bioversions 0.5.320__py3-none-any.whl → 0.7.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- bioversions/__init__.py +7 -3
- bioversions/__main__.py +0 -2
- bioversions/charts.py +3 -7
- bioversions/cli.py +3 -5
- bioversions/py.typed +0 -0
- bioversions/resources/__init__.py +18 -7
- bioversions/resources/update.py +20 -12
- bioversions/resources/versions.json +20536 -0
- bioversions/slack_client.py +2 -5
- bioversions/sources/__init__.py +45 -17
- bioversions/sources/antibodyregistry.py +9 -6
- bioversions/sources/bigg.py +5 -7
- bioversions/sources/biogrid.py +0 -2
- bioversions/sources/cellosaurus.py +3 -5
- bioversions/sources/chebi.py +1 -3
- bioversions/sources/chembl.py +3 -3
- bioversions/sources/chemidplus.py +1 -3
- bioversions/sources/civic.py +46 -0
- bioversions/sources/complexportal.py +0 -2
- bioversions/sources/daily.py +0 -2
- bioversions/sources/depmap.py +1 -3
- bioversions/sources/dgi.py +9 -12
- bioversions/sources/disgenet.py +1 -3
- bioversions/sources/drugbank.py +2 -4
- bioversions/sources/drugcentral.py +2 -4
- bioversions/sources/ensembl.py +4 -6
- bioversions/sources/expasy.py +1 -4
- bioversions/sources/flybase.py +0 -2
- bioversions/sources/gtdb.py +35 -0
- bioversions/sources/guidetopharmacology.py +3 -4
- bioversions/sources/hgnc.py +13 -14
- bioversions/sources/homologene.py +0 -2
- bioversions/sources/icd10.py +30 -0
- bioversions/sources/icd11.py +30 -0
- bioversions/sources/icf.py +30 -0
- bioversions/sources/intact.py +0 -2
- bioversions/sources/interpro.py +1 -3
- bioversions/sources/itis.py +8 -15
- bioversions/sources/kegg.py +7 -6
- bioversions/sources/mesh.py +10 -5
- bioversions/sources/mgi.py +0 -2
- bioversions/sources/mirbase.py +13 -7
- bioversions/sources/moalmanac.py +0 -2
- bioversions/sources/msigdb.py +0 -2
- bioversions/sources/ncit.py +1 -4
- bioversions/sources/npass.py +0 -2
- bioversions/sources/obo.py +4 -6
- bioversions/sources/ols.py +6 -8
- bioversions/sources/omim.py +33 -0
- bioversions/sources/oncotree.py +4 -4
- bioversions/sources/pathbank.py +0 -2
- bioversions/sources/pathwaycommons.py +0 -2
- bioversions/sources/pfam.py +0 -2
- bioversions/sources/pombase.py +0 -2
- bioversions/sources/pr.py +1 -3
- bioversions/sources/pubchem.py +0 -2
- bioversions/sources/reactome.py +0 -2
- bioversions/sources/rfam.py +0 -2
- bioversions/sources/rgd.py +1 -3
- bioversions/sources/rhea.py +1 -6
- bioversions/sources/rxnorm.py +1 -3
- bioversions/sources/sgd.py +0 -2
- bioversions/sources/signor.py +36 -0
- bioversions/sources/slm.py +4 -3
- bioversions/sources/stringdb.py +2 -4
- bioversions/sources/umls.py +0 -2
- bioversions/sources/uniprot.py +1 -3
- bioversions/sources/unversioned.py +0 -2
- bioversions/sources/wikipathways.py +0 -2
- bioversions/sources/zfin.py +0 -2
- bioversions/templates/base.html +28 -0
- bioversions/templates/home.html +60 -0
- bioversions/twitter_client.py +5 -8
- bioversions/utils.py +40 -32
- bioversions/version.py +3 -5
- bioversions/wsgi.py +2 -4
- bioversions-0.7.1.dist-info/METADATA +393 -0
- bioversions-0.7.1.dist-info/RECORD +81 -0
- bioversions-0.7.1.dist-info/WHEEL +4 -0
- {bioversions-0.5.320.dist-info → bioversions-0.7.1.dist-info}/entry_points.txt +1 -0
- {bioversions-0.5.320.dist-info → bioversions-0.7.1.dist-info/licenses}/LICENSE +1 -1
- bioversions-0.5.320.dist-info/METADATA +0 -166
- bioversions-0.5.320.dist-info/RECORD +0 -72
- bioversions-0.5.320.dist-info/WHEEL +0 -5
- bioversions-0.5.320.dist-info/top_level.txt +0 -1
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"""A getter for `SIGNOR <https://signor.uniroma2.it>`_."""
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import datetime
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from typing import ClassVar
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from bioversions.utils import Getter, VersionType, get_soup
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__all__ = [
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"SignorGetter",
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]
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URL = "https://signor.uniroma2.it/downloads.php"
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TEXT = "Click here to download the latest stable release"
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class SignorGetter(Getter):
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"""A getter for SIGNOR."""
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name = "SIGNOR"
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version_type = VersionType.date
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date_fmt = "%B %Y"
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collection: ClassVar[list[str]] = ["signor", "signor.relation"]
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def get(self) -> datetime.datetime:
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"""Get the latest SIGNOR version number."""
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soup = get_soup(URL)
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for p in soup.find_all("p"):
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if TEXT in p.text:
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_, _, after = p.text.partition(TEXT)
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after = after.strip().lstrip("(").rstrip(")")
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return datetime.datetime.strptime(after, "%B %Y")
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raise RuntimeError
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if __name__ == "__main__":
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SignorGetter.print()
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bioversions/sources/slm.py
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# -*- coding: utf-8 -*-
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"""A getter for SwissLipids."""
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import datetime
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"SwissLipidGetter",
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]
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# View docs at https://www.swisslipids.org/#/api
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URL = "https://www.swisslipids.org/api/index.php/downloadData"
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class SwissLipidGetter(Getter):
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"""A getter for SwissLipids."""
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def get(self):
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"""Get the latest SwissLipids version number."""
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res = requests.get(
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res = requests.get(URL, timeout=15).json()
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record = next(record for record in res if record["file"] == "lipids.tsv")
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return datetime.datetime.strptime(record["date"], "%B %d %Y")
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bioversions/sources/stringdb.py
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# -*- coding: utf-8 -*-
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"""A getter for StringDB."""
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from bioversions.utils import Getter, VersionType, get_soup
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soup = get_soup("https://string-db.org/cgi/access")
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table = soup.find(**{"class": "footer_access_archive_table"})
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rows = table.find_all(**{"class": "row"})
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version, date, link, _summary =
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version, date, link, _summary = (row.text for row in rows[1].find_all(**{"class": "cell"}))
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date = date[len("current: since ") :]
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return
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return {"version": version, "date": date}
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if __name__ == "__main__":
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bioversions/sources/umls.py
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bioversions/sources/uniprot.py
CHANGED
bioversions/sources/zfin.py
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<!doctype html>
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<html lang="en">
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<head>
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{% block head %}
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<!-- Required meta tags -->
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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{% block styles %}
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<!-- Bootstrap CSS -->
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{{ bootstrap.load_css() }}
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{% endblock %}
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<script src="https://kit.fontawesome.com/4c86883252.js" crossorigin="anonymous"></script>
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<title>{% block title %}{% endblock %}</title>
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{% endblock %}
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</head>
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<body>
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<!-- Your page content -->
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{% block content %}{% endblock %}
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{% block scripts %}
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<!-- Optional JavaScript -->
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{{ bootstrap.load_js() }}
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{% endblock %}
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</body>
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</html>
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{% extends "base.html" %}
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{% block title %}Bioversions{% endblock %}
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{% block content %}
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<div class="container" style="margin-top: 50px; margin-bottom: 50px">
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<div class="row justify-content-center">
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<div class="card">
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<h5 class="card-header text-center">Biological Database Latest Versions</h5>
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<div class="card-body">
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<p>
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This web application lists the latest versions for biological databases.
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It refreshes once per day.
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</p>
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</div>
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<table class="table table-striped table-hover">
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<thead>
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<tr>
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<th>Name</th>
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<th>Version</th>
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<th>Date</th>
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<th class="text-center">JSON</th>
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</tr>
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</thead>
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<tbody>
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{% for row in rows %}
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<tr>
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<td>{{ row.name }}</td>
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<td>
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{% if row.homepage %}
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<a href="{{ row.homepage }}">{{ row.version }} <i class="fas fa-link"></i></a>
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{% else %}
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{{ row.version }}
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{% endif %}
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</td>
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<td>
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{% if row.date %}{{ row.date }}{% endif %}
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</td>
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<td class="text-center">
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<a href="{{ url_for('database', name=row.name.lower().replace(" ", "")) }}">
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<i class="fas fa-download"></i>
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</a>
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</td>
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</tr>
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{% endfor %}
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</tbody>
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</table>
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<div class="card-footer">
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<p style="text-align: center">
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Developed with ❤️ by the <a href="https://indralab.github.io">INDRA Lab</a> in the
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<a href="https://hits.harvard.edu">Harvard Program in Therapeutic Science (HiTS)</a>.<br/>
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Funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).<br/>
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Point of contact: <a href="https://github.com/cthoyt">@cthoyt</a>.
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(<a href="https://github.com/biopragmatics/bioversions">Source code</a>)
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</p>
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</div>
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</div>
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</div>
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</div>
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{% endblock %}
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bioversions/twitter_client.py
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"""Utilities for interacting with Twitter."""
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import pystow
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import tweepy
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@lru_cache(maxsize=1)
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def _get_api(
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consumer_key:
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consumer_secret:
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access_token:
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access_token_secret:
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) ->
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consumer_key: str | None = None,
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consumer_secret: str | None = None,
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access_token: str | None = None,
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access_token_secret: str | None = None,
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) -> tweepy.API | None:
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consumer_key = pystow.get_config("bioversions", "consumer_key", passthrough=consumer_key)
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consumer_secret = pystow.get_config(
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"bioversions", "consumer_secret", passthrough=consumer_secret
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bioversions/utils.py
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"""Utilities and implementation for bioversions."""
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from typing import Any, ClassVar
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import bioregistry
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import pydantic
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import requests
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import requests_ftp
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from cachier import cachier
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DOCS = os.path.abspath(os.path.join(HERE, os.pardir, os.pardir, "docs"))
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class VersionType(enum.Enum):
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"""Different types of versions."""
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) -> BeautifulSoup:
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:param timeout: How many integer seconds to wait for a response?
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:param user_agent: A custom user-agent to set, e.g., to avoid anti-crawling mechanisms
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date_fmt: str | None
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homepage_fmt: str | None
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@property
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@property
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-
def date(cls) ->
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+
def date(cls) -> datetime.date | None:
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"""Get the date if it's set."""
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vp = cls.version_date_parsed
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if vp is not None:
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@@ -116,10 +118,12 @@ class MetaGetter(type):
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try:
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return datetime.datetime.strptime(date, cls.date_fmt).date()
|
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except ValueError:
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-
raise ValueError(
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+
raise ValueError(
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f"Issue in {cls.__name__} with date {date} and fmt {cls.date_fmt}"
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) from None
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@property
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-
def version_date_parsed(cls) ->
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def version_date_parsed(cls) -> datetime.date | None:
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"""Get the date as a parsed class there's a format string."""
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if cls.date_version_fmt is None:
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return None
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@@ -127,11 +131,12 @@ class MetaGetter(type):
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|
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return datetime.datetime.strptime(cls.version, cls.date_version_fmt).date()
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except ValueError:
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raise ValueError(
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f"Issue parsing {cls.__name__} version {cls.version}
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-
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f"Issue parsing {cls.__name__} version {cls.version} "
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f"with fmt {cls.date_version_fmt}"
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) from None
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@property
|
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|
-
def homepage(cls) ->
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+
def homepage(cls) -> str | None:
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|
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"""Get the homepage's URL if a format string was specified."""
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if cls.homepage_fmt is None:
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return None
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@@ -157,11 +162,11 @@ class Bioversion(pydantic.BaseModel):
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#: The version type
|
|
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vtype: VersionType
|
|
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#: The date of the current release
|
|
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|
-
date:
|
|
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|
+
date: datetime.date | None
|
|
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166
|
#: The URL for the homepage of the specific version of the database
|
|
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|
-
homepage:
|
|
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|
+
homepage: str | None
|
|
163
168
|
#: The database prefix
|
|
164
|
-
bioregistry_id:
|
|
169
|
+
bioregistry_id: str | None
|
|
165
170
|
|
|
166
171
|
|
|
167
172
|
class Getter(metaclass=MetaGetter):
|
|
@@ -173,32 +178,35 @@ class Getter(metaclass=MetaGetter):
|
|
|
173
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|
version_type: ClassVar[VersionType]
|
|
174
179
|
|
|
175
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|
#: The URL with `{version}` to format in the version. Specify this in the inheriting class.
|
|
176
|
-
homepage_fmt: ClassVar[
|
|
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|
+
homepage_fmt: ClassVar[str | None] = None
|
|
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182
|
|
|
178
|
-
date_fmt: ClassVar[
|
|
183
|
+
date_fmt: ClassVar[str | None] = None
|
|
179
184
|
|
|
180
|
-
date_version_fmt: ClassVar[
|
|
185
|
+
date_version_fmt: ClassVar[str | None] = None
|
|
181
186
|
|
|
182
|
-
bioregistry_id: ClassVar[
|
|
187
|
+
bioregistry_id: ClassVar[str | None] = None
|
|
183
188
|
|
|
184
189
|
# The following are automatically calculated based on the metaclass
|
|
185
190
|
version: ClassVar[str]
|
|
186
191
|
date: ClassVar[str]
|
|
187
192
|
homepage: ClassVar[str]
|
|
188
193
|
|
|
189
|
-
|
|
194
|
+
#: Prefixes this getter works for
|
|
195
|
+
collection: ClassVar[list[str] | None] = None
|
|
196
|
+
|
|
197
|
+
def get(self) -> str | Mapping[str, str] | datetime.datetime:
|
|
190
198
|
"""Get the latest of this database."""
|
|
191
199
|
raise NotImplementedError
|
|
192
200
|
|
|
193
201
|
@classmethod
|
|
194
|
-
def print(cls, sep: str = "\t", file=None):
|
|
202
|
+
def print(cls, sep: str = "\t", file=None):
|
|
195
203
|
"""Print the latest version of this database."""
|
|
196
204
|
x = [cls.bioregistry_id, cls.name, cls.version]
|
|
197
205
|
if cls.date:
|
|
198
206
|
x.append(f"({cls.date})")
|
|
199
207
|
if cls.homepage:
|
|
200
208
|
x.append(cls.homepage)
|
|
201
|
-
print(*x, sep=sep, file=file)
|
|
209
|
+
print(*x, sep=sep, file=file)
|
|
202
210
|
|
|
203
211
|
@classmethod
|
|
204
212
|
def resolve(cls) -> Bioversion:
|
|
@@ -216,7 +224,7 @@ class Getter(metaclass=MetaGetter):
|
|
|
216
224
|
@classmethod
|
|
217
225
|
def to_dict(cls) -> Mapping[str, Any]:
|
|
218
226
|
"""Get a dict with the data for this database."""
|
|
219
|
-
return cls.resolve().
|
|
227
|
+
return cls.resolve().model_dump()
|
|
220
228
|
|
|
221
229
|
|
|
222
230
|
class DailyGetter(Getter):
|
|
@@ -224,7 +232,7 @@ class DailyGetter(Getter):
|
|
|
224
232
|
|
|
225
233
|
version_type = VersionType.daily
|
|
226
234
|
|
|
227
|
-
def get(self) ->
|
|
235
|
+
def get(self) -> str | Mapping[str, str]:
|
|
228
236
|
"""Return a constant "daily" string."""
|
|
229
237
|
return "daily"
|
|
230
238
|
|
|
@@ -237,14 +245,14 @@ class UnversionedGetter(Getter):
|
|
|
237
245
|
#: Has this database been apparently abandoned (true) or is it still updated (false)
|
|
238
246
|
abandoned: ClassVar[bool]
|
|
239
247
|
|
|
240
|
-
def get(self) ->
|
|
248
|
+
def get(self) -> str | Mapping[str, str]:
|
|
241
249
|
"""Return a constant unversioned string."""
|
|
242
250
|
return "unversioned"
|
|
243
251
|
|
|
244
252
|
|
|
245
253
|
def get_obo_version(url: str) -> str:
|
|
246
254
|
"""Get the data version from an OBO file."""
|
|
247
|
-
with requests.get(url, stream=True) as res:
|
|
255
|
+
with requests.get(url, stream=True, timeout=60) as res:
|
|
248
256
|
for line in res.iter_lines():
|
|
249
257
|
line = line.decode("utf-8")
|
|
250
258
|
if line.startswith("data-version:"):
|
|
@@ -270,7 +278,7 @@ class OBOFoundryGetter(Getter):
|
|
|
270
278
|
|
|
271
279
|
def get(self) -> str:
|
|
272
280
|
"""Get the OBO version."""
|
|
273
|
-
url = f"
|
|
281
|
+
url = f"https://purl.obolibrary.org/obo/{self.key}.obo"
|
|
274
282
|
return self.process(get_obo_version(url))
|
|
275
283
|
|
|
276
284
|
def process(self, version: str) -> str:
|
bioversions/version.py
CHANGED
|
@@ -1,22 +1,20 @@
|
|
|
1
|
-
# -*- coding: utf-8 -*-
|
|
2
|
-
|
|
3
1
|
"""Version information for bioversions."""
|
|
4
2
|
|
|
5
3
|
import os
|
|
6
|
-
from subprocess import CalledProcessError, check_output
|
|
4
|
+
from subprocess import CalledProcessError, check_output
|
|
7
5
|
|
|
8
6
|
__all__ = [
|
|
9
7
|
"VERSION",
|
|
10
8
|
]
|
|
11
9
|
|
|
12
|
-
VERSION = "0.
|
|
10
|
+
VERSION = "0.7.1"
|
|
13
11
|
|
|
14
12
|
|
|
15
13
|
def get_git_hash() -> str:
|
|
16
14
|
"""Get the bioversions git hash."""
|
|
17
15
|
with open(os.devnull, "w") as devnull:
|
|
18
16
|
try:
|
|
19
|
-
ret = check_output(
|
|
17
|
+
ret = check_output(
|
|
20
18
|
["git", "rev-parse", "HEAD"],
|
|
21
19
|
cwd=os.path.dirname(__file__),
|
|
22
20
|
stderr=devnull,
|
bioversions/wsgi.py
CHANGED
|
@@ -1,8 +1,6 @@
|
|
|
1
|
-
# -*- coding: utf-8 -*-
|
|
2
|
-
|
|
3
1
|
"""A web application for listing database versions."""
|
|
4
2
|
|
|
5
|
-
from typing import Any
|
|
3
|
+
from typing import Any
|
|
6
4
|
|
|
7
5
|
import flask
|
|
8
6
|
from flask_bootstrap import Bootstrap
|
|
@@ -22,7 +20,7 @@ def home():
|
|
|
22
20
|
@app.route("/database/<name>.json")
|
|
23
21
|
def database(name: str):
|
|
24
22
|
"""Resolve information about a given database."""
|
|
25
|
-
rv:
|
|
23
|
+
rv: dict[str, Any] = {"query": name}
|
|
26
24
|
try:
|
|
27
25
|
bioversion = resolve(name)
|
|
28
26
|
except KeyError:
|