pyobo 0.11.1__py3-none-any.whl → 0.11.2__py3-none-any.whl

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.11.1"
+VERSION = "0.11.2"
 
 
 def get_git_hash() -> str:

{pyobo-0.11.1.dist-info → pyobo-0.11.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.11.1
+Version: 0.11.2
 Summary: A python package for handling and generating OBO
 Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
@@ -49,40 +49,40 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: obonet >=0.3.0
+Requires-Dist: obonet>=0.3.0
 Requires-Dist: click
 Requires-Dist: tqdm
 Requires-Dist: pyyaml
 Requires-Dist: pandas
 Requires-Dist: requests
 Requires-Dist: protmapper
-Requires-Dist: more-itertools
-Requires-Dist: more-click >=0.0.2
+Requires-Dist: more_itertools
+Requires-Dist: more_click>=0.0.2
 Requires-Dist: humanize
 Requires-Dist: tabulate
 Requires-Dist: cachier
-Requires-Dist: pystow >=0.2.7
-Requires-Dist: bioversions >=0.5.535
-Requires-Dist: bioregistry >=0.11.23
-Requires-Dist: bioontologies >=0.4.0
-Requires-Dist: zenodo-client >=0.0.5
-Requires-Dist: class-resolver
+Requires-Dist: pystow>=0.2.7
+Requires-Dist: bioversions>=0.5.535
+Requires-Dist: bioregistry>=0.11.23
+Requires-Dist: bioontologies>=0.4.0
+Requires-Dist: zenodo-client>=0.0.5
+Requires-Dist: class_resolver
 Requires-Dist: psycopg2-binary
-Requires-Dist: pydantic >=2.0
-Requires-Dist: drugbank-downloader
-Requires-Dist: chembl-downloader
-Requires-Dist: umls-downloader >=0.1.3
-Requires-Dist: typing-extensions
+Requires-Dist: pydantic>=2.0
+Requires-Dist: requests-ftp
+Requires-Dist: drugbank_downloader
+Requires-Dist: chembl_downloader
+Requires-Dist: umls_downloader>=0.1.3
+Requires-Dist: typing_extensions
 Requires-Dist: rdflib
-Provides-Extra: docs
-Requires-Dist: sphinx >=8 ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme >=3.0 ; extra == 'docs'
-Requires-Dist: sphinx-click ; extra == 'docs'
-Requires-Dist: sphinx-automodapi ; extra == 'docs'
 Provides-Extra: tests
-Requires-Dist: pytest ; extra == 'tests'
-Requires-Dist: coverage ; extra == 'tests'
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: coverage; extra == "tests"
+Provides-Extra: docs
+Requires-Dist: sphinx>=8; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=3.0; extra == "docs"
+Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: sphinx_automodapi; extra == "docs"
 
 <!--
 <p align="center">

{pyobo-0.11.1.dist-info → pyobo-0.11.2.dist-info}/RECORD

@@ -12,7 +12,7 @@ pyobo/plugins.py,sha256=UyEnXxFP2q9IdYp5o7DDXPBrcExvTx4LkvhvWXx-XQc,1227
 pyobo/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyobo/reader.py,sha256=C_-Dz0ScyFdr8DivHTYyDhIVg8SOwS_Y0DIuqKT2EJI,21292
 pyobo/resource_utils.py,sha256=8ZQx8d-HbmPyc_WHUhqx1yjUKFZMF101FopZwZPghoE,4273
-pyobo/version.py,sha256=QvIJIOoOcrMgtVzkvER3psDs709LKt9w5I-rKlbzVcI,919
+pyobo/version.py,sha256=5XT91psNM717pWEmUHFJc4A_TdbD4AvRx-gAxK9qm4Y,919
 pyobo/api/__init__.py,sha256=7_uVqbZVEWrKNBYxVJb86K9-dLsGD2d2H5wjLzIP1wU,1301
 pyobo/api/alts.py,sha256=fYA3S3odeem2-HvzeqUn0jkAFGdmbL1SYXCjIqKmRqs,2836
 pyobo/api/hierarchy.py,sha256=-zgM4n0n0h5v5aPOhG0AR3isOt10Vtpo6EwVYN00ngI,9509
@@ -24,21 +24,6 @@ pyobo/api/species.py,sha256=Ze1yr3n9jCVQVYXmn_hw_FiziTYchddCNTW9ChDH85U,2259
 pyobo/api/typedefs.py,sha256=Z4IZ5ggJe1N7lKMMrng5P8WnZo0nalsaLTMLmQT0w2Y,1130
 pyobo/api/utils.py,sha256=zM56HjlYNPXjnhIe3oS7Yv5mAEfHHbhnf1gpJOnem1M,3274
 pyobo/api/xrefs.py,sha256=InnBazYid5SBoRCMfE3lrBIRtdvwNi2oozjlGaX06ls,6007
-pyobo/apps/__init__.py,sha256=iACi86TkTiGxwneGmfaudZOIEqZ45YjPXng7XjPE38Y,72
-pyobo/apps/cli.py,sha256=gnXBAaESw1T1BvgMpTv-0P26hM2vKCAXPy0SOskgUwU,335
-pyobo/apps/gilda/__init__.py,sha256=jpLIHJOmR_66tdXXUWFP9NiZnpQKvjv5YpCJWoAKnUI,54
-pyobo/apps/gilda/__main__.py,sha256=9EEwzUlwcFHrfAEzveIvmqHiPu52wLt8o4Xe_vFcWf0,124
-pyobo/apps/gilda/app.py,sha256=rHqGR52fnbhqRPWktbIZc8ZZcFEIKp6rq7ledFuN_Lg,1315
-pyobo/apps/gilda/cli.py,sha256=OteTZy060Elmg38sl091kHfaHjjLTJaAtLdUpWgr6ug,702
-pyobo/apps/gilda/templates/base.html,sha256=MxFNPgWW4wYzXXS3RwXMcMJAc1_lUhguQvVYQYjSjLY,888
-pyobo/apps/gilda/templates/home.html,sha256=ZAqegzBGgVct9UzmfC0dfGJ6_jbDSCpbwqe2WB-00AA,273
-pyobo/apps/gilda/templates/matches.html,sha256=x3mvMCevr8IoXSXmm_aOQlKNBycvMpBedLLCt2znNXQ,934
-pyobo/apps/mapper/__init__.py,sha256=9PK1LtsCTVcQQzSPtpa6f1dgjsoeygq9cAP7AXqEiJY,56
-pyobo/apps/mapper/__main__.py,sha256=XScQCj6oK2OslWyZ8yzcaietLJm_XxDLA22CMoyy6dM,169
-pyobo/apps/mapper/cli.py,sha256=AHPPXqSd3LTMhHIsmhErMB_gpfDeDs6IGlPdHQKMIq0,682
-pyobo/apps/mapper/mapper.py,sha256=yVIHGlTwFNtKEF07K-oqsqy8ggIalN6SfmyzB4E--2I,5787
-pyobo/apps/mapper/templates/base.html,sha256=w9d8e8qKnVy_h7RT5hWV9EwghgPqn0y3xJ-tZw0v9TQ,982
-pyobo/apps/mapper/templates/mapper_home.html,sha256=XugUb76C6B1JGQTCb2tDhZ-XyY-636qeZJODUTrpjdw,2785
 pyobo/cli/__init__.py,sha256=pTiLuzjjpi0P69yVjQ2kE6nBUmZuYFnqdJNDZLDkgvk,71
 pyobo/cli/aws.py,sha256=_S08OhNY-vdx-KIT4ix3Zluey9lVY0RWJhDjwcwrw2M,964
 pyobo/cli/cli.py,sha256=gWEMOWEfjpTdCjxJm1F3Kq73FD1xoGfG9p_8r0YJ4Ro,3522
@@ -165,9 +150,8 @@ pyobo/xrefdb/sources/intact.py,sha256=l2gqxm9OLPpQqhNqAIT_jk7AHx61itsUCz-5dowwMb
 pyobo/xrefdb/sources/ncit.py,sha256=QTo9BSGuurvy9M54viS6_v6dF36O8DbUGU6iiyqKsPI,3729
 pyobo/xrefdb/sources/pubchem.py,sha256=VK_yPCaoa-CKQNkq9iAF0Zh0D_zxqa92YG4OBbvnA9c,771
 pyobo/xrefdb/sources/wikidata.py,sha256=JSrl3YWMQA_gxw7IXJRnxWWetcAV82aM5-5J3IHFzoQ,3562
-pyobo-0.11.1.dist-info/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-pyobo-0.11.1.dist-info/METADATA,sha256=llPe8alNZWukCFjhvVKIEL6s2Vri9vfaSWRZE2DxMQg,24927
-pyobo-0.11.1.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-pyobo-0.11.1.dist-info/entry_points.txt,sha256=YfZYzQyXBZ5dGiy4GsOUCOKKlNRNDcmR4vnlpD50q08,41
-pyobo-0.11.1.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
-pyobo-0.11.1.dist-info/RECORD,,
+pyobo-0.11.2.dist-info/METADATA,sha256=OhM135rj_cy5fzwcUBqk0Hfm4ItzYdR7DjKVt5pX8Hg,24916
+pyobo-0.11.2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pyobo-0.11.2.dist-info/entry_points.txt,sha256=YfZYzQyXBZ5dGiy4GsOUCOKKlNRNDcmR4vnlpD50q08,41
+pyobo-0.11.2.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
+pyobo-0.11.2.dist-info/RECORD,,

{pyobo-0.11.1.dist-info → pyobo-0.11.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pyobo/apps/__init__.py

@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""A collection of web apps built on PyOBO."""

pyobo/apps/cli.py

@@ -1,24 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO apps."""
-
-import click
-
-from .gilda.cli import main as gilda_main
-from .mapper.cli import main as mapper_main
-
-__all__ = [
-    "main",
-]
-
-
-@click.group(name="apps")
-def main():
-    """Apps."""
-
-
-main.add_command(gilda_main)
-main.add_command(mapper_main)
-
-if __name__ == "__main__":
-    main()

pyobo/apps/gilda/__init__.py

@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Gilda Service."""

pyobo/apps/gilda/__main__.py

@@ -1,8 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Gilda Service."""
-
-from .cli import main
-
-if __name__ == "__main__":
-    main()

pyobo/apps/gilda/app.py

@@ -1,48 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Gilda Service."""
-
-from typing import Iterable, Union
-
-import flask
-from flask_bootstrap import Bootstrap
-from flask_wtf import FlaskForm
-from wtforms.fields import StringField, SubmitField
-from wtforms.validators import DataRequired
-
-from pyobo.gilda_utils import get_grounder
-
-
-class Form(FlaskForm):
-    """Form for submitting a query."""
-
-    text = StringField("Text", validators=[DataRequired()])
-    submit = SubmitField()
-
-    def make_response(self):
-        """Make a response with the text."""
-        return flask.redirect(flask.url_for("ground", text=self.text.data))
-
-
-def get_app(prefix: Union[str, Iterable[str]]):
-    """Make an app for grounding the text."""
-    grounder = get_grounder(prefix)
-
-    app = flask.Flask(__name__)
-    app.config["WTF_CSRF_ENABLED"] = False
-    Bootstrap(app)
-
-    @app.route("/", methods=["GET", "POST"])
-    def home():
-        """Ground the given text."""
-        form = Form()
-        if form.validate_on_submit():
-            return form.make_response()
-        return flask.render_template("home.html", form=form)
-
-    @app.route("/ground/<text>")
-    def ground(text: str):
-        """Ground the given text."""
-        return flask.jsonify([scored_match.to_json() for scored_match in grounder.ground(text)])
-
-    return app

pyobo/apps/gilda/cli.py

@@ -1,36 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Gilda Service."""
-
-import click
-from more_click import (
-    host_option,
-    port_option,
-    run_app,
-    verbose_option,
-    with_gunicorn_option,
-    workers_option,
-)
-
-__all__ = [
-    "main",
-]
-
-
-@click.command(name="gilda")
-@click.argument("prefix", nargs=-1)
-@verbose_option
-@host_option
-@workers_option
-@port_option
-@with_gunicorn_option
-def main(prefix: str, host: str, port: str, with_gunicorn: bool, workers: int):
-    """Run the Gilda service for this database."""
-    from .app import get_app
-
-    app = get_app(prefix)
-    run_app(app, host=host, port=port, with_gunicorn=with_gunicorn, workers=workers)
-
-
-if __name__ == "__main__":
-    main()

pyobo/apps/gilda/templates/base.html

@@ -1,33 +0,0 @@
-<!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>
-<div class="container" style="margin-top: 50px; margin-bottom: 50px">
-    <div class="row">
-        <div class="card">
-            <!-- Your page content -->
-            {% block content %}{% endblock %}
-        </div>
-    </div>
-</div>
-{% block scripts %}
-    <!-- Optional JavaScript -->
-    {{ bootstrap.load_js() }}
-{% endblock %}
-</body>
-</html>

pyobo/apps/gilda/templates/home.html

@@ -1,11 +0,0 @@
-{% extends "base.html" %}
-
-{% block content %}
-    <h5 class="card-header">Gilda</h5>
-    <div class="card-body">
-        <p>
-            This is the Gilda grounding service.
-        </p>
-        {{ wtf.quick_form(form, form_type='horizontal') }}
-    </div>
-{% endblock %}

pyobo/apps/gilda/templates/matches.html

@@ -1,32 +0,0 @@
-{% extends "base.html" %}
-
-{% block content %}
-    <h5 class="card-header">Gilda</h5>
-    <div class="card-body">
-        <p>
-            Results for <code>{{ form.text.data }}</code>
-            {% if form.context.data %} with context
-                <i>{{ form.context.data }}</i>{% endif %}
-        </p>
-    </div>
-    <table class="table table-striped table-hover">
-        <thead>
-        <tr>
-            <th>Database</th>
-            <th>Identifier</th>
-            <th>Name</th>
-            <th>Score</th>
-        </tr>
-        </thead>
-        <tbody>
-        {% for match in matches %}
-            <tr>
-                <td>{{ match['term']['db'] }}</td>
-                <td>{{ match['term']['id'] }}</td>
-                <td>{{ match['term']['entry_name'] }}</td>
-                <td class="text-right">{{ match['score'] | round(4) }}</td>
-            </tr>
-        {% endfor %}
-        </tbody>
-    </table>
-{% endblock %}

pyobo/apps/mapper/__init__.py

@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Mapping Service."""

pyobo/apps/mapper/__main__.py

@@ -1,11 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Mapping Service.
-
-Run with ``python -m pyobo.apps.mapper``
-"""
-
-from .cli import main
-
-if __name__ == "__main__":
-    main()

pyobo/apps/mapper/cli.py

@@ -1,37 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""CLI for PyOBO's Mapping Service.
-
-Run with ``python -m pyobo.apps.mapper``.
-"""
-
-import click
-from more_click import (
-    host_option,
-    port_option,
-    run_app,
-    verbose_option,
-    with_gunicorn_option,
-)
-
-__all__ = [
-    "main",
-]
-
-
-@click.command(name="mapper")
-@click.option("-x", "--mappings-file")
-@port_option
-@host_option
-@with_gunicorn_option
-@verbose_option
-def main(mappings_file, host: str, port: str, with_gunicorn: bool):
-    """Run the mappings app."""
-    from .mapper import get_app
-
-    app = get_app(mappings_file)
-    run_app(app=app, host=host, port=port, with_gunicorn=with_gunicorn)
-
-
-if __name__ == "__main__":
-    main()

pyobo/apps/mapper/mapper.py

@@ -1,187 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""PyOBO's Mapping Service.
-
-Run with ``python -m pyobo.apps.mapper``.
-"""
-
-import logging
-from functools import lru_cache
-from typing import Any, Dict, Iterable, List, Mapping, Optional, Union
-
-import bioregistry
-import pandas as pd
-from flasgger import Swagger
-from flask import (
-    Blueprint,
-    Flask,
-    abort,
-    current_app,
-    jsonify,
-    render_template,
-    url_for,
-)
-from flask_bootstrap import VERSION_BOOTSTRAP, Bootstrap
-from werkzeug.local import LocalProxy
-
-from pyobo import Canonicalizer
-from pyobo.constants import PROVENANCE, SOURCE_PREFIX, TARGET_PREFIX
-from pyobo.identifier_utils import normalize_curie
-from pyobo.resource_utils import ensure_inspector_javert_df
-
-__all__ = [
-    "get_app",
-]
-
-logger = logging.getLogger(__name__)
-
-summary_df = LocalProxy(lambda: current_app.config["summary"])
-canonicalizer: Canonicalizer = LocalProxy(lambda: current_app.config["canonicalizer"])
-
-
-@lru_cache()
-def _single_source_shortest_path(curie: str) -> Optional[Mapping[str, List[Mapping[str, str]]]]:
-    return canonicalizer.single_source_shortest_path(curie=curie)
-
-
-@lru_cache()
-def _all_shortest_paths(source_curie: str, target_curie: str) -> List[List[Mapping[str, str]]]:
-    return canonicalizer.all_shortest_paths(source_curie=source_curie, target_curie=target_curie)
-
-
-#: The blueprint that gets added to the app
-search_blueprint = Blueprint("search", __name__)
-
-
-@search_blueprint.route("/")
-def home():
-    """Show the home page."""
-    return render_template("mapper_home.html")
-
-
-@search_blueprint.route("/mappings/<curie>")
-def single_source_mappings(curie: str):
-    """Return all length xrefs from the given identifier."""
-    if curie not in canonicalizer.graph:
-        return jsonify(
-            success=False,
-            query=dict(curie=curie),
-            message="could not find curie",
-        )
-    return jsonify(_single_source_shortest_path(curie))
-
-
-@search_blueprint.route("/mappings/<source_curie>/<target_curie>")
-def all_mappings(source_curie: str, target_curie: str):
-    """Return all shortest paths of xrefs between the two identifiers."""
-    if source_curie not in canonicalizer.graph:
-        return jsonify(
-            success=False,
-            query=dict(source_curie=source_curie, target_curie=target_curie),
-            message="could not find source curie",
-        )
-    if target_curie not in canonicalizer.graph:
-        return jsonify(
-            success=False,
-            query=dict(source_curie=source_curie, target_curie=target_curie),
-            message="could not find target curie",
-        )
-
-    return jsonify(_all_shortest_paths(source_curie, target_curie))
-
-
-@search_blueprint.route("/mappings/summarize")
-def summarize():
-    """Summarize the mappings."""
-    return summary_df.to_html(index=False)
-
-
-@search_blueprint.route("/mappings/summarize_by/<prefix>")
-def summarize_one(prefix: str):
-    """Summarize the mappings."""
-    norm_prefix = bioregistry.normalize_prefix(prefix)
-    if norm_prefix is None:
-        return abort(500, f"invalid prefix: {prefix}")
-    in_df = summary_df.loc[summary_df[TARGET_PREFIX] == norm_prefix, [SOURCE_PREFIX, "count"]]
-    out_df = summary_df.loc[summary_df[SOURCE_PREFIX] == norm_prefix, [TARGET_PREFIX, "count"]]
-    return f"""
-    <h1>Incoming Mappings to {norm_prefix}</h1>
-    {in_df.to_html(index=False)}
-    <h1>Outgoing Mappings from {norm_prefix}</h1>
-    {out_df.to_html(index=False)}
-    """
-
-
-@search_blueprint.route("/canonicalize/<curie>")
-def canonicalize(curie: str):
-    """Return the best CURIE."""
-    # TODO maybe normalize the curie first?
-    norm_prefix, norm_identifier = normalize_curie(curie)
-    if norm_prefix is None or norm_identifier is None:
-        return jsonify(
-            query=curie,
-            normalizable=False,
-        )
-
-    norm_curie = f"{norm_prefix}:{norm_identifier}"
-
-    rv: Dict[str, Any] = dict(query=curie)
-    if norm_curie != curie:
-        rv["norm_curie"] = norm_curie
-
-    if norm_curie not in canonicalizer.graph:
-        rv["found"] = False
-    else:
-        result_curie = canonicalizer.canonicalize(norm_curie)
-        rv.update(
-            found=True,
-            result=result_curie,
-            mappings=url_for(
-                f".{all_mappings.__name__}",
-                source_curie=norm_curie,
-                target_curie=result_curie,
-            ),
-        )
-
-    return jsonify(rv)
-
-
-def get_app(paths: Union[None, str, Iterable[str]] = None) -> Flask:
-    """Build the Flask app."""
-    app = Flask(__name__)
-    Swagger(app)
-
-    logger.info("using bootstrap_flask %s", VERSION_BOOTSTRAP)
-    Bootstrap(app)
-
-    if paths is None:
-        df = ensure_inspector_javert_df()
-    elif isinstance(paths, str):
-        df = pd.read_csv(paths, sep="\t", dtype=str)
-    else:
-        df = pd.concat(pd.read_csv(path, sep="\t", dtype=str) for path in paths)
-
-    app.config["summary"] = summarize_xref_df(df)
-    app.config["summary_provenances"] = summarize_xref_provenances_df(df)
-    # TODO allow for specification of priorities in the canonicalizer
-    app.config["canonicalizer"] = Canonicalizer.from_df(df)
-    app.register_blueprint(search_blueprint)
-    return app
-
-
-def summarize_xref_df(df: pd.DataFrame) -> pd.DataFrame:
-    """Get all meta-mappings."""
-    return _summarize(df, [SOURCE_PREFIX, TARGET_PREFIX])
-
-
-def summarize_xref_provenances_df(df: pd.DataFrame) -> pd.DataFrame:
-    """Get all meta-mappings."""
-    return _summarize(df, [SOURCE_PREFIX, TARGET_PREFIX, PROVENANCE])
-
-
-def _summarize(df: pd.DataFrame, columns) -> pd.DataFrame:
-    """Get all meta-mappings."""
-    rv = df[columns].groupby(columns).size().reset_index()
-    rv.columns = [*columns, "count"]
-    rv.sort_values("count", inplace=True, ascending=False)
-    return rv

pyobo/apps/mapper/templates/base.html

@@ -1,35 +0,0 @@
-<!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>
-<div class="container" style="margin-top: 25px; margin-bottom: 25px">
-    <div class="row justify-content-center">
-        <div class="col-md-8 col-lg-8">
-            <div class="card">
-                <!-- Your page content -->
-                {% block content %}{% endblock %}
-            </div>
-        </div>
-    </div>
-</div>
-{% block scripts %}
-    <!-- Optional JavaScript -->
-    {{ bootstrap.load_js() }}
-{% endblock %}
-</body>
-</html>

pyobo/apps/mapper/templates/mapper_home.html

@@ -1,64 +0,0 @@
-{% extends "base.html" %}
-
-{% block content %}
-    <h5 class="card-header">Inspector Javert's Mapper</h5>
-    <div class="card-body">
-        <p class="card-text">
-            This service resolves <a href="https://en.wikipedia.org/wiki/CURIE">CURIEs</a>
-            to the best CURIE that's mapped to it.
-        </p>
-        <p>
-            A summary of all of the xrefs can be found <a href="{{ url_for('.summarize') }}">here</a>.
-            You can also look at a summary for a specific prefix like <a
-                href="{{ url_for('.summarize_one', prefix='umls') }}"><code>UMLS</code></a>.
-        </p>
-        <ul>
-            <li>
-                Use the <code>/mappings</code> endpoint to look up equivalent entities,
-                for example, <a
-                    href="{{ url_for('.single_source_mappings', curie='hgnc:6893') }}"><code>hgnc:6893</code></a>.
-            </li>
-            <li>
-                Use the <code>/mappings</code> endpoint to look up all mappings between two entities,
-                for example, <a
-                    href="{{ url_for('.all_mappings', source_curie='hgnc:6893', target_curie='ensembl:ENSG00000186868') }}"><code>hgnc:6893</code>
-                and <code>ensembl:ENSG00000186868</code></a>.
-            </li>
-        </ul>
-    </div>
-    <table class="table">
-        <thead>
-        <tr>
-            <th scope="col">CURIE</th>
-            <th scope="col">Description</th>
-        </tr>
-        </thead>
-        <tr>
-            <td><a href="{{ url_for('.canonicalize', curie='hgnc:6893') }}">hgnc:6893</a></td>
-            <td>✅ maps correct identifier to higher priority namespace (ncbigene)</td>
-        </tr>
-        <tr>
-            <td><a href="{{ url_for('.canonicalize', curie='ncbigene:4137') }}">ncbigene:4137</a></td>
-            <td>✅ already priority namespace</td>
-        </tr>
-        <tr>
-            <td><a href="{{ url_for('.canonicalize', curie='DOID:00000') }}">DOID:00000</a></td>
-            <td>❌ invalid identifier</td>
-        </tr>
-        <tr>
-            <td><a href="{{ url_for('.canonicalize', curie='NNN:00000') }}">NNN:00000</a></td>
-            <td>❌ invalid prefix</td>
-        </tr>
-        <tr>
-            <td><a href="{{ url_for('.canonicalize', curie='wikidata:Q42') }}">wikidata:Q42</a></td>
-            <td>❌ unmapped prefix</td>
-        </tr>
-    </table>
-    <div class="card-footer text-center">
-        Developed with ❤️ in 🇩🇪 by <a href="https://github.com/cthoyt">@cthoyt</a>.
-
-        (<span class="text-muted"><a href="https://github.com/pyobo/pyobo">source code</a></span> |
-        <span class="text-muted"><a
-                href="https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html">blog post</a></span>)
-    </div>
-{% endblock %}

pyobo-0.11.1.dist-info/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-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
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.