From 7b4ba6076ef6fafe5866e7a75aab7dc95b0af282 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Mon, 11 Sep 2023 17:48:14 -0400
Subject: [PATCH 1/8] Update package.json
---
package.json | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/package.json b/package.json
index 7fcc0d8..dab6b6f 100644
--- a/package.json
+++ b/package.json
@@ -12,7 +12,9 @@
"author": "Mark Keller",
"license": "MIT",
"dependencies": {
- "zarr": "^0.4.0"
+ "@zarrita/core": "^0.0.3",
+ "@zarrita/storage": "^0.0.2",
+ "@zarrita/indexing": "^0.0.3"
},
"devDependencies": {
"@babel/core": "^7.9.0",
From f0dea27b05074fd7ab98c45d75f6a75ace83c6b6 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Mon, 11 Sep 2023 17:56:59 -0400
Subject: [PATCH 2/8] Update ZarrMultivecDataFetcher.js
---
src/ZarrMultivecDataFetcher.js | 33 +++++++++++++++------------------
1 file changed, 15 insertions(+), 18 deletions(-)
diff --git a/src/ZarrMultivecDataFetcher.js b/src/ZarrMultivecDataFetcher.js
index 03aae60..46fa799 100644
--- a/src/ZarrMultivecDataFetcher.js
+++ b/src/ZarrMultivecDataFetcher.js
@@ -1,4 +1,6 @@
-import { HTTPStore, openArray, slice } from 'zarr';
+import { FetchStore } from '@zarrita/storage';
+import { open as zarrOpen, root as zarrRoot } from '@zarrita/core';
+import { slice, get as zarrGet } from '@zarrita/indexing';
function multivecChunksToTileDenseArray(chunks, tileShape, isRow) {
// Allocate a Float32Array for the tile (with length tile_size).
@@ -55,7 +57,8 @@ const ZarrMultivecDataFetcher = function ZarrMultivecDataFetcher(HGC, ...args) {
if (dataConfig.url) {
// console.assert(dataConfig.url.endsWith('.zarr'));
// S3 bucket must have a CORS policy to allow reading from any origin.
- this.store = new HTTPStore(dataConfig.url, { supportedMethods: ['GET'] });
+ this.store = new FetchStore(dataConfig.url);
+ this.storeRoot = zarrRoot(this.store);
}
if(dataConfig.row !== undefined) {
@@ -67,14 +70,10 @@ const ZarrMultivecDataFetcher = function ZarrMultivecDataFetcher(HGC, ...args) {
this.tilesetInfoLoading = true;
// Use the tileset_info stored as JSON in file.zarr/.zattrs
- return this.store
- .getItem('.zattrs')
- .then(bytes => {
- const decoder = new TextDecoder('utf-8');
- const json = JSON.parse(decoder.decode(bytes));
- return json;
- })
- .then(attrs => {
+ return this.storeRoot
+ .then(root => zarrOpen(root))
+ .then(grp => {
+ const attrs = grp.attrs;
this.tilesetInfoLoading = false;
const chromSizes = attrs.multiscales.map(d => ([d.name, d.metadata.chromsize]));
@@ -142,7 +141,7 @@ const ZarrMultivecDataFetcher = function ZarrMultivecDataFetcher(HGC, ...args) {
}
tile(z, x, tileId) {
- const { store } = this;
+ const { storeRoot } = this;
return this.tilesetInfo().then(tsInfo => {
// const multiscales = tsInfo.multiscales;
@@ -186,13 +185,11 @@ const ZarrMultivecDataFetcher = function ZarrMultivecDataFetcher(HGC, ...args) {
// since data for each chromosome is stored in a separate zarr array.
return Promise.all(
chrChunks.map(([chrName, zStart, zEnd]) => {
- return openArray({
- store,
- path: `/chromosomes/${chrName}/${resolution}/`,
- mode: 'r',
- }).then(arr => (this.row !== undefined
- ? arr.getRaw([this.row, slice(zStart, zEnd)])
- : arr.get([null, slice(zStart, zEnd)])
+ return (await storeRoot)
+ .then(root => zarrOpen(root.resolve(`/chromosomes/${chrName}/${resolution}/`), { kind: "array" }))
+ .then(arr => (this.row !== undefined
+ ? zarrGet(arr, [this.row, slice(zStart, zEnd)])
+ : zarrGet(arr, [null, slice(zStart, zEnd)])
));
}),
).then(chunks => {
From 345255264bba841c7a3dd465a24c2a34ac2730ce Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Mon, 18 Sep 2023 18:38:23 -0400
Subject: [PATCH 3/8] Use same config as higlass-bigwig-datafetchers
---
.gitignore | 3 +-
babel.config.js | 22 -
bundle.mjs | 19 +
src/demo/viewconfig.js => index.html | 68 +-
package-lock.json | 4288 ++++++++++++
package.json | 72 +-
rollup.demo.config.js | 141 -
rollup.demo.utils.js | 22 -
rollup.pkg.config.js | 88 -
src/ZarrMultivecDataFetcher.js | 17 +-
src/demo/Demo.js | 16 -
src/demo/index.js | 11 -
src/demo/index.scss | 3 -
vite-demo.config.js | 6 +
vite-test.config.js | 34 +
yarn.lock | 9175 --------------------------
16 files changed, 4459 insertions(+), 9526 deletions(-)
delete mode 100644 babel.config.js
create mode 100644 bundle.mjs
rename src/demo/viewconfig.js => index.html (69%)
create mode 100644 package-lock.json
delete mode 100644 rollup.demo.config.js
delete mode 100644 rollup.demo.utils.js
delete mode 100644 rollup.pkg.config.js
delete mode 100644 src/demo/Demo.js
delete mode 100644 src/demo/index.js
delete mode 100644 src/demo/index.scss
create mode 100644 vite-demo.config.js
create mode 100644 vite-test.config.js
delete mode 100644 yarn.lock
diff --git a/.gitignore b/.gitignore
index 1e98f09..ca23b5b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
node_modules/
.DS_Store
build-demo/
-build-pkg/
\ No newline at end of file
+build-pkg/
+dist/
\ No newline at end of file
diff --git a/babel.config.js b/babel.config.js
deleted file mode 100644
index d262a58..0000000
--- a/babel.config.js
+++ /dev/null
@@ -1,22 +0,0 @@
-module.exports = {
- env: {
- test: {
- presets: [
- ["@babel/preset-env", { modules: "commonjs" }],
- "@babel/preset-react"
- ]
- },
- production: {
- presets: [
- ["@babel/preset-env", { modules: false }],
- "@babel/preset-react"
- ]
- },
- development: {
- presets: [
- ["@babel/preset-env", { modules: false }],
- "@babel/preset-react"
- ]
- }
- }
-};
\ No newline at end of file
diff --git a/bundle.mjs b/bundle.mjs
new file mode 100644
index 0000000..643a286
--- /dev/null
+++ b/bundle.mjs
@@ -0,0 +1,19 @@
+import * as esbuild from "esbuild";
+
+const env = process.env.APP_ENV || 'development';
+
+import { NodeGlobalsPolyfillPlugin as globals } from '@esbuild-plugins/node-globals-polyfill';
+import { NodeModulesPolyfillPlugin as builtins } from '@esbuild-plugins/node-modules-polyfill';
+
+esbuild.build({
+ entryPoints: ["src/index.js"],
+ target: 'es2020',
+ format: 'esm',
+ sourcemap: true,
+ bundle: true,
+ minify: env === 'production',
+ outfile: env === 'production' ? 'dist/index.min.js' : 'dist/index.js',
+ plugins: [],
+ external: ['zarrita'],
+ watch: process.env.ESBUILD_MODE === 'watch',
+});
\ No newline at end of file
diff --git a/src/demo/viewconfig.js b/index.html
similarity index 69%
rename from src/demo/viewconfig.js
rename to index.html
index c5af6e9..7f2c334 100644
--- a/src/demo/viewconfig.js
+++ b/index.html
@@ -1,4 +1,58 @@
-const viewconfig = {
+
+
+
+
+ HiGlass Zarr Data Fetcher
+
+
+
+
+
+
+
+
+
+
+
+Here's some text
+
+
+And some other text
+
+
+
+
+