Skip to content

Commit ae3f64f

Browse files
manztmanzt
authored
Bump Gosling.js to v0.16.0 (#143)
Co-authored-by: manzt <manzt@users.noreply.github.com>
1 parent c1292b9 commit ae3f64f

File tree

5 files changed

+906
-429
lines changed

5 files changed

+906
-429
lines changed

‎gosling/display.py

+35-89
Original file line numberDiff line numberDiff line change
@@ -1,79 +1,39 @@
1+
from __future__ import annotations
2+
13
import json
24
import uuid
3-
from dataclasses import dataclass
4-
from typing import Any, Dict, Optional
5+
from typing import Any, Dict
56

67
import jinja2
78

89
from gosling.plugin_registry import PluginRegistry
910
from gosling.schema import SCHEMA_VERSION, THEMES
1011

11-
# TODO: This is kind of a mess. Gosling.js can be very finky with its
12-
# peer dependencies in various Jupyter-like environments. This is a
13-
# hacky way to get things working in JupyterLab, Jupyter Notebook,
14-
# VSCode, and Colab consistently.
12+
# TODO: Ideally we could use a single import but this seems to work ok.
1513
HTML_TEMPLATE = jinja2.Template(
1614
"""
1715
<!DOCTYPE html>
1816
<html>
1917
<head>
2018
<style>.error { color: red; }</style>
21-
<link rel="stylesheet" href="{{ higlass_css_url }}">
2219
</head>
2320
<body>
2421
<div id="{{ output_div }}"></div>
2522
<script type="module">
26-
async function loadScript(src) {
27-
return new Promise(resolve => {
28-
const script = document.createElement('script');
29-
script.onload = resolve;
30-
script.src = src;
31-
script.async = false;
32-
document.head.appendChild(script);
33-
});
34-
}
35-
async function loadGosling() {
36-
// Manually load scripts from window namespace since requirejs might not be
37-
// available in all browser environments.
38-
// https://github.com/DanielHreben/requirejs-toggle
39-
if (!window.gosling) {
40-
// https://github.com/DanielHreben/requirejs-toggle
41-
window.__requirejsToggleBackup = {
42-
define: window.define,
43-
require: window.require,
44-
requirejs: window.requirejs,
45-
};
46-
for (const field of Object.keys(window.__requirejsToggleBackup)) {
47-
window[field] = undefined;
48-
}
49-
// load dependencies sequentially
50-
const sources = [
51-
"{{ react_url }}",
52-
"{{ react_dom_url }}",
53-
"{{ pixijs_url }}",
54-
"{{ higlass_js_url }}",
55-
"{{ gosling_url }}",
56-
];
57-
for (const src of sources) await loadScript(src);
58-
// restore requirejs after scripts have loaded
59-
Object.assign(window, window.__requirejsToggleBackup);
60-
delete window.__requirejsToggleBackup;
61-
}
62-
return window.gosling;
63-
};
64-
var el = document.getElementById('{{ output_div }}');
65-
var spec = {{ spec }};
66-
var opt = {{ embed_options }};
67-
loadGosling()
68-
.then(gosling => gosling.embed(el, spec, opt))
69-
.catch(err => {
70-
el.innerHTML = `\
71-
<div class="error">
72-
<p>JavaScript Error: ${error.message}</p>
73-
<p>This usually means there's a typo in your Gosling specification. See the javascript console for the full traceback.</p>
74-
</div>`;
75-
throw error;
76-
});
23+
import { importWithMap } from "https://unpkg.com/dynamic-importmap@0.1.0";
24+
let importMap = {{ import_map }};
25+
let gosling = await importWithMap("gosling.js", importMap);
26+
let el = document.getElementById('{{ output_div }}');
27+
let spec = {{ spec }};
28+
let opt = {{ embed_options }};
29+
gosling.embed(el, spec, opt).catch((err) => {
30+
el.innerHTML = `\
31+
<div class="error">
32+
<p>JavaScript Error: ${error.message}</p>
33+
<p>This usually means there's a typo in your Gosling specification. See the javascript console for the full traceback.</p>
34+
</div>`;
35+
throw error;
36+
});
7737
</script>
7838
</body>
7939
</html>
@@ -83,54 +43,40 @@
8343
GoslingSpec = Dict[str, Any]
8444

8545

86-
@dataclass
87-
class GoslingBundle:
88-
react: str
89-
react_dom: str
90-
pixijs: str
91-
higlass_js: str
92-
higlass_css: str
93-
gosling: str
94-
95-
96-
def get_display_dependencies(
46+
def get_gosling_import_map(
9747
gosling_version: str = SCHEMA_VERSION.lstrip("v"),
98-
higlass_version: str = "~1.12",
99-
react_version: str = "17",
48+
higlass_version: str = "1.13",
49+
react_version: str = "18",
10050
pixijs_version: str = "6",
101-
base_url: str = "https://unpkg.com",
102-
) -> GoslingBundle:
103-
return GoslingBundle(
104-
react=f"{ base_url }/react@{ react_version }/umd/react.production.min.js",
105-
react_dom=f"{ base_url }/react-dom@{ react_version }/umd/react-dom.production.min.js",
106-
pixijs=f"{ base_url }/pixi.js@{ pixijs_version }/dist/browser/pixi.min.js",
107-
higlass_js=f"{ base_url }/higlass@{ higlass_version }/dist/hglib.js",
108-
higlass_css=f"{ base_url }/higlass@{ higlass_version }/dist/hglib.css",
109-
gosling=f"{ base_url }/gosling.js@{ gosling_version }/dist/gosling.js",
110-
)
51+
) -> dict:
52+
return {
53+
"imports": {
54+
"react": f"https://esm.sh/react@{react_version}",
55+
"react-dom": f"https://esm.sh/react-dom@{react_version}",
56+
"pixi": f"https://esm.sh/pixi.js@{pixijs_version}",
57+
"higlass": f"https://esm.sh/higlass@{higlass_version}?external=react,react-dom,pixi",
58+
"gosling.js": f"https://esm.sh/gosling.js@{gosling_version}?external=react,react-dom,pixi,higlass",
59+
}
60+
}
11161

11262

11363
def spec_to_html(
11464
spec: GoslingSpec,
11565
output_div: str = "vis",
116-
embed_options: Optional[Dict[str, Any]] = None,
66+
embed_options: Dict[str, Any] | None = None,
11767
**kwargs,
11868
):
11969
embed_options = embed_options or dict(padding=0, theme=themes.get())
120-
deps = get_display_dependencies(**kwargs)
70+
deps = get_gosling_import_map(**kwargs)
12171

12272
return HTML_TEMPLATE.render(
12373
spec=json.dumps(spec),
12474
embed_options=json.dumps(embed_options),
12575
output_div=output_div,
126-
react_url=deps.react,
127-
react_dom_url=deps.react_dom,
128-
pixijs_url=deps.pixijs,
129-
higlass_js_url=deps.higlass_js,
130-
higlass_css_url=deps.higlass_css,
131-
gosling_url=deps.gosling,
76+
import_map=json.dumps(deps),
13277
)
13378

79+
13480
class Renderer:
13581
def __init__(self, output_div: str = "jupyter-gosling-{}", **kwargs: Any):
13682
self._output_div = output_div

‎gosling/schema/__init__.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
# flake8: noqa
22
from .core import *
33
from .channels import *
4-
SCHEMA_VERSION = 'v0.9.31'
5-
SCHEMA_URL = 'https://raw.githubusercontent.com/gosling-lang/gosling.js/v0.9.31/schema/gosling.schema.json'
4+
SCHEMA_VERSION = 'v0.16.0'
5+
SCHEMA_URL = 'https://raw.githubusercontent.com/gosling-lang/gosling.js/v0.16.0/src/gosling-schema/gosling.schema.json'
66
THEMES = {'dark', 'ensembl', 'excel', 'ggplot', 'google', 'igv', 'jbrowse', 'light', 'ucsc', 'warm', 'washu'}

0 commit comments

Comments
 (0)