diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index a9506cde6..b9fe5e21e 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -84,6 +84,8 @@ jobs: #---------------------------------------------- - name: Run tests run: poetry run python -m unittest discover + env: + BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }} #---------------------------------------------- # coverage report @@ -93,6 +95,8 @@ jobs: poetry run coverage run -m unittest discover poetry run coverage xml poetry run coverage report -m + env: + BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }} #---------------------------------------------- # upload coverage results diff --git a/README.md b/README.md index 7ebfc6e21..913cc6511 100644 --- a/README.md +++ b/README.md @@ -218,6 +218,16 @@ runoak -i obolibrary:go.obo viz GO:0005773 ## Configuration +Configuration for an arbitrary `key` (e.g., `bioportal_api_token`) +can be set in the following ways: + +1. Set `OAKLIB_` in the environment +2. Create a configuration file `~/.config/oaklib.ini` + and set the `[oaklib]` section in it with the given key-value pair like + ` = ` +3. Use the CLI command `runoak set-apikey ` to automatically create + and populate the appropriate configuration file. + OAK uses [`pystow`](https://github.com/cthoyt/pystow) for caching. By default, this goes inside `~/.data/`, but can be configured following [these instructions](https://github.com/cthoyt/pystow#%EF%B8%8F%EF%B8%8F-configuration). diff --git a/poetry.lock b/poetry.lock index a28dcabf9..fc8208e1f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -51,7 +51,7 @@ frozenlist = ">=1.1.0" name = "alabaster" version = "0.7.12" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -125,7 +125,7 @@ tests = ["pytest"] name = "argparse" version = "1.4.0" description = "Python command-line parsing library" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -153,7 +153,7 @@ python-versions = ">=3.6" [[package]] name = "atomicwrites" -version = "1.4.0" +version = "1.4.1" description = "Atomic file writes." category = "dev" optional = false @@ -177,7 +177,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (> name = "babel" version = "2.10.3" description = "Internationalization utilities" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -217,7 +217,7 @@ lxml = ["lxml"] [[package]] name = "bioregistry" -version = "0.5.36" +version = "0.5.47" description = "Integrated registry of biological databases and nomenclatures" category = "main" optional = false @@ -237,7 +237,7 @@ charts = ["matplotlib", "matplotlib-venn", "seaborn", "pandas"] docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi", "autodoc-pydantic"] export = ["pyyaml", "rdflib", "rdflib-jsonld", "ndex2"] gha = ["more-itertools"] -health = ["click-default-group", "pandas"] +health = ["click-default-group", "pandas", "tabulate"] tests = ["coverage", "pytest", "more-itertools"] web = ["pyyaml", "rdflib", "rdflib-jsonld", "flask", "flasgger", "bootstrap-flask (<=2.0.0)", "markdown"] @@ -259,14 +259,14 @@ dev = ["build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "pip-tools (= [[package]] name = "boto3" -version = "1.24.25" +version = "1.24.37" description = "The AWS SDK for Python" category = "main" optional = true python-versions = ">= 3.7" [package.dependencies] -botocore = ">=1.27.25,<1.28.0" +botocore = ">=1.27.37,<1.28.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -275,7 +275,7 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.27.25" +version = "1.27.37" description = "Low-level, data-driven core of boto 3." category = "main" optional = true @@ -312,7 +312,7 @@ pycparser = "*" name = "cfgraph" version = "0.2.1" description = "rdflib collections flattening graph" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -377,7 +377,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "coverage" -version = "6.4.1" +version = "6.4.2" description = "Code coverage measurement for Python" category = "dev" optional = false @@ -439,13 +439,13 @@ packaging = "*" name = "docutils" version = "0.17.1" description = "Docutils -- Python Documentation Utilities" -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "dominate" -version = "2.6.0" +version = "2.7.0" description = "Dominate is a Python library for creating and manipulating HTML documents using an elegant DOM API." category = "main" optional = true @@ -463,13 +463,13 @@ python-versions = ">=3.6" name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" [[package]] name = "executing" -version = "0.8.3" +version = "0.9.0" description = "Get the currently executing AST node of a frame, and other information" category = "dev" optional = false @@ -477,7 +477,7 @@ python-versions = "*" [[package]] name = "fastjsonschema" -version = "2.15.3" +version = "2.16.1" description = "Fastest Python implementation of JSON schema" category = "dev" optional = false @@ -496,7 +496,7 @@ python-versions = ">=3.7" [[package]] name = "flask" -version = "2.1.2" +version = "2.1.3" description = "A simple framework for building complex web applications." category = "main" optional = true @@ -623,7 +623,7 @@ rfc3987 = "*" [[package]] name = "gilda" -version = "0.10.1" +version = "0.10.3" description = "Grounding for biomedical entities with contextual disambiguation" category = "main" optional = true @@ -649,15 +649,15 @@ test = ["pytest", "pytest-cov"] [[package]] name = "graphviz" -version = "0.20" +version = "0.20.1" description = "Simple Python interface for Graphviz" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" [package.extras] dev = ["tox (>=3)", "flake8", "pep8-naming", "wheel", "twine"] -docs = ["sphinx (>=4)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"] +docs = ["sphinx (>=5)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"] test = ["pytest (>=7)", "pytest-mock (>=3)", "mock (>=4)", "pytest-cov", "coverage"] [[package]] @@ -691,7 +691,7 @@ python-versions = ">=3.5" name = "imagesize" version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" @@ -899,7 +899,7 @@ hbreader = "*" name = "jsonpatch" version = "1.32" description = "Apply JSON-Patches (RFC 6902)" -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" @@ -910,7 +910,7 @@ jsonpointer = ">=1.9" name = "jsonpath-ng" version = "1.5.3" description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming." -category = "dev" +category = "main" optional = false python-versions = "*" @@ -923,13 +923,13 @@ six = "*" name = "jsonpointer" version = "2.3" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "jsonschema" -version = "4.6.2" +version = "4.7.2" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -1069,9 +1069,9 @@ regex = ["regex"] [[package]] name = "linkml" -version = "1.2.15" +version = "1.3.1" description = "Linked Open Data Modeling Language" -category = "dev" +category = "main" optional = false python-versions = ">=3.7.6,<4.0.0" @@ -1086,7 +1086,7 @@ jinja2 = "*" jsonasobj2 = ">=1.0.3,<2.0.0" jsonschema = ">=3.0.1" linkml-dataops = "*" -linkml-runtime = "1.2.16" +linkml-runtime = ">=1.3.0,<2.0.0" myst-parser = "*" openpyxl = "*" parse = "*" @@ -1104,13 +1104,13 @@ sqlalchemy = ">=1.4.31" watchdog = ">=0.9.0" [package.extras] -docs = ["sphinx-rtd-theme", "sphinx"] +docs = ["sphinx", "sphinx-rtd-theme"] [[package]] name = "linkml-dataops" version = "0.1.0" description = "LinkML Data Operations API" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1123,7 +1123,7 @@ linkml-runtime = ">=1.1.6" [[package]] name = "linkml-runtime" -version = "1.2.16" +version = "1.3.1" description = "Runtime environment for LinkML, the Linked open data modeling language" category = "main" optional = false @@ -1136,7 +1136,7 @@ hbreader = "*" json-flattener = ">=0.1.9" jsonasobj2 = ">=1.0.4,<2.0.0" jsonschema = ">=3.2.0" -prefixcommons = "*" +prefixcommons = "0.1.11" pyyaml = "*" rdflib = ">=6.0.0" requests = "*" @@ -1145,7 +1145,7 @@ requests = "*" name = "markdown-it-py" version = "2.1.0" description = "Python port of markdown-it. Markdown parsing, done right!" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1185,7 +1185,7 @@ traitlets = "*" name = "mdit-py-plugins" version = "0.3.0" description = "Collection of plugins for markdown-it-py" -category = "dev" +category = "main" optional = false python-versions = "~=3.6" @@ -1201,7 +1201,7 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] name = "mdurl" version = "0.1.1" description = "Markdown URL utilities" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1244,7 +1244,7 @@ python-versions = ">=3.7" name = "myst-parser" version = "0.17.2" description = "An extended commonmark compliant parser, with bridges to docutils & sphinx." -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1341,7 +1341,7 @@ python-versions = ">=3.5" [[package]] name = "networkx" -version = "2.8.4" +version = "2.8.5" description = "Python package for creating and manipulating graphs and networks" category = "main" optional = false @@ -1408,7 +1408,7 @@ test = ["pytest", "coverage", "requests", "testpath", "nbval", "selenium", "pyte [[package]] name = "numpy" -version = "1.23.0" +version = "1.23.1" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -1458,14 +1458,14 @@ pystow = "*" typing-extensions = "*" [package.extras] -docs = ["sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints", "sphinx-automodapi"] -tests = ["pytest", "coverage", "unittest-templates"] +tests = ["unittest-templates", "coverage", "pytest"] +docs = ["sphinx-automodapi", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "sphinx"] [[package]] name = "openpyxl" version = "3.0.10" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1529,7 +1529,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" name = "parse" version = "1.19.0" description = "parse() is the opposite of format()" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -1579,7 +1579,7 @@ dev = ["pre-commit", "tox"] name = "ply" version = "3.11" description = "Python Lex & Yacc" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -1695,7 +1695,7 @@ email = ["email-validator (>=1.0.3)"] name = "pygments" version = "2.12.0" description = "Pygments is a syntax highlighting package written in Python." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1731,7 +1731,7 @@ python-versions = ">=3.7" name = "pyshex" version = "0.8.1" description = "Python ShEx Implementation" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1750,7 +1750,7 @@ urllib3 = "*" name = "pyshexc" version = "0.9.1" description = "PyShExC - Python ShEx compiler" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1946,7 +1946,7 @@ rdflib-jsonld = "0.6.1" [[package]] name = "regex" -version = "2022.6.2" +version = "2022.7.25" description = "Alternative regular expression module, to replace re." category = "main" optional = true @@ -1982,7 +1982,7 @@ python-versions = "*" name = "ruamel.yaml" version = "0.17.21" description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" -category = "dev" +category = "main" optional = false python-versions = ">=3" @@ -1997,7 +1997,7 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"] name = "ruamel.yaml.clib" version = "0.2.6" description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml" -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -2076,7 +2076,7 @@ win32 = ["pywin32"] name = "shexjsg" version = "0.8.2" description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -2095,7 +2095,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." -category = "dev" +category = "main" optional = false python-versions = "*" @@ -2111,7 +2111,7 @@ python-versions = ">=3.6" name = "sparqlslurper" version = "0.5.1" description = "SPARQL Slurper for rdflib" -category = "dev" +category = "main" optional = false python-versions = ">=3.7.4" @@ -2141,7 +2141,7 @@ pandas = ["pandas (>=1.3.5)"] name = "sphinx" version = "4.5.0" description = "Python documentation generator" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -2173,7 +2173,7 @@ test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"] name = "sphinx-click" version = "3.1.0" description = "Sphinx extension that automatically documents click applications" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -2201,7 +2201,7 @@ dev = ["transifex-client", "sphinxcontrib-httpdomain", "bump2version"] name = "sphinxcontrib-applehelp" version = "1.0.2" description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books" -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -2213,7 +2213,7 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -2225,7 +2225,7 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -2237,7 +2237,7 @@ test = ["pytest", "html5lib"] name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -2256,7 +2256,7 @@ python-versions = "*" name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -2268,7 +2268,7 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -2310,15 +2310,14 @@ sqlcipher = ["sqlcipher3-binary"] [[package]] name = "sqlalchemy-utils" -version = "0.38.2" +version = "0.38.3" description = "Various utility functions for SQLAlchemy." category = "main" optional = false -python-versions = "~=3.4" +python-versions = "~=3.6" [package.dependencies] -six = "*" -SQLAlchemy = ">=1.0" +SQLAlchemy = ">=1.3" [package.extras] arrow = ["arrow (>=0.3.4)"] @@ -2329,14 +2328,14 @@ intervals = ["intervals (>=0.7.1)"] password = ["passlib (>=1.6,<2.0)"] pendulum = ["pendulum (>=2.0.5)"] phone = ["phonenumbers (>=5.9.2)"] -test = ["pytest (>=2.7.1)", "Pygments (>=1.2)", "Jinja2 (>=2.3)", "docutils (>=0.10)", "flexmock (>=0.9.7)", "mock (==2.0.0)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pg8000 (>=1.12.4)", "pytz (>=2014.2)", "python-dateutil (>=2.6)", "pymysql", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pyodbc", "backports.zoneinfo"] -test_all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "mock (==2.0.0)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)", "backports.zoneinfo"] +test = ["pytest (>=2.7.1)", "Pygments (>=1.2)", "Jinja2 (>=2.3)", "docutils (>=0.10)", "flexmock (>=0.9.7)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pg8000 (>=1.12.4)", "pytz (>=2014.2)", "python-dateutil (>=2.6)", "pymysql", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pyodbc", "backports.zoneinfo"] +test_all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)", "backports.zoneinfo"] timezone = ["python-dateutil"] url = ["furl (>=0.4.1)"] [[package]] name = "sssom" -version = "0.3.12" +version = "0.3.13" description = "Operations on SSSOM mapping tables" category = "main" optional = false @@ -2346,7 +2345,7 @@ python-versions = ">=3.7" bioregistry = "*" click = "*" deprecation = "*" -linkml-runtime = ">=1.1.12" +linkml = "*" networkx = "*" numpy = "*" pandas = "*" @@ -2486,7 +2485,7 @@ python-versions = ">=3.5" [[package]] name = "urllib3" -version = "1.26.10" +version = "1.26.11" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false @@ -2523,7 +2522,7 @@ python-versions = "*" name = "watchdog" version = "2.1.9" description = "Filesystem events monitoring" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -2548,12 +2547,15 @@ python-versions = "*" [[package]] name = "werkzeug" -version = "2.1.2" +version = "2.2.0" description = "The comprehensive WSGI web application library." category = "main" optional = true python-versions = ">=3.7" +[package.dependencies] +MarkupSafe = ">=2.1.1" + [package.extras] watchdog = ["watchdog"] @@ -2604,15 +2606,15 @@ multidict = ">=4.0" [[package]] name = "zipp" -version = "3.8.0" +version = "3.8.1" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] [extras] docs = [] @@ -2624,7 +2626,9 @@ python-versions = "^3.9" content-hash = "cea8459ba7eed7cc6d12a1661e048cb79098b92241785138b273d20594962841" [metadata.files] -adeft = [] +adeft = [ + {file = "adeft-0.11.1.tar.gz", hash = "sha256:72664c098ad0a6fae940c3750583addaaec5012a0d31626809773d3d7469f349"}, +] aiohttp = [ {file = "aiohttp-3.8.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:1ed0b6477896559f17b9eaeb6d38e07f7f9ffe40b9f0f9627ae8b9926ae260a8"}, {file = "aiohttp-3.8.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7dadf3c307b31e0e61689cbf9e06be7a867c563d5a63ce9dca578f956609abf8"}, @@ -2707,7 +2711,10 @@ alabaster = [ {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"}, {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"}, ] -aniso8601 = [] +aniso8601 = [ + {file = "aniso8601-9.0.1-py2.py3-none-any.whl", hash = "sha256:1d2b7ef82963909e93c4f24ce48d4de9e66009a21bf1c1e1c85bdd0812fe412f"}, + {file = "aniso8601-9.0.1.tar.gz", hash = "sha256:72e3117667eedf66951bb2d93f4296a56b94b078a8a95905a052611fb3f1b973"}, +] antlr4-python3-runtime = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] @@ -2758,10 +2765,7 @@ async-timeout = [ {file = "async-timeout-4.0.2.tar.gz", hash = "sha256:2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15"}, {file = "async_timeout-4.0.2-py3-none-any.whl", hash = "sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c"}, ] -atomicwrites = [ - {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"}, - {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"}, -] +atomicwrites = [] attrs = [ {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"}, {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"}, @@ -2870,7 +2874,10 @@ charset-normalizer = [ {file = "charset-normalizer-2.1.0.tar.gz", hash = "sha256:575e708016ff3a5e3681541cb9d79312c416835686d054a23accb873b254f413"}, {file = "charset_normalizer-2.1.0-py3-none-any.whl", hash = "sha256:5189b6f22b01957427f35b6a08d9a0bc45b46d3788ef5a92e978433c7a35f8a5"}, ] -class-resolver = [] +class-resolver = [ + {file = "class_resolver-0.3.10-py3-none-any.whl", hash = "sha256:041c8706abb5a7f0ac3b1067e973e65a0571a59198717b440d7c0052fb75ec4e"}, + {file = "class_resolver-0.3.10.tar.gz", hash = "sha256:cc26438ec4d7e27852ece0db638058454ac76055413996a78678bbd72b0343c3"}, +] click = [ {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"}, {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"}, @@ -2910,19 +2917,21 @@ et-xmlfile = [ {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"}, {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"}, ] -executing = [ - {file = "executing-0.8.3-py2.py3-none-any.whl", hash = "sha256:d1eef132db1b83649a3905ca6dd8897f71ac6f8cac79a7e58a1a09cf137546c9"}, - {file = "executing-0.8.3.tar.gz", hash = "sha256:c6554e21c6b060590a6d3be4b82fb78f8f0194d809de5ea7df1c093763311501"}, -] -fastjsonschema = [ - {file = "fastjsonschema-2.15.3-py3-none-any.whl", hash = "sha256:ddb0b1d8243e6e3abb822bd14e447a89f4ab7439342912d590444831fa00b6a0"}, - {file = "fastjsonschema-2.15.3.tar.gz", hash = "sha256:0a572f0836962d844c1fc435e200b2e4f4677e4e6611a2e3bdd01ba697c275ec"}, -] +executing = [] +fastjsonschema = [] fastobo = [] flask = [] -flask-bootstrap = [] -flask-restx = [] -flask-wtf = [] +flask-bootstrap = [ + {file = "Flask-Bootstrap-3.3.7.1.tar.gz", hash = "sha256:cb08ed940183f6343a64e465e83b3a3f13c53e1baabb8d72b5da4545ef123ac8"}, +] +flask-restx = [ + {file = "flask-restx-0.5.1.tar.gz", hash = "sha256:63c69a61999a34f1774eaccc6fc8c7f504b1aad7d56a8ec672264e52d9ac05f4"}, + {file = "flask_restx-0.5.1-py2.py3-none-any.whl", hash = "sha256:96157547acaa8892adcefd8c60abf9040212ac2a8634937a82946e07b46147fd"}, +] +flask-wtf = [ + {file = "Flask-WTF-1.0.1.tar.gz", hash = "sha256:34fe5c6fee0f69b50e30f81a3b7ea16aa1492a771fe9ad0974d164610c09a6c9"}, + {file = "Flask_WTF-1.0.1-py3-none-any.whl", hash = "sha256:9d733658c80be551ce7d5bc13c7a7ac0d80df509be1e23827c847d9520f4359a"}, +] frozenlist = [ {file = "frozenlist-1.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d2257aaba9660f78c7b1d8fea963b68f3feffb1a9d5d05a18401ca9eb3e8d0a3"}, {file = "frozenlist-1.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:4a44ebbf601d7bac77976d429e9bdb5a4614f9f4027777f9e54fd765196e9d3b"}, @@ -2993,10 +3002,7 @@ funowl = [ {file = "funowl-0.1.12.tar.gz", hash = "sha256:3316c37ecde08cdfa96ebcbcc02ed53c355dc56845d654a8f37aa7a913ca6f71"}, ] gilda = [] -graphviz = [ - {file = "graphviz-0.20-py3-none-any.whl", hash = "sha256:62c5f48bcc534a45b4588c548ff75e419c1f1f3a33d31a91796ae80a7f581e4a"}, - {file = "graphviz-0.20.zip", hash = "sha256:76bdfb73f42e72564ffe9c7299482f9d72f8e6cb8d54bce7b48ab323755e9ba5"}, -] +graphviz = [] greenlet = [ {file = "greenlet-1.1.2-cp27-cp27m-macosx_10_14_x86_64.whl", hash = "sha256:58df5c2a0e293bf665a51f8a100d3e9956febfbf1d9aaf8c0677cf70218910c6"}, {file = "greenlet-1.1.2-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:aec52725173bd3a7b56fe91bc56eccb26fbdff1386ef123abb63c84c5b43b63a"}, @@ -3071,17 +3077,26 @@ importlib-metadata = [ {file = "importlib_metadata-4.12.0.tar.gz", hash = "sha256:637245b8bab2b6502fcbc752cc4b7a6f6243bb02b31c5c26156ad103d3d45670"}, ] ipykernel = [] -ipython = [] +ipython = [ + {file = "ipython-8.4.0-py3-none-any.whl", hash = "sha256:7ca74052a38fa25fe9bedf52da0be7d3fdd2fb027c3b778ea78dfe8c212937d1"}, + {file = "ipython-8.4.0.tar.gz", hash = "sha256:f2db3a10254241d9b447232cec8b424847f338d9d36f9a577a6192c332a46abd"}, +] ipython-genutils = [ {file = "ipython_genutils-0.2.0-py2.py3-none-any.whl", hash = "sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8"}, {file = "ipython_genutils-0.2.0.tar.gz", hash = "sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"}, ] -ipywidgets = [] +ipywidgets = [ + {file = "ipywidgets-7.7.1-py2.py3-none-any.whl", hash = "sha256:aa1076ab7102b2486ae2607c43c243200a07c17d6093676c419d4b6762489a50"}, + {file = "ipywidgets-7.7.1.tar.gz", hash = "sha256:5f2fa1b7afae1af32c88088c9828ad978de93ddda393d7ed414e553fee93dcab"}, +] isodate = [ {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"}, {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"}, ] -itsdangerous = [] +itsdangerous = [ + {file = "itsdangerous-2.1.2-py3-none-any.whl", hash = "sha256:2c2349112351b88699d8d4b6b075022c0808887cb7ad10069318a8b0bc88db44"}, + {file = "itsdangerous-2.1.2.tar.gz", hash = "sha256:5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a"}, +] jedi = [ {file = "jedi-0.18.1-py2.py3-none-any.whl", hash = "sha256:637c9635fcf47945ceb91cd7f320234a7be540ded6f3e99a50cb6febdfd1ba8d"}, {file = "jedi-0.18.1.tar.gz", hash = "sha256:74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab"}, @@ -3090,7 +3105,10 @@ jinja2 = [ {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"}, {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"}, ] -jmespath = [] +jmespath = [ + {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"}, + {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"}, +] joblib = [ {file = "joblib-1.1.0-py2.py3-none-any.whl", hash = "sha256:f21f109b3c7ff9d95f8387f752d0d9c34a02aa2f7060c2135f465da0e5160ff6"}, {file = "joblib-1.1.0.tar.gz", hash = "sha256:4158fcecd13733f8be669be0683b96ebdbbd38d23559f54dca7205aea1bf1e35"}, @@ -3120,24 +3138,33 @@ jsonpointer = [ {file = "jsonpointer-2.3-py2.py3-none-any.whl", hash = "sha256:51801e558539b4e9cd268638c078c6c5746c9ac96bc38152d443400e4f3793e9"}, {file = "jsonpointer-2.3.tar.gz", hash = "sha256:97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a"}, ] -jsonschema = [ - {file = "jsonschema-4.6.2-py3-none-any.whl", hash = "sha256:e331e32e29743014fa59fa77895b5d8669382a4904c8ef23144f7f078ec031c7"}, - {file = "jsonschema-4.6.2.tar.gz", hash = "sha256:b19f62322b0f06927e8ae6215c01654e1885857cdcaf58ae1772b1aa97f1faf2"}, -] +jsonschema = [] jupyter = [ {file = "jupyter-1.0.0-py2.py3-none-any.whl", hash = "sha256:5b290f93b98ffbc21c0c7e749f054b3267782166d72fa5e3ed1ed4eaf34a2b78"}, {file = "jupyter-1.0.0.tar.gz", hash = "sha256:d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f"}, {file = "jupyter-1.0.0.zip", hash = "sha256:3e1f86076bbb7c8c207829390305a2b1fe836d471ed54be66a3b8c41e7f46cc7"}, ] -jupyter-client = [] -jupyter-console = [] +jupyter-client = [ + {file = "jupyter_client-7.3.4-py3-none-any.whl", hash = "sha256:17d74b0d0a7b24f1c8c527b24fcf4607c56bee542ffe8e3418e50b21e514b621"}, + {file = "jupyter_client-7.3.4.tar.gz", hash = "sha256:aa9a6c32054b290374f95f73bb0cae91455c58dfb84f65c8591912b8f65e6d56"}, +] +jupyter-console = [ + {file = "jupyter_console-6.4.4-py3-none-any.whl", hash = "sha256:756df7f4f60c986e7bc0172e4493d3830a7e6e75c08750bbe59c0a5403ad6dee"}, + {file = "jupyter_console-6.4.4.tar.gz", hash = "sha256:172f5335e31d600df61613a97b7f0352f2c8250bbd1092ef2d658f77249f89fb"}, +] jupyter-core = [] jupyterlab-pygments = [ {file = "jupyterlab_pygments-0.2.2-py2.py3-none-any.whl", hash = "sha256:2405800db07c9f770863bcf8049a529c3dd4d3e28536638bd7c1c01d2748309f"}, {file = "jupyterlab_pygments-0.2.2.tar.gz", hash = "sha256:7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d"}, ] -jupyterlab-widgets = [] -kgcl-rdflib = [] +jupyterlab-widgets = [ + {file = "jupyterlab_widgets-1.1.1-py3-none-any.whl", hash = "sha256:90ab47d99da03a3697074acb23b2975ead1d6171aa41cb2812041a7f2a08177a"}, + {file = "jupyterlab_widgets-1.1.1.tar.gz", hash = "sha256:67d0ef1e407e0c42c8ab60b9d901cd7a4c68923650763f75bf17fb06c1943b79"}, +] +kgcl-rdflib = [ + {file = "kgcl-rdflib-0.2.0.tar.gz", hash = "sha256:dcf9c53ddceef77d49a152d941b1ec249052981a40a100c677b8d081e761fc8d"}, + {file = "kgcl_rdflib-0.2.0-py3-none-any.whl", hash = "sha256:1517e3e51551810a2f9f525de587b11bc0da8ac5265e5c3c6b62587d8c169599"}, +] kgcl-schema = [ {file = "kgcl_schema-0.2.0-py3-none-any.whl", hash = "sha256:5fa8036386368b3de16a5e034c7c5a785f1f614ec32f98a0f7bf94357475bc41"}, {file = "kgcl_schema-0.2.0.tar.gz", hash = "sha256:753b1cf717efb3c8a3ee78edb7a0af0353561f55a82731a9ab067b0c75c9799c"}, @@ -3146,10 +3173,7 @@ lark = [ {file = "lark-1.1.2-py2.py3-none-any.whl", hash = "sha256:c1ab213fc5e2d273fe2d91da218ccc8b5b92d065b17faa5e743499cb16594b7d"}, {file = "lark-1.1.2.tar.gz", hash = "sha256:7a8d0c07d663da9391d7faee1bf1d7df4998c47ca43a593cbef5c7566acd057a"}, ] -linkml = [ - {file = "linkml-1.2.15-py3-none-any.whl", hash = "sha256:3da9470da7271742058c6da497bdf227d5f329868bec76d1317371d0e7570bb0"}, - {file = "linkml-1.2.15.tar.gz", hash = "sha256:d49125f2ee9aaf8865bade3d3cddd2be5a29c4f247249133582875f61037db8f"}, -] +linkml = [] linkml-dataops = [ {file = "linkml_dataops-0.1.0-py3-none-any.whl", hash = "sha256:193cf7f659e5f07946d2c2761896910d5f7151d91282543b1363801f68307f4c"}, {file = "linkml_dataops-0.1.0.tar.gz", hash = "sha256:4550eab65e78b70dc3b9c651724a94ac2b1d1edb2fbe576465f1d6951a54ed04"}, @@ -3290,7 +3314,10 @@ myst-parser = [ {file = "myst-parser-0.17.2.tar.gz", hash = "sha256:4c076d649e066f9f5c7c661bae2658be1ca06e76b002bb97f02a09398707686c"}, {file = "myst_parser-0.17.2-py3-none-any.whl", hash = "sha256:1635ce3c18965a528d6de980f989ff64d6a1effb482e1f611b1bfb79e38f3d98"}, ] -nbclient = [] +nbclient = [ + {file = "nbclient-0.6.6-py3-none-any.whl", hash = "sha256:09bae4ea2df79fa6bc50aeb8278d8b79d2036792824337fa6eee834afae17312"}, + {file = "nbclient-0.6.6.tar.gz", hash = "sha256:0df76a7961d99a681b4796c74a1f2553b9f998851acc01896dce064ad19a9027"}, +] nbconvert = [ {file = "nbconvert-6.5.0-py3-none-any.whl", hash = "sha256:c56dd0b8978a1811a5654f74c727ff16ca87dd5a43abd435a1c49b840fcd8360"}, {file = "nbconvert-6.5.0.tar.gz", hash = "sha256:223e46e27abe8596b8aed54301fadbba433b7ffea8196a68fd7b1ff509eee99d"}, @@ -3303,41 +3330,24 @@ nest-asyncio = [ {file = "nest_asyncio-1.5.5-py3-none-any.whl", hash = "sha256:b98e3ec1b246135e4642eceffa5a6c23a3ab12c82ff816a92c612d68205813b2"}, {file = "nest_asyncio-1.5.5.tar.gz", hash = "sha256:e442291cd942698be619823a17a86a5759eabe1f8613084790de189fe9e16d65"}, ] -networkx = [ - {file = "networkx-2.8.4-py3-none-any.whl", hash = "sha256:6933b9b3174a0bdf03c911bb4a1ee43a86ce3edeb813e37e1d4c553b3f4a2c4f"}, - {file = "networkx-2.8.4.tar.gz", hash = "sha256:5e53f027c0d567cf1f884dbb283224df525644e43afd1145d64c9d88a3584762"}, +networkx = [] +nltk = [ + {file = "nltk-3.7-py3-none-any.whl", hash = "sha256:ba3de02490308b248f9b94c8bc1ac0683e9aa2ec49ee78536d8667afb5e3eec8"}, + {file = "nltk-3.7.zip", hash = "sha256:d6507d6460cec76d70afea4242a226a7542f85c669177b9c7f562b7cf1b05502"}, ] -nltk = [] -notebook = [] -numpy = [ - {file = "numpy-1.23.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:58bfd40eb478f54ff7a5710dd61c8097e169bc36cc68333d00a9bcd8def53b38"}, - {file = "numpy-1.23.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:196cd074c3f97c4121601790955f915187736f9cf458d3ee1f1b46aff2b1ade0"}, - {file = "numpy-1.23.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f1d88ef79e0a7fa631bb2c3dda1ea46b32b1fe614e10fedd611d3d5398447f2f"}, - {file = "numpy-1.23.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d54b3b828d618a19779a84c3ad952e96e2c2311b16384e973e671aa5be1f6187"}, - {file = "numpy-1.23.0-cp310-cp310-win32.whl", hash = "sha256:2b2da66582f3a69c8ce25ed7921dcd8010d05e59ac8d89d126a299be60421171"}, - {file = "numpy-1.23.0-cp310-cp310-win_amd64.whl", hash = "sha256:97a76604d9b0e79f59baeca16593c711fddb44936e40310f78bfef79ee9a835f"}, - {file = "numpy-1.23.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:d8cc87bed09de55477dba9da370c1679bd534df9baa171dd01accbb09687dac3"}, - {file = "numpy-1.23.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:f0f18804df7370571fb65db9b98bf1378172bd4e962482b857e612d1fec0f53e"}, - {file = "numpy-1.23.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ac86f407873b952679f5f9e6c0612687e51547af0e14ddea1eedfcb22466babd"}, - {file = "numpy-1.23.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ae8adff4172692ce56233db04b7ce5792186f179c415c37d539c25de7298d25d"}, - {file = "numpy-1.23.0-cp38-cp38-win32.whl", hash = "sha256:fe8b9683eb26d2c4d5db32cd29b38fdcf8381324ab48313b5b69088e0e355379"}, - {file = "numpy-1.23.0-cp38-cp38-win_amd64.whl", hash = "sha256:5043bcd71fcc458dfb8a0fc5509bbc979da0131b9d08e3d5f50fb0bbb36f169a"}, - {file = "numpy-1.23.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:1c29b44905af288b3919803aceb6ec7fec77406d8b08aaa2e8b9e63d0fe2f160"}, - {file = "numpy-1.23.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:98e8e0d8d69ff4d3fa63e6c61e8cfe2d03c29b16b58dbef1f9baa175bbed7860"}, - {file = "numpy-1.23.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:79a506cacf2be3a74ead5467aee97b81fca00c9c4c8b3ba16dbab488cd99ba10"}, - {file = "numpy-1.23.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:092f5e6025813e64ad6d1b52b519165d08c730d099c114a9247c9bb635a2a450"}, - {file = "numpy-1.23.0-cp39-cp39-win32.whl", hash = "sha256:d6ca8dabe696c2785d0c8c9b0d8a9b6e5fdbe4f922bde70d57fa1a2848134f95"}, - {file = "numpy-1.23.0-cp39-cp39-win_amd64.whl", hash = "sha256:fc431493df245f3c627c0c05c2bd134535e7929dbe2e602b80e42bf52ff760bc"}, - {file = "numpy-1.23.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:f9c3fc2adf67762c9fe1849c859942d23f8d3e0bee7b5ed3d4a9c3eeb50a2f07"}, - {file = "numpy-1.23.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d0d2094e8f4d760500394d77b383a1b06d3663e8892cdf5df3c592f55f3bff66"}, - {file = "numpy-1.23.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:94b170b4fa0168cd6be4becf37cb5b127bd12a795123984385b8cd4aca9857e5"}, - {file = "numpy-1.23.0.tar.gz", hash = "sha256:bd3fa4fe2e38533d5336e1272fc4e765cabbbde144309ccee8675509d5cd7b05"}, +notebook = [ + {file = "notebook-6.4.12-py3-none-any.whl", hash = "sha256:8c07a3bb7640e371f8a609bdbb2366a1976c6a2589da8ef917f761a61e3ad8b1"}, + {file = "notebook-6.4.12.tar.gz", hash = "sha256:6268c9ec9048cff7a45405c990c29ac9ca40b0bc3ec29263d218c5e01f2b4e86"}, ] +numpy = [] nxontology = [ {file = "nxontology-0.4.1-py3-none-any.whl", hash = "sha256:74cc228adcbbde49c4b35eb40c8b69db40e0a07757533573a775e88b7b2d29f9"}, {file = "nxontology-0.4.1.tar.gz", hash = "sha256:8f1e5d6d7787542e9414be4ae34bb09e369dbaf2d6c646bba2d18b122c083d44"}, ] -obonet = [] +obonet = [ + {file = "obonet-0.3.0-py3-none-any.whl", hash = "sha256:d436eb4f57afa6f1a48992c3a4132126da9793e1439f667ab23cc74d8e957aee"}, + {file = "obonet-0.3.0.tar.gz", hash = "sha256:fd801166cd28a2ef86126f22c8e3da30f5c3b6a3adfc62536abea1aa9956a2b4"}, +] ontoportal-client = [] openpyxl = [ {file = "openpyxl-3.0.10-py2.py3-none-any.whl", hash = "sha256:0ab6d25d01799f97a9464630abacbb34aafecdcaa0ef3cba6d6b3499867d0355"}, @@ -3406,9 +3416,45 @@ prometheus-client = [ {file = "prometheus_client-0.14.1-py3-none-any.whl", hash = "sha256:522fded625282822a89e2773452f42df14b5a8e84a86433e3f8a189c1d54dc01"}, {file = "prometheus_client-0.14.1.tar.gz", hash = "sha256:5459c427624961076277fdc6dc50540e2bacb98eebde99886e59ec55ed92093a"}, ] -prompt-toolkit = [] +prompt-toolkit = [ + {file = "prompt_toolkit-3.0.30-py3-none-any.whl", hash = "sha256:d8916d3f62a7b67ab353a952ce4ced6a1d2587dfe9ef8ebc30dd7c386751f289"}, + {file = "prompt_toolkit-3.0.30.tar.gz", hash = "sha256:859b283c50bde45f5f97829f77a4674d1c1fcd88539364f1b28a37805cfd89c0"}, +] pronto = [] -psutil = [] +psutil = [ + {file = "psutil-5.9.1-cp27-cp27m-manylinux2010_i686.whl", hash = "sha256:799759d809c31aab5fe4579e50addf84565e71c1dc9f1c31258f159ff70d3f87"}, + {file = "psutil-5.9.1-cp27-cp27m-manylinux2010_x86_64.whl", hash = "sha256:9272167b5f5fbfe16945be3db475b3ce8d792386907e673a209da686176552af"}, + {file = "psutil-5.9.1-cp27-cp27m-win32.whl", hash = "sha256:0904727e0b0a038830b019551cf3204dd48ef5c6868adc776e06e93d615fc5fc"}, + {file = "psutil-5.9.1-cp27-cp27m-win_amd64.whl", hash = "sha256:e7e10454cb1ab62cc6ce776e1c135a64045a11ec4c6d254d3f7689c16eb3efd2"}, + {file = "psutil-5.9.1-cp27-cp27mu-manylinux2010_i686.whl", hash = "sha256:56960b9e8edcca1456f8c86a196f0c3d8e3e361320071c93378d41445ffd28b0"}, + {file = "psutil-5.9.1-cp27-cp27mu-manylinux2010_x86_64.whl", hash = "sha256:44d1826150d49ffd62035785a9e2c56afcea66e55b43b8b630d7706276e87f22"}, + {file = "psutil-5.9.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c7be9d7f5b0d206f0bbc3794b8e16fb7dbc53ec9e40bbe8787c6f2d38efcf6c9"}, + {file = "psutil-5.9.1-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:abd9246e4cdd5b554a2ddd97c157e292ac11ef3e7af25ac56b08b455c829dca8"}, + {file = "psutil-5.9.1-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:29a442e25fab1f4d05e2655bb1b8ab6887981838d22effa2396d584b740194de"}, + {file = "psutil-5.9.1-cp310-cp310-win32.whl", hash = "sha256:20b27771b077dcaa0de1de3ad52d22538fe101f9946d6dc7869e6f694f079329"}, + {file = "psutil-5.9.1-cp310-cp310-win_amd64.whl", hash = "sha256:58678bbadae12e0db55186dc58f2888839228ac9f41cc7848853539b70490021"}, + {file = "psutil-5.9.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:3a76ad658641172d9c6e593de6fe248ddde825b5866464c3b2ee26c35da9d237"}, + {file = "psutil-5.9.1-cp36-cp36m-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a6a11e48cb93a5fa606306493f439b4aa7c56cb03fc9ace7f6bfa21aaf07c453"}, + {file = "psutil-5.9.1-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:068935df39055bf27a29824b95c801c7a5130f118b806eee663cad28dca97685"}, + {file = "psutil-5.9.1-cp36-cp36m-win32.whl", hash = "sha256:0f15a19a05f39a09327345bc279c1ba4a8cfb0172cc0d3c7f7d16c813b2e7d36"}, + {file = "psutil-5.9.1-cp36-cp36m-win_amd64.whl", hash = "sha256:db417f0865f90bdc07fa30e1aadc69b6f4cad7f86324b02aa842034efe8d8c4d"}, + {file = "psutil-5.9.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:91c7ff2a40c373d0cc9121d54bc5f31c4fa09c346528e6a08d1845bce5771ffc"}, + {file = "psutil-5.9.1-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:fea896b54f3a4ae6f790ac1d017101252c93f6fe075d0e7571543510f11d2676"}, + {file = "psutil-5.9.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3054e923204b8e9c23a55b23b6df73a8089ae1d075cb0bf711d3e9da1724ded4"}, + {file = "psutil-5.9.1-cp37-cp37m-win32.whl", hash = "sha256:d2d006286fbcb60f0b391741f520862e9b69f4019b4d738a2a45728c7e952f1b"}, + {file = "psutil-5.9.1-cp37-cp37m-win_amd64.whl", hash = "sha256:b14ee12da9338f5e5b3a3ef7ca58b3cba30f5b66f7662159762932e6d0b8f680"}, + {file = "psutil-5.9.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:19f36c16012ba9cfc742604df189f2f28d2720e23ff7d1e81602dbe066be9fd1"}, + {file = "psutil-5.9.1-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:944c4b4b82dc4a1b805329c980f270f170fdc9945464223f2ec8e57563139cf4"}, + {file = "psutil-5.9.1-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4b6750a73a9c4a4e689490ccb862d53c7b976a2a35c4e1846d049dcc3f17d83b"}, + {file = "psutil-5.9.1-cp38-cp38-win32.whl", hash = "sha256:a8746bfe4e8f659528c5c7e9af5090c5a7d252f32b2e859c584ef7d8efb1e689"}, + {file = "psutil-5.9.1-cp38-cp38-win_amd64.whl", hash = "sha256:79c9108d9aa7fa6fba6e668b61b82facc067a6b81517cab34d07a84aa89f3df0"}, + {file = "psutil-5.9.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:28976df6c64ddd6320d281128817f32c29b539a52bdae5e192537bc338a9ec81"}, + {file = "psutil-5.9.1-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:b88f75005586131276634027f4219d06e0561292be8bd6bc7f2f00bdabd63c4e"}, + {file = "psutil-5.9.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:645bd4f7bb5b8633803e0b6746ff1628724668681a434482546887d22c7a9537"}, + {file = "psutil-5.9.1-cp39-cp39-win32.whl", hash = "sha256:32c52611756096ae91f5d1499fe6c53b86f4a9ada147ee42db4991ba1520e574"}, + {file = "psutil-5.9.1-cp39-cp39-win_amd64.whl", hash = "sha256:f65f9a46d984b8cd9b3750c2bdb419b2996895b005aefa6cbaba9a143b1ce2c5"}, + {file = "psutil-5.9.1.tar.gz", hash = "sha256:57f1819b5d9e95cdfb0c881a8a5b7d542ed0b7c522d575706a80bedc848c8954"}, +] ptyprocess = [ {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"}, {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"}, @@ -3537,7 +3583,13 @@ pywin32 = [ {file = "pywin32-304-cp39-cp39-win32.whl", hash = "sha256:25746d841201fd9f96b648a248f731c1dec851c9a08b8e33da8b56148e4c65cc"}, {file = "pywin32-304-cp39-cp39-win_amd64.whl", hash = "sha256:d24a3382f013b21aa24a5cfbfad5a2cd9926610c0affde3e8ab5b3d7dbcf4ac9"}, ] -pywinpty = [] +pywinpty = [ + {file = "pywinpty-2.0.6-cp310-none-win_amd64.whl", hash = "sha256:7fadc5265484c7d7c84554b9f1cfd7acf6383a877c1cfb3ee77d51179145b3ce"}, + {file = "pywinpty-2.0.6-cp37-none-win_amd64.whl", hash = "sha256:906a3048ecfec6ece1b141594ebbbcd5c4751960714c50524e8e907bb77c9207"}, + {file = "pywinpty-2.0.6-cp38-none-win_amd64.whl", hash = "sha256:5e4b2167e813575bf495b46adb2d88be5c470d9daf49d488900350853e95248f"}, + {file = "pywinpty-2.0.6-cp39-none-win_amd64.whl", hash = "sha256:f7ae5d29f1c3d028e06032f8d267b51fd72ea219b9bba3e2a972a7bc26a25a87"}, + {file = "pywinpty-2.0.6.tar.gz", hash = "sha256:a91a77d23f29a58b44f62a9474a31ed67df1277cddb69665275f8d22429046ac"}, +] pyyaml = [ {file = "PyYAML-6.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d4db7c7aef085872ef65a8fd7d6d09a14ae91f691dec3e87ee5ee0539d516f53"}, {file = "PyYAML-6.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9df7ed3b3d2e0ecfe09e14741b857df43adb5a3ddadc919a2d94fbdf78fea53c"}, @@ -3573,8 +3625,69 @@ pyyaml = [ {file = "PyYAML-6.0-cp39-cp39-win_amd64.whl", hash = "sha256:b3d267842bf12586ba6c734f89d1f5b871df0273157918b0ccefa29deb05c21c"}, {file = "PyYAML-6.0.tar.gz", hash = "sha256:68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2"}, ] -pyzmq = [] -qtconsole = [] +pyzmq = [ + {file = "pyzmq-23.2.0-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:22ac0243a41798e3eb5d5714b28c2f28e3d10792dffbc8a5fca092f975fdeceb"}, + {file = "pyzmq-23.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f685003d836ad0e5d4f08d1e024ee3ac7816eb2f873b2266306eef858f058133"}, + {file = "pyzmq-23.2.0-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:d4651de7316ec8560afe430fb042c0782ed8ac54c0be43a515944d7c78fddac8"}, + {file = "pyzmq-23.2.0-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:bcc6953e47bcfc9028ddf9ab2a321a3c51d7cc969db65edec092019bb837959f"}, + {file = "pyzmq-23.2.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0e08671dc202a1880fa522f921f35ca5925ba30da8bc96228d74a8f0643ead9c"}, + {file = "pyzmq-23.2.0-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:de727ea906033b30527b4a99498f19aca3f4d1073230a958679a5b726e2784e0"}, + {file = "pyzmq-23.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f5aa9da520e4bb8cee8189f2f541701405e7690745094ded7a37b425d60527ea"}, + {file = "pyzmq-23.2.0-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:f3ff6abde52e702397949054cb5b06c1c75b5d6542f6a2ce029e46f71ffbbbf2"}, + {file = "pyzmq-23.2.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:e2e2db5c6ef376e97c912733dfc24406f5949474d03e800d5f07b6aca4d870af"}, + {file = "pyzmq-23.2.0-cp310-cp310-win32.whl", hash = "sha256:e669913cb2179507628419ec4f0e453e48ce6f924de5884d396f18c31836089c"}, + {file = "pyzmq-23.2.0-cp310-cp310-win_amd64.whl", hash = "sha256:a3dc339f7bc185d5fd0fd976242a5baf35de404d467e056484def8a4dd95868b"}, + {file = "pyzmq-23.2.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:30c365e60c39c53f8eea042b37ea28304ffa6558fb7241cf278745095a5757da"}, + {file = "pyzmq-23.2.0-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8c2d8b69a2bf239ae3d987537bf3fbc2b044a405394cf4c258fc684971dd48b2"}, + {file = "pyzmq-23.2.0-cp36-cp36m-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:602835e5672ca9ca1d78e6c148fb28c4f91b748ebc41fbd2f479d8763d58bc9b"}, + {file = "pyzmq-23.2.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:831da96ba3f36cc892f0afbb4fb89b28b61b387261676e55d55a682addbd29f7"}, + {file = "pyzmq-23.2.0-cp36-cp36m-musllinux_1_1_i686.whl", hash = "sha256:c8dec8a2f3f0bb462e6439df436cd8c7ec37968e90b4209ac621e7fbc0ed3b00"}, + {file = "pyzmq-23.2.0-cp36-cp36m-musllinux_1_1_x86_64.whl", hash = "sha256:814e5aaf0c3be9991a59066eafb2d6e117aed6b413e3e7e9be45d4e55f5e2748"}, + {file = "pyzmq-23.2.0-cp36-cp36m-win32.whl", hash = "sha256:8496a2a5efd055c61ac2c6a18116c768a25c644b6747dcfde43e91620ab3453c"}, + {file = "pyzmq-23.2.0-cp36-cp36m-win_amd64.whl", hash = "sha256:60746a7e8558655420a69441c0a1d47ed225ed3ac355920b96a96d0554ef7e6b"}, + {file = "pyzmq-23.2.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:5cb642e94337b0c76c9c8cb9bfb0f8a78654575847d080d3e1504f312d691fc3"}, + {file = "pyzmq-23.2.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:444f7d615d5f686d0ef508b9edfa8a286e6d89f449a1ba37b60ef69d869220a3"}, + {file = "pyzmq-23.2.0-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:c9638e0057e3f1a8b7c5ce33c7575349d9183a033a19b5676ad55096ae36820b"}, + {file = "pyzmq-23.2.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:004a431dfa0459123e6f4660d7e3c4ac19217d134ca38bacfffb2e78716fe944"}, + {file = "pyzmq-23.2.0-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:5592fb4316f895922b1cacb91b04a0fa09d6f6f19bbab4442b4d0a0825177b93"}, + {file = "pyzmq-23.2.0-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:c0a5f987d73fd9b46c3d180891f829afda714ab6bab30a1218724d4a0a63afd8"}, + {file = "pyzmq-23.2.0-cp37-cp37m-win32.whl", hash = "sha256:d11628212fd731b8986f1561d9bb3f8c38d9c15b330c3d8a88963519fbcd553b"}, + {file = "pyzmq-23.2.0-cp37-cp37m-win_amd64.whl", hash = "sha256:558f5f636e3e65f261b64925e8b190e8689e334911595394572cc7523879006d"}, + {file = "pyzmq-23.2.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:61b97f624da42813f74977425a3a6144d604ea21cf065616d36ea3a866d92c1c"}, + {file = "pyzmq-23.2.0-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:693c96ae4d975eb8efa1639670e9b1fac0c3f98b7845b65c0f369141fb4bb21f"}, + {file = "pyzmq-23.2.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:2b054525c9f7e240562185bf21671ca16d56bde92e9bd0f822c07dec7626b704"}, + {file = "pyzmq-23.2.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:859059caf564f0c9398c9005278055ed3d37af4d73de6b1597821193b04ca09b"}, + {file = "pyzmq-23.2.0-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:8355744fdbdeac5cfadfa4f38b82029b5f2b8cab7472a33453a217a7f3a9dce2"}, + {file = "pyzmq-23.2.0-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:420b9abd1a7330687a095373b8280a20cdee04342fbc8ccb3b56d9ec8efd4e62"}, + {file = "pyzmq-23.2.0-cp38-cp38-win32.whl", hash = "sha256:59928dfebe93cf1e203e3cb0fd5d5dd384da56b99c8305f2e1b0a933751710f6"}, + {file = "pyzmq-23.2.0-cp38-cp38-win_amd64.whl", hash = "sha256:c882f1d4f96fbd807e92c334251d8ebd159a1ef89059ccd386ddea83fdb91bd8"}, + {file = "pyzmq-23.2.0-cp39-cp39-macosx_10_15_universal2.whl", hash = "sha256:ced12075cdf3c7332ecc1960f77f7439d5ebb8ea20bbd3c34c8299e694f1b0a1"}, + {file = "pyzmq-23.2.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:3a4d87342c2737fbb9eee5c33c792db27b36b04957b4e6b7edd73a5b239a2a13"}, + {file = "pyzmq-23.2.0-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:99cedf38eaddf263cf7e2a50e405f12c02cedf6d9df00a0d9c5d7b9417b57f76"}, + {file = "pyzmq-23.2.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:d1610260cc672975723fcf7705c69a95f3b88802a594c9867781bedd9b13422c"}, + {file = "pyzmq-23.2.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c223a13555444707a0a7ebc6f9ee63053147c8c082bd1a31fd1207a03e8b0500"}, + {file = "pyzmq-23.2.0-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:f5fdb00d65ec44b10cc6b9b6318ef1363b81647a4aa3270ca39565eadb2d1201"}, + {file = "pyzmq-23.2.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:984b232802eddf9f0be264a4d57a10b3a1fd7319df14ee6fc7b41c6d155a3e6c"}, + {file = "pyzmq-23.2.0-cp39-cp39-win32.whl", hash = "sha256:f146648941cadaaaf01254a75651a23c08159d009d36c5af42a7cc200a5e53ec"}, + {file = "pyzmq-23.2.0-cp39-cp39-win_amd64.whl", hash = "sha256:83005d8928f8a5cebcfb33af3bfb84b1ad65d882b899141a331cc5d07d89f093"}, + {file = "pyzmq-23.2.0-pp37-pypy37_pp73-macosx_10_9_x86_64.whl", hash = "sha256:fee86542dc4ee8229e023003e3939b4d58cc2453922cf127778b69505fc9064b"}, + {file = "pyzmq-23.2.0-pp37-pypy37_pp73-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:5d57542429df6acff02ff022067aa75b677603cee70e3abb9742787545eec966"}, + {file = "pyzmq-23.2.0-pp37-pypy37_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:057b154471e096e2dda147f7b057041acc303bb7ca4aa24c3b88c6cecdd78717"}, + {file = "pyzmq-23.2.0-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:5d92e7cbeab7f70b08cc0f27255b0bb2500afc30f31075bca0b1cb87735d186c"}, + {file = "pyzmq-23.2.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:eb4a573a8499685d62545e806d8fd143c84ac8b3439f925cd92c8763f0ed9bd7"}, + {file = "pyzmq-23.2.0-pp38-pypy38_pp73-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:da338e2728410d74ddeb1479ec67cfba73311607037455a40f92b6f5c62bf11d"}, + {file = "pyzmq-23.2.0-pp38-pypy38_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:1b2a21f595f8cc549abd6c8de1fcd34c83441e35fb24b8a59bf161889c62a486"}, + {file = "pyzmq-23.2.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:8c0f4d6f8c985bab83792be26ff3233940ba42e22237610ac50cbcfc10a5c235"}, + {file = "pyzmq-23.2.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:bbabd1df23bf63ae829e81200034c0e433499275a6ed29ca1a912ea7629426d9"}, + {file = "pyzmq-23.2.0-pp39-pypy39_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:21552624ce69e69f7924f413b802b1fb554f4c0497f837810e429faa1cd4f163"}, + {file = "pyzmq-23.2.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c616893a577e9d6773a3836732fd7e2a729157a108b8fccd31c87512fa01671a"}, + {file = "pyzmq-23.2.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:ce4f71e17fa849de41a06109030d3f6815fcc33338bf98dd0dde6d456d33c929"}, + {file = "pyzmq-23.2.0.tar.gz", hash = "sha256:a51f12a8719aad9dcfb55d456022f16b90abc8dde7d3ca93ce3120b40e3fa169"}, +] +qtconsole = [ + {file = "qtconsole-5.3.1-py3-none-any.whl", hash = "sha256:d364592d7ede3257f1e17fcdbfd339c26e2cc638ca4fa4ee56a724e26ea13c81"}, + {file = "qtconsole-5.3.1.tar.gz", hash = "sha256:b73723fac43938b684dcb237a88510dc7721c43a726cea8ade179a2927c0a2f3"}, +] qtpy = [ {file = "QtPy-2.1.0-py3-none-any.whl", hash = "sha256:aee0586081f943029312becece9f63977b0a9e3788f77a6ac8cc74802bb173d6"}, {file = "QtPy-2.1.0.tar.gz", hash = "sha256:ca8cd4217175186344299ee4c0f7e7adcf362c70852ba35b255a534077025c06"}, @@ -3634,7 +3747,10 @@ rfc3987 = [ {file = "ruamel.yaml.clib-0.2.6-cp39-cp39-win_amd64.whl", hash = "sha256:825d5fccef6da42f3c8eccd4281af399f21c02b32d98e113dbc631ea6a6ecbc7"}, {file = "ruamel.yaml.clib-0.2.6.tar.gz", hash = "sha256:4ff604ce439abb20794f05613c374759ce10e3595d1867764dd1ae675b85acbd"}, ] -s3transfer = [] +s3transfer = [ + {file = "s3transfer-0.6.0-py3-none-any.whl", hash = "sha256:06176b74f3a15f61f1b4f25a1fc29a4429040b7647133a463da8fa5bd28d5ecd"}, + {file = "s3transfer-0.6.0.tar.gz", hash = "sha256:2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947"}, +] scikit-learn = [ {file = "scikit-learn-1.1.1.tar.gz", hash = "sha256:3e77b71e8e644f86c8b5be7f1c285ef597de4c384961389ee3e9ca36c445b256"}, {file = "scikit_learn-1.1.1-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:102f51797cd8944bf44a038d106848ddf2804f2c1edf7aea45fba81a4fdc4d80"}, @@ -3786,14 +3902,17 @@ sqlalchemy = [ {file = "SQLAlchemy-1.4.39-cp39-cp39-win_amd64.whl", hash = "sha256:8b773c9974c272aae0fa7e95b576d98d17ee65f69d8644f9b6ffc90ee96b4d19"}, {file = "SQLAlchemy-1.4.39.tar.gz", hash = "sha256:8194896038753b46b08a0b0ae89a5d80c897fb601dd51e243ed5720f1f155d27"}, ] -sqlalchemy-utils = [ - {file = "SQLAlchemy-Utils-0.38.2.tar.gz", hash = "sha256:9e01d6d3fb52d3926fcd4ea4a13f3540701b751aced0316bff78264402c2ceb4"}, - {file = "SQLAlchemy_Utils-0.38.2-py3-none-any.whl", hash = "sha256:622235b1598f97300e4d08820ab024f5219c9a6309937a8b908093f487b4ba54"}, -] +sqlalchemy-utils = [] sssom = [] sssom-schema = [] -stack-data = [] -terminado = [] +stack-data = [ + {file = "stack_data-0.3.0-py3-none-any.whl", hash = "sha256:aa1d52d14d09c7a9a12bb740e6bdfffe0f5e8f4f9218d85e7c73a8c37f7ae38d"}, + {file = "stack_data-0.3.0.tar.gz", hash = "sha256:77bec1402dcd0987e9022326473fdbcc767304892a533ed8c29888dacb7dddbc"}, +] +terminado = [ + {file = "terminado-0.15.0-py3-none-any.whl", hash = "sha256:0d5f126fbfdb5887b25ae7d9d07b0d716b1cc0ccaacc71c1f3c14d228e065197"}, + {file = "terminado-0.15.0.tar.gz", hash = "sha256:ab4eeedccfcc1e6134bfee86106af90852c69d602884ea3a1e8ca6d4486e9bfe"}, +] threadpoolctl = [ {file = "threadpoolctl-3.1.0-py3-none-any.whl", hash = "sha256:8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b"}, {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"}, @@ -3802,22 +3921,42 @@ tinycss2 = [ {file = "tinycss2-1.1.1-py3-none-any.whl", hash = "sha256:fe794ceaadfe3cf3e686b22155d0da5780dd0e273471a51846d0a02bc204fec8"}, {file = "tinycss2-1.1.1.tar.gz", hash = "sha256:b2e44dd8883c360c35dd0d1b5aad0b610e5156c2cb3b33434634e539ead9d8bf"}, ] -tornado = [] +tornado = [ + {file = "tornado-6.2-cp37-abi3-macosx_10_9_universal2.whl", hash = "sha256:20f638fd8cc85f3cbae3c732326e96addff0a15e22d80f049e00121651e82e72"}, + {file = "tornado-6.2-cp37-abi3-macosx_10_9_x86_64.whl", hash = "sha256:87dcafae3e884462f90c90ecc200defe5e580a7fbbb4365eda7c7c1eb809ebc9"}, + {file = "tornado-6.2-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ba09ef14ca9893954244fd872798b4ccb2367c165946ce2dd7376aebdde8e3ac"}, + {file = "tornado-6.2-cp37-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:b8150f721c101abdef99073bf66d3903e292d851bee51910839831caba341a75"}, + {file = "tornado-6.2-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d3a2f5999215a3a06a4fc218026cd84c61b8b2b40ac5296a6db1f1451ef04c1e"}, + {file = "tornado-6.2-cp37-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:5f8c52d219d4995388119af7ccaa0bcec289535747620116a58d830e7c25d8a8"}, + {file = "tornado-6.2-cp37-abi3-musllinux_1_1_i686.whl", hash = "sha256:6fdfabffd8dfcb6cf887428849d30cf19a3ea34c2c248461e1f7d718ad30b66b"}, + {file = "tornado-6.2-cp37-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:1d54d13ab8414ed44de07efecb97d4ef7c39f7438cf5e976ccd356bebb1b5fca"}, + {file = "tornado-6.2-cp37-abi3-win32.whl", hash = "sha256:5c87076709343557ef8032934ce5f637dbb552efa7b21d08e89ae7619ed0eb23"}, + {file = "tornado-6.2-cp37-abi3-win_amd64.whl", hash = "sha256:e5f923aa6a47e133d1cf87d60700889d7eae68988704e20c75fb2d65677a8e4b"}, + {file = "tornado-6.2.tar.gz", hash = "sha256:9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13"}, +] tqdm = [ {file = "tqdm-4.64.0-py2.py3-none-any.whl", hash = "sha256:74a2cdefe14d11442cedf3ba4e21a3b84ff9a2dbdc6cfae2c34addb2a14a5ea6"}, {file = "tqdm-4.64.0.tar.gz", hash = "sha256:40be55d30e200777a307a7585aee69e4eabb46b4ec6a4b4a5f2d9f11e7d5408d"}, ] -traitlets = [] +traitlets = [ + {file = "traitlets-5.3.0-py3-none-any.whl", hash = "sha256:65fa18961659635933100db8ca120ef6220555286949774b9cfc106f941d1c7a"}, + {file = "traitlets-5.3.0.tar.gz", hash = "sha256:0bb9f1f9f017aa8ec187d8b1b2a7a6626a2a1d877116baba52a129bfa124f8e2"}, +] typing-extensions = [ {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"}, {file = "typing_extensions-4.3.0.tar.gz", hash = "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"}, ] -unidecode = [] +unidecode = [ + {file = "Unidecode-1.3.4-py3-none-any.whl", hash = "sha256:afa04efcdd818a93237574791be9b2817d7077c25a068b00f8cff7baa4e59257"}, + {file = "Unidecode-1.3.4.tar.gz", hash = "sha256:8e4352fb93d5a735c788110d2e7ac8e8031eb06ccbfe8d324ab71735015f9342"}, +] urllib3 = [] validators = [ {file = "validators-0.20.0.tar.gz", hash = "sha256:24148ce4e64100a2d5e267233e23e7afeb55316b47d30faae7eb6e7292bc226a"}, ] -visitor = [] +visitor = [ + {file = "visitor-0.1.3.tar.gz", hash = "sha256:2c737903b2b6864ebc6167eef7cf3b997126f1aa94bdf590f90f1436d23e480a"}, +] watchdog = [ {file = "watchdog-2.1.9-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a735a990a1095f75ca4f36ea2ef2752c99e6ee997c46b0de507ba40a09bf7330"}, {file = "watchdog-2.1.9-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6b17d302850c8d412784d9246cfe8d7e3af6bcd45f958abb2d08a6f8bedf695d"}, @@ -3854,7 +3993,10 @@ webencodings = [ {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, ] werkzeug = [] -widgetsnbextension = [] +widgetsnbextension = [ + {file = "widgetsnbextension-3.6.1-py2.py3-none-any.whl", hash = "sha256:954e0faefdd414e4e013f17dbc7fd86f24cf1d243a3ac85d5f0fc2c2d2b50c66"}, + {file = "widgetsnbextension-3.6.1.tar.gz", hash = "sha256:9c84ae64c2893c7cbe2eaafc7505221a795c27d68938454034ac487319a75b10"}, +] wrapt = [ {file = "wrapt-1.14.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:1b376b3f4896e7930f1f772ac4b064ac12598d1c38d04907e696cc4d794b43d3"}, {file = "wrapt-1.14.1-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:903500616422a40a98a5a3c4ff4ed9d0066f3b4c951fa286018ecdf0750194ef"}, @@ -3921,7 +4063,10 @@ wrapt = [ {file = "wrapt-1.14.1-cp39-cp39-win_amd64.whl", hash = "sha256:dee60e1de1898bde3b238f18340eec6148986da0455d8ba7848d50470a7a32fb"}, {file = "wrapt-1.14.1.tar.gz", hash = "sha256:380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d"}, ] -wtforms = [] +wtforms = [ + {file = "WTForms-3.0.1-py3-none-any.whl", hash = "sha256:837f2f0e0ca79481b92884962b914eba4e72b7a2daaf1f939c890ed0124b834b"}, + {file = "WTForms-3.0.1.tar.gz", hash = "sha256:6b351bbb12dd58af57ffef05bc78425d08d1914e0fd68ee14143b7ade023c5bc"}, +] yarl = [ {file = "yarl-1.7.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f2a8508f7350512434e41065684076f640ecce176d262a7d54f0da41d99c5a95"}, {file = "yarl-1.7.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:da6df107b9ccfe52d3a48165e48d72db0eca3e3029b5b8cb4fe6ee3cb870ba8b"}, @@ -3996,7 +4141,4 @@ yarl = [ {file = "yarl-1.7.2-cp39-cp39-win_amd64.whl", hash = "sha256:797c2c412b04403d2da075fb93c123df35239cd7b4cc4e0cd9e5839b73f52c58"}, {file = "yarl-1.7.2.tar.gz", hash = "sha256:45399b46d60c253327a460e99856752009fcee5f5d3c80b2f7c0cae1c38d56dd"}, ] -zipp = [ - {file = "zipp-3.8.0-py3-none-any.whl", hash = "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"}, - {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"}, -] +zipp = [] diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 66777a558..350cee773 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -2213,7 +2213,7 @@ def set_apikey(endpoint, keyval): Sets an API key Example: - oak set-apikey -e bioportal MY-KEY-VALUE + runoak set-apikey -e bioportal MY-KEY-VALUE This is stored in an OS-dependent path """ diff --git a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py index 554617a0b..2359f0e71 100644 --- a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py +++ b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py @@ -18,7 +18,6 @@ ) from oaklib.interfaces.basic_ontology_interface import METADATA_MAP, PREFIX_MAP from oaklib.types import CURIE, URI -from oaklib.utilities.apikey_manager import get_apikey_value from oaklib.utilities.rate_limiter import check_limit SEARCH_CONFIG = SearchConfiguration() @@ -51,8 +50,7 @@ def __post_init__(self): self.focus_ontology = self.resource.slug if not self.ontoportal_client_class: raise NotImplementedError("ontoportal_client_class not specified") - api_key = get_apikey_value(self.ontoportal_client_class.name) - self.client = self.ontoportal_client_class(api_key=api_key) + self.client = self.ontoportal_client_class() def prefix_map(self) -> PREFIX_MAP: # TODO diff --git a/src/oaklib/utilities/apikey_manager.py b/src/oaklib/utilities/apikey_manager.py index 64e75c73e..1727e3a31 100644 --- a/src/oaklib/utilities/apikey_manager.py +++ b/src/oaklib/utilities/apikey_manager.py @@ -1,54 +1,42 @@ """ -Functions for managing and accessing API keys - -See ``_ +Functions for managing and accessing API keys via :mod:`pystow`. """ -import logging -from pathlib import Path - -from appdirs import user_config_dir +import pystow -from oaklib.datamodels.vocabulary import APP_NAME +__all__ = [ + "get_apikey_value", + "set_apikey_value", +] -APIKEY_SUFFIX = "apikey.txt" +APP_NAME = "oaklib" -def get_apikey_path(system: str) -> Path: +def get_apikey_value(key: str, raise_on_missing: bool = False) -> str: """ - Gets the path to where the API key is stored + Get the value of the given configuration key. - :param system: e.g "bioportal" - :return: - """ - p = Path(user_config_dir(APP_NAME)) / f"{system}-{APIKEY_SUFFIX}" - logging.info(f"API KEY path = {p}") - return p + :param key: e.g "bioportal" for the BioPortal API token + :param raise_on_missing: If true, will raise a value error if no data is found and no default + is given + :return: The API key associated with the system + Configuration can be set in the following ways: -def get_apikey_value(system: str) -> str: - """ - Gets the value of a specific API key - - :param system: e.g "bioportal" - :return: + 1. Set `OAKLIB_{key}` in the environment + 2. Create a configuration file `~/.config/oaklib.ini` + and set the `[oaklib]` section in it with the given key + 3. Use the :func:`set_apikey_value` function to directly + create a configuration file """ - path = get_apikey_path(system) - if not path.exists(): - raise ValueError(f"No API key found in: {path}") - with open(path) as stream: - return stream.readlines()[0].strip() + return pystow.get_config(APP_NAME, key, raise_on_missing=raise_on_missing) -def set_apikey_value(system: str, val: str) -> None: +def set_apikey_value(key: str, value: str) -> None: """ - Sets the value for a specific API key + Set the value for a given configuration key. - :param system: e.g. "bioportal" - :param val: API key value - :return: + :param key: e.g. "bioportal" + :param value: API key value """ - dir = Path(user_config_dir(APP_NAME)) - dir.mkdir(exist_ok=True, parents=True) - with open(get_apikey_path(system), "w", encoding="utf-8") as stream: - stream.write(val) + pystow.write_config(APP_NAME, key, value)