null +++ b/tests/resources/day/dog-simple.csv @@ -0,0 +1,14 @@ +meal,subcat,id,grams,notes,desired_kcal +breakfast,base,20044,90,"rice, uncooked [55g cooked]",120 +breakfast,base,16042,50,"pinto beans, raw [cooked: ¼ cup or 56g]",60 +breakfast,base,5062,50,chicken breast,50 +breakfast,cooked (veg),11507,25,"sweet potato, raw",20 +breakfast,cooked (veg),11233,10,"kale, raw OR broccoli, boiled, w/o salt",5 +breakfast,soaked,12220,10,flax [½ tbsp],30 +breakfast,chopped,11297,3,"parsley, fresh",1 +breakfast,supplements,,0.075,milk thistle extract, +breakfast,supplements,,0.15,"calcium citrate, [1/8 tsp]", +,,,,, +,,,,, +,,,,, +TOTAL,,,,,286 \ No newline at end of file diff --git a/tests/resources/day/dog.csv b/tests/resources/day/dog.csv new file mode 100644 index 0000000..89c9151 --- /dev/null +++ b/tests/resources/day/dog.csv @@ -0,0 +1,20 @@ +meal,id,grams,notes,desired_kcal +breakfast,20044,19,"rice, uncooked",70 +breakfast,8120,13,"oats, raw",50 +breakfast,16042,14,"pinto beans, raw",50 +breakfast,5062,33,chicken breast,40 +breakfast,11304,16,"peas, green, raw",15 +breakfast,11507,23,"sweet potato, raw",20 +breakfast,11091,14,"broccoli, boiled, w/o salt",5 +breakfast,12155,6,walnut,40 +breakfast,12220,6,flax,30 +breakfast,1289,35,kefir,15 +breakfast,9050,18,blueberries,10 +breakfast,9040,23,banana,20 +breakfast,11297,7,"parsley, fresh", +breakfast,2064,5,"peppermint, fresh", +breakfast,,0.075,milk thistle extract, +,,,, +,,,, +,,,, +TOTAL,,,,365 diff --git a/tests/resources/day/human-test.csv b/tests/resources/day/human-test.csv new file mode 100644 index 0000000..a2cd57e --- /dev/null +++ b/tests/resources/day/human-test.csv @@ -0,0 +1,23 @@ +meal,id,grams,serving_id,serving_qty +breakfast,13047,100,, +breakfast,1270,28,, +breakfast,9038,55,, +breakfast,11251,20,, +breakfast,11529,35,, +breakfast,11282,15,, +breakfast,11828,210,, +breakfast,28313,40,, +breakfast,9112,100,, +lunch,20137,140,, +lunch,5062,100,, +lunch,12136,45,, +lunch,11821,50,, +lunch,44005,15,, +dinner,20545,150,, +dinner,16146,85,, +dinner,1270,40,, +dinner,9037,60,, +dinner,15076,100,, +dinner,11090,60,, +dinner,11938,35,, +dinner,11282,25,, diff --git a/tests/resources/day/original-dog-simple.csv b/tests/resources/day/original-dog-simple.csv new file mode 100644 index 0000000..8206c40 --- /dev/null +++ b/tests/resources/day/original-dog-simple.csv @@ -0,0 +1,10 @@ +meal,id,grams,notes +breakfast,20046,500,"rice, uncooked" +breakfast,5306,400,ground turkey +breakfast,23572,400,ground beef +breakfast,5028,400,chicken liver +breakfast,5062,400,chicken breast +breakfast,15048,400,canned mackerel +breakfast,11422,800,"pumpkin, raw [canned]" +breakfast,11304,400,"Peas, green, raw" +breakfast,11090,400,broccoli diff --git a/tests/resources/prefs.json b/tests/resources/prefs.json new file mode 100644 index 0000000..27b8920 --- /dev/null +++ b/tests/resources/prefs.json @@ -0,0 +1,3 @@ +{ + "current_user": 1 +} diff --git a/tests/resources/rda/dog-18lbs.csv b/tests/resources/rda/dog-18lbs.csv new file mode 100644 index 0000000..3614f94 --- /dev/null +++ b/tests/resources/rda/dog-18lbs.csv @@ -0,0 +1,83 @@ +# Revised Mon 10 Aug 2020 10:11:09 AM EDT,,,, +# nutra version 0.1.0.dev1,,,, +#,,,, +id,rda,units,tagname,nutr_desc +203,18,g,PRO,Protein +204,25,g,FAT,Total lipid (fat) +205,60,g,CARB,"Carbohydrate, by difference" +208,501,kcal,CAL,Energy +269,15,g,SUGAR,"Sugars, total" +291,9,g,FIBTG,"Fiber, total dietary" +301,300,mg,CA,"Calcium, Ca" +303,4,mg,FE,"Iron, Fe" +304,100,mg,MG,"Magnesium, Mg" +305,250,mg,P,"Phosphorus, P" +306,1300,mg,K,"Potassium, K" +307,350,mg,NA,"Sodium, Na" +309,3,mg,ZN,"Zinc, Zn" +312,0.2,mg,CU,"Copper, Cu" +315,0.6,mg,MN,"Manganese, Mn" +317,15,µg,SE,"Selenium, Se" +318,1000,IU,VITA_IU,"Vitamin A, IU" +320,250,µg,VITA_RAE,"Vitamin A, RAE" +324,100,IU,VITD_IU,Vitamin D +328,5,µg,VITD,Vitamin D (D2 + D3) +337,900,µg,LYCPN,Lycopene +338,2000,µg,LUTZEA,Lutein + zeaxanthin +401,30,mg,VITC,"Vitamin C, total ascorbic acid" +404,0.3,mg,B1,Thiamin +405,0.35,mg,B2,Riboflavin +406,4,mg,B3,Niacin +410,1.25,mg,B5,Pantothenic acid +415,0.4,mg,B6,Vitamin B-6 +417,100,µg,B9,"Folate, total" +418,0.6,µg,B12,Vitamin B-12 +421,110,mg,CHO,"Choline, total" +430,30,µg,VITK,Vitamin K (phylloquinone) +501,0.1,g,TRP_G,Tryptophan +502,0.3,g,THR_G,Threonine +503,0.5,g,ILE_G,Isoleucine +504,1,g,LEU_G,Leucine +505,0.8,g,LYS_G,Lysine +506,0.3,g,MET_G,Methionine +508,0.3,g,PHE_G,Phenylalanine +509,0.4,g,TYR_G,Tyrosine +510,0.5,g,VAL_G,Valine +511,0.3,g,ARG_G,Arginine +512,0.2,g,HISTN_G,Histidine +513,0.3,g,ALA_G,Alanine +514,0.3,g,ASP_G,Aspartic acid +515,0.5,g,GLU_G,Glutamic acid +516,0.2,g,GLY_G,Glycine +517,0.2,g,PRO_G,Proline +518,0.4,g,SER_G,Serine +601,50,mg,CHOLEST,Cholesterol +605,0,g,FATRN,"Fatty acids, total trans" +606,7,g,FASAT,"Fatty acids, total saturated" +621,0.1,g,F22D6,22:6 n-3 (DHA) +629,0.05,g,F20D5,20:5 n-3 (EPA) +645,10,g,FAMS,"Fatty acids, total monounsaturated" +646,6,g,FAPU,"Fatty acids, total polyunsaturated" +710,8,mg,DAID,Daidzein +711,4,mg,GENI,Genistein +713,11,mg,TOTISO,Total isoflavones +731,5,mg,CYAD,Cyanidin +734,10,mg,PAdimer,Proanthocyanidin dimers +735,5,mg,PAtrimer,Proanthocyanidin trimers +736,5,mg,PA4-6mer,Proanthocyanidin 4-6mers +737,2,mg,PA7-10mer,Proanthocyanidin 7-10mers +738,1,mg,PApolymer,Proanthocyanidin polymers (>10mers) +749,10,mg,CATE,(+)-Catechin +750,10,mg,EPICATEGC,(-)-Epigallocatechin +751,10,mg,EPICATEC,(-)-Epicatechin +752,10,mg,EPICATECG3,(-)-Epicatechin 3-gallate +753,15,mg,EGCG,(-)-Epigallocatechin 3-gallate +759,20,mg,HESPT,Hesperetin +762,15,mg,NARING,Naringenin +770,8,mg,APIGEN,Apigenin +773,5,mg,LUTEOL,Luteolin +785,5,mg,ISORHAM,Isorhamnetin +786,1.5,mg,KAEMF,Kaempferol +788,0.5,mg,MYRIC,Myricetin +789,5,mg,QUERCE,Quercetin +851,0.3,g,F18D3CN3,"18:3 n-3 c,c,c (ALA)" diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..1d314cf --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,286 @@ +# -*- coding: utf-8 -*- +""" +Created on Fri Jan 31 15:19:53 2020 + +@author: shane +""" +import os +import sqlite3 +import sys + +import pytest + +from ntclient import ( + NTSQLITE_BUILDPATH, + NUTRA_DIR, + USDA_DB_NAME, + __db_target_nt__, + __db_target_usda__, + set_flags, +) +from ntclient.__main__ import build_argparser +from ntclient.__main__ import main as nt_main +from ntclient.core import nutprogbar +from ntclient.ntsqlite.sql import build_ntsqlite +from ntclient.persistence.sql.nt import funcs as nt_funcs +from ntclient.persistence.sql.nt import nt_ver +from ntclient.persistence.sql.usda import funcs as usda_funcs +from ntclient.persistence.sql.usda import sql as _usda_sql +from ntclient.persistence.sql.usda import usda_ver +from ntclient.services import init +from ntclient.utils.exceptions import SqlInvalidVersionError + +# TODO: integration tests.. create user, recipe, log.. analyze & compare +arg_parser = build_argparser() +TEST_HOME = os.path.dirname(os.path.abspath(__file__)) + + +def test_000_init(): + """Tests the SQL/persistence init in real time""" + code, result = init(yes=True) + assert code == 0 + assert result + + +def test_100_usda_sql_funcs(): + """Performs cursory inspection (sanity checks) of usda.sqlite3 image""" + version = usda_ver() + assert version == __db_target_usda__ + result = usda_funcs.sql_nutrients_details() + assert len(result[1]) == 186 + + result = usda_funcs.sql_servings([9050, 9052]) + assert len(result) == 3 + + result = usda_funcs.sql_analyze_foods([23567, 23293]) + assert len(result) == 188 + + result = usda_funcs.sql_sort_foods(789) + assert len(result) == 415 + # result = usda_funcs.sql_sort_foods(789, fdgrp_ids=[100]) + # assert len(result) == 1 + + result = usda_funcs.sql_sort_foods_by_kcal(789) + assert len(result) == 246 + # result = usda_funcs.sql_sort_foods_by_kcal(789, fdgrp_ids=[1100]) + # assert len(result) == 127 + + +def test_200_nt_sql_funcs(): + """Performs cursory inspection (sanity check) of nt.sqlite3 image""" + version = nt_ver() + assert version == __db_target_nt__ + + headers, rows = nt_funcs.sql_biometrics() + assert headers == ["id", "name", "unit", "created"] + assert len(rows) == 29 + + +def test_300_argparser_debug_no_paging(): + """Verifies the debug and no_paging flags are set""" + args = arg_parser.parse_args(args=["-d", "--no-pager"]) + set_flags(args) + + assert args.debug is True + assert args.no_paging is True + + from ntclient import DEBUG, PAGING # pylint: disable=import-outside-toplevel + + assert DEBUG is True + assert PAGING is False + + +def test_400_usda_argparser_funcs(): + """Tests udsa functions in argparser.funcs (to varying degrees each)""" + # Init + args = arg_parser.parse_args(args=["init", "-y"]) + assert args.yes is True + code, result = args.func(args=args) + assert code == 0 + assert result + + # Nutrients ( and `--no-pager` flag) + args = arg_parser.parse_args(args=["--no-pager", "nt"]) + set_flags(args) # unnecessary due to already happening, but hey + code, result = args.func() + assert code == 0 + assert len(result) == 186 + + # Search + args = arg_parser.parse_args(args=["search", "grass", "beef"]) + code, result = args.func(args) + assert code == 0 + assert result + # Top 20 (beats injecting BUFFER_HT/DEFAULT_RESULT_LIMIT) + args = arg_parser.parse_args(args=["search", "grass", "beef", "-t", "20"]) + code, result = args.func(args) + assert code == 0 + assert len(result) == 20 + assert result[0]["long_desc"] is not None + + # Sort + args = arg_parser.parse_args(args=["sort", "789"]) + code, result = args.func(args) + assert code == 0 + assert result + # Top 20 + args = arg_parser.parse_args(args=["sort", "789", "-t", "20"]) + code, result = args.func(args) + assert code == 0 + assert len(result) == 20 + assert result[0][4] == "Capers, raw" + + # Anl + args = arg_parser.parse_args(args=["anl", "9053"]) + code, nutrients_rows, servings_rows = args.func(args) + assert code == 0 + assert len(nutrients_rows[0]) == 30 + assert len(servings_rows[0]) == 1 + + # Day + rda_csv_path = os.path.join(TEST_HOME, "resources", "rda", "dog-18lbs.csv") + day_csv_path = os.path.join(TEST_HOME, "resources", "day", "dog.csv") + args = arg_parser.parse_args(args=["day", "-r", rda_csv_path, day_csv_path]) + code, result = args.func(args) + assert code == 0 + assert result[0][213] == 1.295 + assert len(result[0]) == 177 + + +def test_401_invalid_path_day_throws_error(): + """Ensures invalid path throws exception in `day` subcommand""" + invalid_day_csv_path = os.path.join( + TEST_HOME, "resources", "day", "__NONEXISTENT_CSV_FILE__.csv" + ) + with pytest.raises(SystemExit) as sys_exit: + arg_parser.parse_args(args=["day", invalid_day_csv_path]) + assert sys_exit.value.code == 2 + + invalid_rda_csv_path = os.path.join( + TEST_HOME, "resources", "rda", "__NONEXISTENT_CSV_FILE__.csv" + ) + with pytest.raises(SystemExit) as sys_exit: + arg_parser.parse_args( + args=["day", "-r", invalid_rda_csv_path, invalid_day_csv_path] + ) + assert sys_exit.value.code == 2 + + +def test_402_nt_argparser_funcs(): + """Tests nt functions in argparser.funcs (to varying degrees each)""" + + +def test_500_main_module(): + """Tests execution of main() and __main__, in __main__.py""" + code = nt_main(args=["--no-pager", "nt"]) + assert code == 0 + + sys.argv = ["./nutra"] + code = nt_main() + assert code == 1 + + with pytest.raises(SystemExit) as system_exit: + nt_main(args=["-h"]) + assert system_exit.value.code == 0 + + # __main__: if args_dict + code = nt_main(args=["anl", "9053", "-g", "80"]) + assert code == 0 + + +def test_600_sql_integrity_error__service_wip(): + """Provokes IntegrityError in nt.sqlite3""" + from ntclient.services import biometrics # pylint: disable=import-outside-toplevel + + args = arg_parser.parse_args(args=["-d", "bio", "log", "add", "12,12"]) + biometrics.input = ( + lambda x: "y" + ) # mocks input, could also pass `-y` flag or set yes=True + + with pytest.raises(sqlite3.IntegrityError) as integrity_error: + args.func(args) + assert ( + integrity_error.value.args[0] + == "NOT NULL constraint failed: biometric_log.profile_id" + ) + + +def test_700_build_ntsqlite_succeeds(): + """Verifies the service level call for git submodule""" + try: + os.remove(NTSQLITE_BUILDPATH) + except FileNotFoundError: + pass + assert not os.path.exists(NTSQLITE_BUILDPATH) + + result = build_ntsqlite(verbose=True) + assert result is True + assert os.path.isfile(NTSQLITE_BUILDPATH) + os.remove(NTSQLITE_BUILDPATH) + + +def test_800_usda_upgrades_or_downgrades(): + """Ensures the static usda.sqlite3 file can be upgraded/downgraded as needed""" + version = usda_ver() + major, minor, release = version.split(".") + new_release = str(int(release) + 1) + new_version = ".".join([major, minor, new_release]) + _usda_sql( + "INSERT INTO version (version) VALUES (?)", + values=(new_version,), + version_check=False, + ) + + code, successful = init(yes=True) + assert code == 0 + assert successful is True + + +def test_801_sql_invalid_version_error_if_version_old(): + """Throws base custom SqlException... + TODO: why lines still missing in `coverage` for __main__ ?""" + _usda_sql( + "DELETE FROM version WHERE version=?", + values=(__db_target_usda__,), + version_check=False, + ) + + with pytest.raises(SqlInvalidVersionError) as sql_invalid_version_error: + nt_main(["-d", "nt"]) + assert sql_invalid_version_error is not None + + +def test_802_usda_downloads_fresh_if_missing_or_deleted(): + """Ensure download of usda.sqlite3.tar.xz, if usda.sqlite3 is missing""" + from ntclient.persistence.sql import usda # pylint: disable=import-outside-toplevel + + # TODO: similar for nt.sqlite3? Define development standards.. rebuilding, deleting, preserving + # remove whole `.nutra` in a special test? + try: + # TODO: export USDA_DB_PATH at package level, don't pepper os.path.join() throughout code? + usda_path = os.path.join(NUTRA_DIR, USDA_DB_NAME) + os.remove(usda_path) + except (FileNotFoundError, PermissionError) as err: + # TODO: resolve PermissionError on Windows + print(repr(err)) + _usda_sql( + "INSERT INTO version (version) VALUES (?)", + values=(__db_target_usda__,), + version_check=False, + ) + pytest.xfail("PermissionError, are you using Microsoft Windows?") + + usda.input = lambda x: "y" # mocks input, could also pass `-y` flag or set yes=True + code, successful = init() + assert code == 0 + assert successful is True + + +def test_900_nut_rda_bar(): + """Verifies colored/visual output is correctly generated""" + analysis = usda_funcs.sql_analyze_foods(food_ids=[1001]) + nutrients = usda_funcs.sql_nutrients_overview() + output = nutprogbar.nutprogbar( + food_amts={1001: 100}, food_analyses=analysis, nutrients=nutrients + ) + assert output -- 2.52.0