bioversions 0.5.552__py3-none-any.whl → 0.5.553__py3-none-any.whl

bioversions/sources/ncit.py

@@ -1,9 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """A getter for the NCI Thesaurus."""
 
 import re
-from typing import Dict
 
 from ..utils import Getter, VersionType, get_soup
 
@@ -25,7 +22,7 @@ class NCItGetter(Getter):
     date_fmt = "%Y-%m-%d"
     version_type = VersionType.other
 
-    def get(self) -> Dict[str, str]:
+    def get(self) -> dict[str, str]:
         """Get the latest NCIt version number."""
         soup = get_soup(URL)
         version_str = soup.find("span", {"class": "vocabularynamelong_ncit"}).contents[0]

bioversions/sources/npass.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for NPASS."""
 
 from bioversions.utils import Getter, VersionType, get_soup

bioversions/sources/obo.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """Getters for OBO ontologies."""
 
-from typing import Iterable, Type
+from collections.abc import Iterable
 
 from bioversions.utils import Getter, OBOFoundryGetter, VersionType
 
@@ -56,7 +54,7 @@ class PrGetter(OBOFoundryGetter):
     homepage_fmt = "https://proconsortium.org/download/release_{version}/"
 
 
-def iter_obo_getters() -> Iterable[Type[Getter]]:
+def iter_obo_getters() -> Iterable[type[Getter]]:
     """Iterate over OBO getters."""
     yield from OBOFoundryGetter.__subclasses__()
 

bioversions/sources/ols.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 """Get versions from the OLS."""
 
 import logging
-from typing import Iterable, List, Mapping, Optional, Type, Union
+from collections.abc import Iterable, Mapping
 
 import bioregistry
 from bioregistry.external.ols import get_ols_processing
@@ -16,7 +14,7 @@ logger = logging.getLogger(__name__)
 ols_processing = get_ols_processing()
 
 
-def _get_version_type(bioregistry_id: str) -> Optional[VersionType]:
+def _get_version_type(bioregistry_id: str) -> VersionType | None:
     ols_id = bioregistry.get_ols_prefix(bioregistry_id)
     ols_config = ols_processing.get(ols_id)
     if ols_config is None:
@@ -33,7 +31,7 @@ def _get_version_type(bioregistry_id: str) -> Optional[VersionType]:
         return None
 
 
-def make_ols_getter(bioregistry_id: str) -> Optional[Type[Getter]]:
+def make_ols_getter(bioregistry_id: str) -> type[Getter] | None:
     """Make a getter from OLS."""
     ols_id = bioregistry.get_ols_prefix(bioregistry_id)
     if ols_id is None:
@@ -66,14 +64,14 @@ def make_ols_getter(bioregistry_id: str) -> Optional[Type[Getter]]:
         name = _name
         version_type = _version_type  # type:ignore
 
-        def get(self) -> Union[str, Mapping[str, str]]:
+        def get(self) -> str | Mapping[str, str]:
             """Get the version from the Bioregistry."""
             return version
 
     return OlsGetter
 
 
-def iter_ols_getters() -> Iterable[Type[Getter]]:
+def iter_ols_getters() -> Iterable[type[Getter]]:
     """Iterate over OLS getters."""
     for bioregistry_id in bioregistry.read_registry():
         yv = make_ols_getter(bioregistry_id)
@@ -81,7 +79,7 @@ def iter_ols_getters() -> Iterable[Type[Getter]]:
             yield yv
 
 
-def extend_ols_getters(getters: List[Type[Getter]]) -> None:
+def extend_ols_getters(getters: list[type[Getter]]) -> None:
     """Extend the getters, without adding duplicates."""
     for ols_getter in iter_ols_getters():
         if any(getter.bioregistry_id == ols_getter.bioregistry_id for getter in getters):

bioversions/sources/omim.py

@@ -1,7 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """A getter for the OMIM."""
 
+from typing import ClassVar
 
 from bioversions.utils import Getter, VersionType, get_soup
 
@@ -16,7 +15,7 @@ class OMIMGetter(Getter):
     name = "Online Mendelian Inheritance in Man"
     date_version_fmt = "%B %d, %Y"
     version_type = VersionType.date
-    collection = ["omim.ps", "omim"]
+    collection: ClassVar[list[str]] = ["omim.ps", "omim"]
 
     def get(self) -> str:
         """Get the latest OMIM version number."""

bioversions/sources/oncotree.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for OncoTree."""
 
 import requests
@@ -22,10 +20,12 @@ class OncoTreeGetter(Getter):
 
     def get(self) -> str:
         """Get the latest OncoTree version number."""
-        res = requests.get("http://oncotree.mskcc.org/api/versions", params={"format": "json"})
+        res = requests.get(
+            "http://oncotree.mskcc.org/api/versions", params={"format": "json"}, timeout=5
+        )
         res_json = res.json()
         version = next(
-            (r["release_date"] for r in res_json if r["api_identifier"] == "oncotree_latest_stable")
+            r["release_date"] for r in res_json if r["api_identifier"] == "oncotree_latest_stable"
         )
         return version
 

bioversions/sources/pathbank.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for PathBank."""
 
 from bioversions.utils import Getter, VersionType, get_soup

bioversions/sources/pathwaycommons.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for Pathway Commons."""
 
 from bioversions.utils import Getter, VersionType, get_soup

bioversions/sources/pfam.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for Rfam."""
 
 import ftplib

bioversions/sources/pombase.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for PomBase."""
 
 from bioversions.utils import Getter, VersionType, get_soup

bioversions/sources/pr.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for the Protein Ontology."""
 
 from bioversions.utils import Getter, VersionType, get_soup
@@ -26,7 +24,7 @@ class PRGetter(Getter):
         rows = soup.find("table", **{"class": "nrm11"}).find_all("tr")
         row = list(rows)[2]
         version_cell, date_cell, *_ = list(row.find_all("td"))
-        return dict(version=version_cell.text.strip(), date=date_cell.text.strip())
+        return {"version": version_cell.text.strip(), "date": date_cell.text.strip()}
 
 
 if __name__ == "__main__":

bioversions/sources/pubchem.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for PubChem."""
 
 import datetime

bioversions/sources/reactome.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for Reactome."""
 
 from ..utils import Getter, VersionType, get_soup

bioversions/sources/rfam.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for Rfam."""
 
 from bioversions.utils import Getter, VersionType, _get_ftp_version

bioversions/sources/rgd.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for RGD."""
 
 import requests

bioversions/sources/rhea.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for Rhea."""
 
 import requests

bioversions/sources/rxnorm.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for RxNorm."""
 
 from datetime import datetime

bioversions/sources/sgd.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for SGD."""
 
 import requests

bioversions/sources/slm.py

@@ -23,7 +23,7 @@ class SwissLipidGetter(Getter):
 
     def get(self):
         """Get the latest SwissLipids version number."""
-        res = requests.get(URL).json()
+        res = requests.get(URL, timeout=15).json()
         record = next(record for record in res if record["file"] == "lipids.tsv")
         return datetime.datetime.strptime(record["date"], "%B %d %Y")
 

bioversions/sources/stringdb.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for StringDB."""
 
 from bioversions.utils import Getter, VersionType, get_soup
@@ -21,9 +19,9 @@ class StringDBGetter(Getter):
         soup = get_soup("https://string-db.org/cgi/access")
         table = soup.find(**{"class": "footer_access_archive_table"})
         rows = table.find_all(**{"class": "row"})
-        version, date, link, _summary = [row.text for row in rows[1].find_all(**{"class": "cell"})]
+        version, date, link, _summary = (row.text for row in rows[1].find_all(**{"class": "cell"}))
         date = date[len("current: since ") :]
-        return dict(version=version, date=date)
+        return {"version": version, "date": date}
 
 
 if __name__ == "__main__":

bioversions/sources/umls.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for UMLS."""
 
 from datetime import datetime

bioversions/sources/uniprot.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """A getter for UniProt."""
 
-from xml.etree import ElementTree  # noqa:S405
+from xml.etree import ElementTree
 
 import requests
 

bioversions/sources/unversioned.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A collection of unversioned resources."""
 
 # TODO

bioversions/sources/wikipathways.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for WikiPathways."""
 
 from bioversions.utils import Getter, VersionType, get_soup

bioversions/sources/zfin.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """A getter for ZFIN."""
 
 from datetime import datetime

bioversions/templates/base.html

@@ -0,0 +1,28 @@
+<!doctype html>
+<html lang="en">
+<head>
+    {% block head %}
+        <!-- Required meta tags -->
+        <meta charset="utf-8">
+        <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+
+        {% block styles %}
+            <!-- Bootstrap CSS -->
+            {{ bootstrap.load_css() }}
+        {% endblock %}
+
+        <script src="https://kit.fontawesome.com/4c86883252.js" crossorigin="anonymous"></script>
+
+        <title>{% block title %}{% endblock %}</title>
+    {% endblock %}
+</head>
+<body>
+<!-- Your page content -->
+{% block content %}{% endblock %}
+
+{% block scripts %}
+    <!-- Optional JavaScript -->
+    {{ bootstrap.load_js() }}
+{% endblock %}
+</body>
+</html>

bioversions/templates/home.html

@@ -0,0 +1,60 @@
+{% extends "base.html" %}
+
+{% block title %}Bioversions{% endblock %}
+
+{% block content %}
+    <div class="container" style="margin-top: 50px; margin-bottom: 50px">
+        <div class="row justify-content-center">
+            <div class="card">
+                <h5 class="card-header text-center">Biological Database Latest Versions</h5>
+                <div class="card-body">
+                    <p>
+                        This web application lists the latest versions for biological databases.
+                        It refreshes once per day.
+                    </p>
+                </div>
+                <table class="table table-striped table-hover">
+                    <thead>
+                    <tr>
+                        <th>Name</th>
+                        <th>Version</th>
+                        <th>Date</th>
+                        <th class="text-center">JSON</th>
+                    </tr>
+                    </thead>
+                    <tbody>
+                    {% for row in rows %}
+                        <tr>
+                            <td>{{ row.name }}</td>
+                            <td>
+                                {% if row.homepage %}
+                                    <a href="{{ row.homepage }}">{{ row.version }} <i class="fas fa-link"></i></a>
+                                {% else %}
+                                    {{ row.version }}
+                                {% endif %}
+                            </td>
+                            <td>
+                                {% if row.date %}{{ row.date }}{% endif %}
+                            </td>
+                            <td class="text-center">
+                                <a href="{{ url_for('database', name=row.name.lower().replace(" ", "")) }}">
+                                    <i class="fas fa-download"></i>
+                                </a>
+                            </td>
+                        </tr>
+                    {% endfor %}
+                    </tbody>
+                </table>
+                <div class="card-footer">
+                    <p style="text-align: center">
+                        Developed with ❤️ by the <a href="https://indralab.github.io">INDRA Lab</a> in the
+                        <a href="https://hits.harvard.edu">Harvard Program in Therapeutic Science (HiTS)</a>.<br/>
+                        Funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).<br/>
+                        Point of contact: <a href="https://github.com/cthoyt">@cthoyt</a>.
+                        (<a href="https://github.com/biopragmatics/bioversions">Source code</a>)
+                    </p>
+                </div>
+            </div>
+        </div>
+    </div>
+{% endblock %}

bioversions/twitter_client.py

@@ -1,9 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """Utilities for interacting with Twitter."""
 
 from functools import lru_cache
-from typing import Optional
 
 import pystow
 import tweepy
@@ -11,11 +8,11 @@ import tweepy
 
 @lru_cache(maxsize=1)
 def _get_api(
-    consumer_key: Optional[str] = None,
-    consumer_secret: Optional[str] = None,
-    access_token: Optional[str] = None,
-    access_token_secret: Optional[str] = None,
-) -> Optional[tweepy.API]:
+    consumer_key: str | None = None,
+    consumer_secret: str | None = None,
+    access_token: str | None = None,
+    access_token_secret: str | None = None,
+) -> tweepy.API | None:
     consumer_key = pystow.get_config("bioversions", "consumer_key", passthrough=consumer_key)
     consumer_secret = pystow.get_config(
         "bioversions", "consumer_secret", passthrough=consumer_secret

bioversions/utils.py

@@ -1,12 +1,11 @@
-# -*- coding: utf-8 -*-
-
 """Utilities and implementation for bioversions."""
 
 import datetime
 import enum
 import ftplib
 import os
-from typing import Any, ClassVar, List, Mapping, Optional, Union
+from collections.abc import Mapping
+from typing import Any, ClassVar
 
 import bioregistry
 import pydantic
@@ -48,7 +47,7 @@ def norm(s: str) -> str:
 
 
 def get_soup(
-    url: str, verify: bool = True, timeout: Optional[int] = None, user_agent: Optional[str] = None
+    url: str, verify: bool = True, timeout: int | None = None, user_agent: str | None = None
 ) -> BeautifulSoup:
     """Get a beautiful soup parsed version of the given web page.
 
@@ -82,9 +81,9 @@ class MetaGetter(type):
 
     _cache = None
 
-    date_fmt: Optional[str]
-    date_version_fmt: Optional[str]
-    homepage_fmt: Optional[str]
+    date_fmt: str | None
+    date_version_fmt: str | None
+    homepage_fmt: str | None
 
     @property
     def _cache_prop(cls):
@@ -105,7 +104,7 @@ class MetaGetter(type):
             raise TypeError(f"_cache_prop was a {type(cls._cache_prop)}")
 
     @property
-    def date(cls) -> Optional[datetime.date]:
+    def date(cls) -> datetime.date | None:
         """Get the date if it's set."""
         vp = cls.version_date_parsed
         if vp is not None:
@@ -122,10 +121,12 @@ class MetaGetter(type):
         try:
             return datetime.datetime.strptime(date, cls.date_fmt).date()
         except ValueError:
-            raise ValueError(f"Issue in {cls.__name__} with date {date} and fmt {cls.date_fmt}")
+            raise ValueError(
+                f"Issue in {cls.__name__} with date {date} and fmt {cls.date_fmt}"
+            ) from None
 
     @property
-    def version_date_parsed(cls) -> Optional[datetime.date]:
+    def version_date_parsed(cls) -> datetime.date | None:
         """Get the date as a parsed class there's a format string."""
         if cls.date_version_fmt is None:
             return None
@@ -133,11 +134,12 @@ class MetaGetter(type):
             return datetime.datetime.strptime(cls.version, cls.date_version_fmt).date()
         except ValueError:
             raise ValueError(
-                f"Issue parsing {cls.__name__} version {cls.version} with fmt {cls.date_version_fmt}"
-            )
+                f"Issue parsing {cls.__name__} version {cls.version} "
+                f"with fmt {cls.date_version_fmt}"
+            ) from None
 
     @property
-    def homepage(cls) -> Optional[str]:
+    def homepage(cls) -> str | None:
         """Get the homepage's URL if a format string was specified."""
         if cls.homepage_fmt is None:
             return None
@@ -163,11 +165,11 @@ class Bioversion(pydantic.BaseModel):
     #: The version type
     vtype: VersionType
     #: The date of the current release
-    date: Optional[datetime.date]
+    date: datetime.date | None
     #: The URL for the homepage of the specific version of the database
-    homepage: Optional[str]
+    homepage: str | None
     #: The database prefix
-    bioregistry_id: Optional[str]
+    bioregistry_id: str | None
 
 
 class Getter(metaclass=MetaGetter):
@@ -179,13 +181,13 @@ class Getter(metaclass=MetaGetter):
     version_type: ClassVar[VersionType]
 
     #: The URL with `{version}` to format in the version. Specify this in the inheriting class.
-    homepage_fmt: ClassVar[Optional[str]] = None
+    homepage_fmt: ClassVar[str | None] = None
 
-    date_fmt: ClassVar[Optional[str]] = None
+    date_fmt: ClassVar[str | None] = None
 
-    date_version_fmt: ClassVar[Optional[str]] = None
+    date_version_fmt: ClassVar[str | None] = None
 
-    bioregistry_id: ClassVar[Optional[str]] = None
+    bioregistry_id: ClassVar[str | None] = None
 
     # The following are automatically calculated based on the metaclass
     version: ClassVar[str]
@@ -193,21 +195,21 @@ class Getter(metaclass=MetaGetter):
     homepage: ClassVar[str]
 
     #: Prefixes this getter works for
-    collection: ClassVar[Optional[List[str]]] = None
+    collection: ClassVar[list[str] | None] = None
 
-    def get(self) -> Union[str, Mapping[str, str], datetime.datetime]:
+    def get(self) -> str | Mapping[str, str] | datetime.datetime:
         """Get the latest of this database."""
         raise NotImplementedError
 
     @classmethod
-    def print(cls, sep: str = "\t", file=None):  # noqa:T202
+    def print(cls, sep: str = "\t", file=None):
         """Print the latest version of this database."""
         x = [cls.bioregistry_id, cls.name, cls.version]
         if cls.date:
             x.append(f"({cls.date})")
         if cls.homepage:
             x.append(cls.homepage)
-        print(*x, sep=sep, file=file)  # noqa:T201
+        print(*x, sep=sep, file=file)
 
     @classmethod
     def resolve(cls) -> Bioversion:
@@ -225,7 +227,7 @@ class Getter(metaclass=MetaGetter):
     @classmethod
     def to_dict(cls) -> Mapping[str, Any]:
         """Get a dict with the data for this database."""
-        return cls.resolve().to_dict()
+        return cls.resolve().model_dump()
 
 
 class DailyGetter(Getter):
@@ -233,7 +235,7 @@ class DailyGetter(Getter):
 
     version_type = VersionType.daily
 
-    def get(self) -> Union[str, Mapping[str, str]]:
+    def get(self) -> str | Mapping[str, str]:
         """Return a constant "daily" string."""
         return "daily"
 
@@ -246,14 +248,14 @@ class UnversionedGetter(Getter):
     #: Has this database been apparently abandoned (true) or is it still updated (false)
     abandoned: ClassVar[bool]
 
-    def get(self) -> Union[str, Mapping[str, str]]:
+    def get(self) -> str | Mapping[str, str]:
         """Return a constant unversioned string."""
         return "unversioned"
 
 
 def get_obo_version(url: str) -> str:
     """Get the data version from an OBO file."""
-    with requests.get(url, stream=True) as res:
+    with requests.get(url, stream=True, timeout=60) as res:
         for line in res.iter_lines():
             line = line.decode("utf-8")
             if line.startswith("data-version:"):

bioversions/version.py

@@ -1,22 +1,20 @@
-# -*- coding: utf-8 -*-
-
 """Version information for bioversions."""
 
 import os
-from subprocess import CalledProcessError, check_output  # noqa: S404
+from subprocess import CalledProcessError, check_output
 
 __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.552"
+VERSION = "0.5.553"
 
 
 def get_git_hash() -> str:
     """Get the bioversions git hash."""
     with open(os.devnull, "w") as devnull:
         try:
-            ret = check_output(  # noqa: S603,S607
+            ret = check_output(
                 ["git", "rev-parse", "HEAD"],
                 cwd=os.path.dirname(__file__),
                 stderr=devnull,

bioversions/wsgi.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """A web application for listing database versions."""
 
-from typing import Any, Dict
+from typing import Any
 
 import flask
 from flask_bootstrap import Bootstrap
@@ -22,7 +20,7 @@ def home():
 @app.route("/database/<name>.json")
 def database(name: str):
     """Resolve information about a given database."""
-    rv: Dict[str, Any] = dict(query=name)
+    rv: dict[str, Any] = {"query": name}
     try:
         bioversion = resolve(name)
     except KeyError:

{bioversions-0.5.552.dist-info → bioversions-0.5.553.dist-info}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Charles Tapley Hoyt
+Copyright (c) 2024 Charles Tapley Hoyt
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal