From 3093da6c0bf6e3d9574fad04c4f5d1d3449db286 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 24 Jun 2022 11:06:47 +0200 Subject: [PATCH 01/12] Update apikey_manager.py --- src/oaklib/utilities/apikey_manager.py | 38 ++++++-------------------- 1 file changed, 8 insertions(+), 30 deletions(-) diff --git a/src/oaklib/utilities/apikey_manager.py b/src/oaklib/utilities/apikey_manager.py index 64e75c73e..68975e423 100644 --- a/src/oaklib/utilities/apikey_manager.py +++ b/src/oaklib/utilities/apikey_manager.py @@ -1,30 +1,15 @@ """ -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 -APIKEY_SUFFIX = "apikey.txt" - - -def get_apikey_path(system: str) -> Path: - """ - Gets the path to where the API key is stored - - :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 - +__all__ = [ + "get_apikey_value", + "set_apikey_value", +] def get_apikey_value(system: str) -> str: """ @@ -33,11 +18,7 @@ def get_apikey_value(system: str) -> str: :param system: e.g "bioportal" :return: """ - 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, system) def set_apikey_value(system: str, val: str) -> None: @@ -48,7 +29,4 @@ def set_apikey_value(system: str, val: str) -> None: :param val: API key value :return: """ - 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, system, val) From 4172dfc2b81b98d000d3e96373248eefea2e54b1 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 24 Jun 2022 11:08:58 +0200 Subject: [PATCH 02/12] Update apikey_manager.py --- src/oaklib/utilities/apikey_manager.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/oaklib/utilities/apikey_manager.py b/src/oaklib/utilities/apikey_manager.py index 68975e423..b0a795c50 100644 --- a/src/oaklib/utilities/apikey_manager.py +++ b/src/oaklib/utilities/apikey_manager.py @@ -11,6 +11,7 @@ "set_apikey_value", ] + def get_apikey_value(system: str) -> str: """ Gets the value of a specific API key From 25f71a12178de91e7b1eec664c72358500befcee Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 24 Jun 2022 11:15:13 +0200 Subject: [PATCH 03/12] Cleanup and add docs --- poetry.lock | 2 +- pyproject.toml | 1 + src/oaklib/cli.py | 2 +- src/oaklib/utilities/apikey_manager.py | 33 ++++++++++++++++---------- 4 files changed, 23 insertions(+), 15 deletions(-) diff --git a/poetry.lock b/poetry.lock index ad0281537..e6ee2bd83 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2480,7 +2480,7 @@ docs = [] [metadata] lock-version = "1.1" python-versions = "^3.9" -content-hash = "70eeeb0764abcca9ca98b32c4247552eda86cfde8664f128c1befd8528da6413" +content-hash = "5744727a2d5f04691deb2efeba7afa9f1505095844f12967be8aa90ddc99b683" [metadata.files] aiohttp = [ diff --git a/pyproject.toml b/pyproject.toml index ebea6ba9a..a10652c7d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ lark = "^1.1.2" kgcl = "^0.1.0" kgcl-schema = "^0.1.1" funowl = "^0.1.12" +pystow = "^0.4.4" [tool.poetry.dev-dependencies] pytest = "^5.2" diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 4cedb68d7..036605a38 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -1876,7 +1876,7 @@ 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/utilities/apikey_manager.py b/src/oaklib/utilities/apikey_manager.py index b0a795c50..3e395bbc0 100644 --- a/src/oaklib/utilities/apikey_manager.py +++ b/src/oaklib/utilities/apikey_manager.py @@ -4,30 +4,37 @@ import pystow -from oaklib.datamodels.vocabulary import APP_NAME - __all__ = [ "get_apikey_value", "set_apikey_value", ] +APP_NAME = "oak" + -def get_apikey_value(system: str) -> str: +def get_apikey_value(key: str) -> str: """ - Gets the value of a specific API key + Get the value of the given configuration key. + + :param key: e.g "bioportal" for the BioPortal API token + :return: The API key associated with the system + + Configuration can be set in the following ways: - :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 """ - return pystow.get_config(APP_NAME, system) + return pystow.get_config(APP_NAME, key) -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 """ - pystow.write_config(APP_NAME, system, val) + pystow.write_config(APP_NAME, key, value) From d213ebec1aa53abe771655191b7203b1d44d98ea Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 24 Jun 2022 11:17:54 +0200 Subject: [PATCH 04/12] Documentation --- README.md | 12 ++++++++++++ src/oaklib/utilities/apikey_manager.py | 2 +- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5d1473c60..15ace9771 100644 --- a/README.md +++ b/README.md @@ -215,6 +215,18 @@ Same using pronto, fetching ontology from obolibrary 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. + ## Potential Refactoring Currently all implementations exist in this repo/module, this results in a lot of dependencies diff --git a/src/oaklib/utilities/apikey_manager.py b/src/oaklib/utilities/apikey_manager.py index 3e395bbc0..b278df066 100644 --- a/src/oaklib/utilities/apikey_manager.py +++ b/src/oaklib/utilities/apikey_manager.py @@ -9,7 +9,7 @@ "set_apikey_value", ] -APP_NAME = "oak" +APP_NAME = "oaklib" def get_apikey_value(key: str) -> str: From 338a2804ac4e908707c370e73e9f0c36e2b08414 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 6 Jul 2022 16:45:03 -0400 Subject: [PATCH 05/12] Update poetry.lock --- poetry.lock | 134 ++++++++++++++++++++-------------------------------- 1 file changed, 52 insertions(+), 82 deletions(-) diff --git a/poetry.lock b/poetry.lock index d3dde7a9c..609630cf1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -188,7 +188,7 @@ lxml = ["lxml"] [[package]] name = "bioregistry" -version = "0.5.33" +version = "0.5.35" description = "Integrated registry of biological databases and nomenclatures" category = "main" optional = false @@ -320,7 +320,7 @@ toml = ["tomli"] [[package]] name = "cryptography" -version = "37.0.3" +version = "37.0.4" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." category = "main" optional = false @@ -537,7 +537,7 @@ python-versions = ">=3.5" [[package]] name = "imagesize" -version = "1.3.0" +version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" category = "main" optional = false @@ -1130,7 +1130,7 @@ testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest [[package]] name = "nbclient" -version = "0.6.5" +version = "0.6.6" description = "A client library for executing notebooks. 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optional = false @@ -375,6 +443,14 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +[[package]] +name = "dominate" +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 +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + [[package]] name = "entrypoints" version = "0.4" @@ -387,13 +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 @@ -401,7 +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 @@ -412,12 +488,81 @@ devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benc [[package]] name = "fastobo" -version = "0.11.1" +version = "0.12.1" description = "Faultless AST for Open Biomedical Ontologies in Python." category = "main" optional = false +python-versions = ">=3.7" + +[[package]] +name = "flask" +version = "2.1.3" +description = "A simple framework for building complex web applications." +category = "main" +optional = true +python-versions = ">=3.7" + +[package.dependencies] +click = ">=8.0" +importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""} +itsdangerous = ">=2.0" +Jinja2 = ">=3.0" +Werkzeug = ">=2.0" + +[package.extras] +async = ["asgiref (>=3.2)"] +dotenv = ["python-dotenv"] + +[[package]] +name = "flask-bootstrap" +version = "3.3.7.1" +description = "An extension that includes Bootstrap in your project, without any boilerplate code." +category = "main" +optional = true +python-versions = "*" + +[package.dependencies] +dominate = "*" +Flask = ">=0.8" +visitor = "*" + +[[package]] +name = "flask-restx" +version = "0.5.1" +description = "Fully featured framework for fast, easy and documented API development with Flask" +category = "main" +optional = true +python-versions = "*" + +[package.dependencies] +aniso8601 = {version = ">=0.82", markers = "python_version >= \"3.5\""} +Flask = ">=0.8,<2.0.0 || >2.0.0" +jsonschema = "*" +pytz = "*" +six = ">=1.3.0" +werkzeug = "!=2.0.0" + +[package.extras] +dev = ["blinker", "Faker (==2.0.0)", "mock (==3.0.5)", "pytest-benchmark (==3.2.2)", "pytest-cov (==2.7.1)", "pytest-flask (==0.15.1)", "pytest-mock (==1.10.4)", "pytest-profiling (==1.7.0)", "tzlocal", "invoke (==1.3.0)", "readme-renderer (==24.0)", "twine (==1.15.0)", "tox", "pytest (==4.6.5)", "pytest (==5.4.1)", "ossaudit", "black"] +doc = ["alabaster (==0.7.12)", "Sphinx (==2.1.2)", "sphinx-issues (==1.2.0)"] +test = ["blinker", "Faker (==2.0.0)", "mock (==3.0.5)", "pytest-benchmark (==3.2.2)", "pytest-cov (==2.7.1)", "pytest-flask (==0.15.1)", "pytest-mock (==1.10.4)", "pytest-profiling (==1.7.0)", "tzlocal", "invoke (==1.3.0)", "readme-renderer (==24.0)", "twine (==1.15.0)", "pytest (==4.6.5)", "pytest (==5.4.1)", "ossaudit"] + +[[package]] +name = "flask-wtf" +version = "1.0.1" +description = "Form rendering, validation, and CSRF protection for Flask with WTForms." +category = "main" +optional = true python-versions = ">=3.6" +[package.dependencies] +Flask = "*" +itsdangerous = "*" +WTForms = "*" + +[package.extras] +email = ["email-validator"] + [[package]] name = "frozenlist" version = "1.3.0" @@ -476,17 +621,43 @@ rdflib = ">=5.0.0" rdflib-shim = "*" rfc3987 = "*" +[[package]] +name = "gilda" +version = "0.10.3" +description = "Grounding for biomedical entities with contextual disambiguation" +category = "main" +optional = true +python-versions = "*" + +[package.dependencies] +adeft = ">=0.11.0" +boto3 = "*" +flask = "*" +flask-bootstrap = "*" +flask-restx = "*" +flask-wtf = "*" +obonet = "*" +pystow = ">=0.1.10" +regex = "*" +unidecode = "*" + +[package.extras] +benchmarks = ["pandas (>=1.0)", "requests", "tabulate", "tqdm", "click"] +docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-rtd-theme"] +terms = ["indra"] +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]] @@ -542,7 +713,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest- [[package]] name = "ipykernel" -version = "6.15.0" +version = "6.15.1" description = "IPython Kernel for Jupyter" category = "dev" optional = false @@ -637,6 +808,14 @@ python-versions = "*" [package.dependencies] six = "*" +[[package]] +name = "itsdangerous" +version = "2.1.2" +description = "Safely pass data to untrusted environments and back." +category = "main" +optional = true +python-versions = ">=3.7" + [[package]] name = "jedi" version = "0.18.1" @@ -666,12 +845,20 @@ MarkupSafe = ">=2.0" [package.extras] i18n = ["Babel (>=2.7)"] +[[package]] +name = "jmespath" +version = "1.0.1" +description = "JSON Matching Expressions" +category = "main" +optional = true +python-versions = ">=3.7" + [[package]] name = "joblib" version = "1.1.0" description = "Lightweight pipelining with Python functions" category = "main" -optional = false +optional = true python-versions = ">=3.6" [[package]] @@ -712,7 +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.*" @@ -723,7 +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 = "*" @@ -736,13 +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 = "4.6.1" +version = "4.7.2" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -813,7 +1000,7 @@ test = ["pexpect"] [[package]] name = "jupyter-core" -version = "4.10.0" +version = "4.11.1" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "dev" optional = false @@ -882,9 +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" @@ -899,7 +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 = "*" @@ -917,13 +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" @@ -936,7 +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 @@ -949,7 +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 = "*" @@ -958,7 +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" @@ -998,7 +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" @@ -1014,7 +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" @@ -1057,7 +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" @@ -1154,7 +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 @@ -1167,6 +1354,28 @@ doc = ["sphinx (>=5)", "pydata-sphinx-theme (>=0.9)", "sphinx-gallery (>=0.10)", extra = ["lxml (>=4.6)", "pygraphviz (>=1.9)", "pydot (>=1.4.2)", "sympy (>=1.10)"] test = ["pytest (>=7.1)", "pytest-cov (>=3.0)", "codecov (>=2.1)"] +[[package]] +name = "nltk" +version = "3.7" +description = "Natural Language Toolkit" +category = "main" +optional = true +python-versions = ">=3.7" + +[package.dependencies] +click = "*" +joblib = "*" +regex = ">=2021.8.3" +tqdm = "*" + +[package.extras] +all = ["numpy", "pyparsing", "scipy", "matplotlib", "twython", "requests", "scikit-learn", "python-crfsuite"] +corenlp = ["requests"] +machine_learning = ["numpy", "python-crfsuite", "scikit-learn", "scipy"] +plot = ["matplotlib"] +tgrep = ["pyparsing"] +twitter = ["twython"] + [[package]] name = "notebook" version = "6.4.12" @@ -1199,7 +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 @@ -1222,11 +1431,41 @@ pronto = ">=2.4.0" dev = ["fire", "pandas", "pre-commit", "pytest"] viz = ["pygraphviz"] +[[package]] +name = "obonet" +version = "0.3.0" +description = "Parse OBO formatted ontologies into networkx" +category = "main" +optional = true +python-versions = ">=3.5" + +[package.dependencies] +networkx = "*" + +[package.extras] +dev = ["pre-commit", "pytest"] + +[[package]] +name = "ontoportal-client" +version = "0.0.3" +description = "A client to BioPortal and other OntoPortal instances." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +pystow = "*" +typing-extensions = "*" + +[package.extras] +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" @@ -1290,7 +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 = "*" @@ -1340,24 +1579,20 @@ dev = ["pre-commit", "tox"] name = "ply" version = "3.11" description = "Python Lex & Yacc" -category = "dev" +category = "main" optional = false python-versions = "*" [[package]] name = "prefixcommons" -version = "0.1.9" -description = "Library for working prefixcommons.org CURIEs" +version = "0.1.11" +description = "A python API for working with ID prefixes" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7,<4.0" [package.dependencies] -pyyaml = "*" -requests = "*" - -[package.extras] -test = ["pytest"] +requests = ">=2.28.1,<3.0.0" [[package]] name = "prometheus-client" @@ -1383,15 +1618,15 @@ wcwidth = "*" [[package]] name = "pronto" -version = "2.4.7" +version = "2.5.0" description = "Python frontend to ontologies." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] chardet = ">=3.0,<5.0" -fastobo = ">=0.11.1,<0.12.0" +fastobo = ">=0.12.1,<0.13.0" networkx = ">=2.3,<3.0" python-dateutil = ">=2.8,<3.0" @@ -1496,7 +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" @@ -1515,7 +1750,7 @@ urllib3 = "*" name = "pyshexc" version = "0.9.1" description = "PyShExC - Python ShEx compiler" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1710,17 +1945,12 @@ rdflib = ">=5.0.0" rdflib-jsonld = "0.6.1" [[package]] -name = "recommonmark" -version = "0.7.1" -description = "A docutils-compatibility bridge to CommonMark, enabling you to write CommonMark inside of Docutils & Sphinx projects." +name = "regex" +version = "2022.7.25" +description = "Alternative regular expression module, to replace re." category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -commonmark = ">=0.8.1" -docutils = ">=0.11" -sphinx = ">=1.3.1" +optional = true +python-versions = ">=3.6" [[package]] name = "requests" @@ -1752,7 +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" @@ -1767,16 +1997,30 @@ 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" +[[package]] +name = "s3transfer" +version = "0.6.0" +description = "An Amazon S3 Transfer Manager" +category = "main" +optional = true +python-versions = ">= 3.7" + +[package.dependencies] +botocore = ">=1.12.36,<2.0a.0" + +[package.extras] +crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"] + [[package]] name = "scikit-learn" version = "1.1.1" description = "A set of python modules for machine learning and data mining" category = "main" -optional = false +optional = true python-versions = ">=3.8" [package.dependencies] @@ -1832,7 +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 = "*" @@ -1867,7 +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" @@ -1929,7 +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" @@ -2066,15 +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)"] @@ -2085,14 +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 = "0.3.11" +version = "0.3.13" description = "Operations on SSSOM mapping tables" category = "main" optional = false @@ -2102,7 +2345,7 @@ python-versions = ">=3.7" bioregistry = "*" click = "*" deprecation = "*" -linkml-runtime = ">=1.1.12" +linkml = "*" networkx = "*" numpy = "*" pandas = "*" @@ -2110,19 +2353,29 @@ pandasql = "*" pyparsing = "2.4.7" pyyaml = "*" rdflib = ">=6" -recommonmark = ">=0.7" -scikit_learn = "*" scipy = "*" sparqlwrapper = "*" +sssom-schema = "*" validators = [ "*", ">=0.0", ] [package.extras] -docs = ["sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints", "sphinx-click"] +docs = ["sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints", "sphinx-click", "recommonmark"] test = ["pytest"] +[[package]] +name = "sssom-schema" +version = "0.9.4" +description = "SSSOM is a Simple Standard for Sharing Ontology Mappings." +category = "main" +optional = false +python-versions = ">=3.7.6,<4.0.0" + +[package.dependencies] +linkml-runtime = ">=1.1.24,<2.0.0" + [[package]] name = "stack-data" version = "0.3.0" @@ -2160,7 +2413,7 @@ name = "threadpoolctl" version = "3.1.0" description = "threadpoolctl" category = "main" -optional = false +optional = true python-versions = ">=3.6" [[package]] @@ -2222,13 +2475,21 @@ category = "main" optional = false python-versions = ">=3.7" +[[package]] +name = "unidecode" +version = "1.3.4" +description = "ASCII transliterations of Unicode text" +category = "main" +optional = true +python-versions = ">=3.5" + [[package]] name = "urllib3" -version = "1.26.9" +version = "1.26.11" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4" [package.extras] brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"] @@ -2249,11 +2510,19 @@ decorator = ">=3.4.0" [package.extras] test = ["pytest (>=2.2.3)", "flake8 (>=2.4.0)", "isort (>=4.2.2)"] +[[package]] +name = "visitor" +version = "0.1.3" +description = "A tiny pythonic visitor implementation." +category = "main" +optional = true +python-versions = "*" + [[package]] name = "watchdog" version = "2.1.9" 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"sha256:24148ce4e64100a2d5e267233e23e7afeb55316b47d30faae7eb6e7292bc226a"}, ] +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"}, @@ -3799,6 +3992,7 @@ webencodings = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, ] +werkzeug = [] widgetsnbextension = [ {file = "widgetsnbextension-3.6.1-py2.py3-none-any.whl", hash = "sha256:954e0faefdd414e4e013f17dbc7fd86f24cf1d243a3ac85d5f0fc2c2d2b50c66"}, {file = 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"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 = [] From 4ca44f9032796d2a484b6d5c79e55d7755a716d7 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 25 Jul 2022 16:31:43 -0400 Subject: [PATCH 08/12] Update apikey_manager.py --- src/oaklib/utilities/apikey_manager.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/oaklib/utilities/apikey_manager.py b/src/oaklib/utilities/apikey_manager.py index b278df066..1727e3a31 100644 --- a/src/oaklib/utilities/apikey_manager.py +++ b/src/oaklib/utilities/apikey_manager.py @@ -12,11 +12,13 @@ APP_NAME = "oaklib" -def get_apikey_value(key: str) -> str: +def get_apikey_value(key: str, raise_on_missing: bool = False) -> str: """ Get the value of the given configuration key. :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: @@ -27,7 +29,7 @@ def get_apikey_value(key: str) -> str: 3. Use the :func:`set_apikey_value` function to directly create a configuration file """ - return pystow.get_config(APP_NAME, key) + return pystow.get_config(APP_NAME, key, raise_on_missing=raise_on_missing) def set_apikey_value(key: str, value: str) -> None: From b94de6d3da0b20315eb71345696af5d317aa1b87 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 25 Jul 2022 16:33:19 -0400 Subject: [PATCH 09/12] Update ontoportal_implementation_base.py --- .../ontoportal/ontoportal_implementation_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py index 554617a0b..cabf77eda 100644 --- a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py +++ b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py @@ -51,7 +51,7 @@ 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) + api_key = get_apikey_value(self.ontoportal_client_class.name, raise_on_missing=True) self.client = self.ontoportal_client_class(api_key=api_key) def prefix_map(self) -> PREFIX_MAP: From b6ae167e650d104a9c19b0ba1738d655fa0f66d6 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 25 Jul 2022 16:40:55 -0400 Subject: [PATCH 10/12] Pass through bioportal config --- .github/workflows/main.yaml | 4 ++++ 1 file changed, 4 insertions(+) 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 From 5d1465c8378ff684d554b7ab7d9c21a20f59b3a7 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 25 Jul 2022 16:49:29 -0400 Subject: [PATCH 11/12] Update ontoportal_implementation_base.py --- .../ontoportal/ontoportal_implementation_base.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py index cabf77eda..3811c01a3 100644 --- a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py +++ b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py @@ -51,8 +51,7 @@ 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, raise_on_missing=True) - self.client = self.ontoportal_client_class(api_key=api_key) + self.client = self.ontoportal_client_class() def prefix_map(self) -> PREFIX_MAP: # TODO From addd7f2505e21dd249d5ad732082037b5c7e37d0 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 25 Jul 2022 17:03:28 -0400 Subject: [PATCH 12/12] Update ontoportal_implementation_base.py --- .../implementations/ontoportal/ontoportal_implementation_base.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py b/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py index 3811c01a3..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()