From d4df7c9cb536ee3f990370ffad66b907aff15f15 Mon Sep 17 00:00:00 2001 From: Matthew McCormick Date: Wed, 7 May 2025 17:30:53 -0400 Subject: [PATCH 01/18] COMP: pnpm-lock updates --- pnpm-lock.yaml | 2929 +++++++++++++++++++++++++++--------------------- 1 file changed, 1680 insertions(+), 1249 deletions(-) diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 02be47e..5eeffbe 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -1,1365 +1,826 @@ -lockfileVersion: '6.0' +lockfileVersion: '9.0' settings: autoInstallPeers: true excludeLinksFromLockfile: false -dependencies: - '@ipld/car': - specifier: ^5.2.6 - version: 5.2.6 - '@ucanto/core': - specifier: ^9.0.1 - version: 9.0.1 - '@ucanto/principal': - specifier: ^9.0.0 - version: 9.0.0 - '@web3-storage/w3up-client': - specifier: ^12.0.0 - version: 12.0.0 - commander: - specifier: ^11.1.0 - version: 11.1.0 - dotenv: - specifier: ^16.3.1 - version: 16.3.1 - files-from-path: - specifier: ^1.0.4 - version: 1.0.4 - imjoy-rpc: - specifier: ^0.5.46 - version: 0.5.46 - -devDependencies: - '@thewtex/setup-micromamba': - specifier: ^1.9.7 - version: 1.9.7 - concurrently: - specifier: ^8.2.2 - version: 8.2.2 - vite: - specifier: ^3.1.4 - version: 3.2.3 +importers: + + .: + dependencies: + '@ipld/car': + specifier: ^5.2.6 + version: 5.4.0 + '@ucanto/core': + specifier: ^9.0.1 + version: 9.0.1 + '@ucanto/principal': + specifier: ^9.0.0 + version: 9.0.2 + '@web3-storage/w3up-client': + specifier: ^12.0.0 + version: 12.5.3(encoding@0.1.13) + commander: + specifier: ^11.1.0 + version: 11.1.0 + dotenv: + specifier: ^16.3.1 + version: 16.5.0 + files-from-path: + specifier: ^1.0.4 + version: 1.1.4 + imjoy-rpc: + specifier: ^0.5.46 + version: 0.5.59 + devDependencies: + '@thewtex/setup-micromamba': + specifier: ^1.9.7 + version: 1.9.7(encoding@0.1.13) + concurrently: + specifier: ^8.2.2 + version: 8.2.2 + vite: + specifier: ^3.1.4 + version: 3.2.11(@types/node@22.15.15) packages: - /@actions/cache@3.2.2: - resolution: {integrity: sha512-6D0Jq5JrLZRQ3VApeQwQkkV20ZZXjXsHNYXd9VjNUdi9E0h93wESpxfMJ2JWLCUCgHNLcfY0v3GjNM+2FdRMlg==} - dependencies: - '@actions/core': 1.10.1 - '@actions/exec': 1.1.1 - '@actions/glob': 0.1.2 - '@actions/http-client': 2.2.0 - '@actions/io': 1.1.3 - '@azure/abort-controller': 1.1.0 - '@azure/ms-rest-js': 2.7.0 - '@azure/storage-blob': 12.17.0 - semver: 6.3.1 - uuid: 3.4.0 - transitivePeerDependencies: - - encoding - dev: true + '@actions/cache@3.3.0': + resolution: {integrity: sha512-+eCsMTIZUEm+QA9GqjollOhCdvRrZ1JV8d9Rp34zVNizBkYITO8dhKczP5Xps1dFzc5n59p7vYVtZrGt18bb5Q==} + deprecated: Please upgrade to v4 or higher. 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github.com/web3-storage/one-webcrypto/5148cd14d5489a8ac4cd38223870e02db15a2382: - resolution: {tarball: https://codeload.github.com/web3-storage/one-webcrypto/tar.gz/5148cd14d5489a8ac4cd38223870e02db15a2382} - name: one-webcrypto - version: 1.0.3 - dev: false + zod@3.24.4: {} From 7664cce31199dd2fece2c4476bc7adc7bacc1167 Mon Sep 17 00:00:00 2001 From: Matthew McCormick Date: Wed, 7 May 2025 17:39:15 -0400 Subject: [PATCH 02/18] ENH: pixi init --- .gitattributes | 2 + .gitignore | 4 + pixi.lock | 260 +++++++++++++++++++++++++++++++++++++++++++++++++ pixi.toml | 11 +++ 4 files changed, 277 insertions(+) create mode 100644 .gitattributes create mode 100644 pixi.lock create mode 100644 pixi.toml diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..887a2c1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore index 9586cf5..f959b6d 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,7 @@ micromamba/ .env oauth2_creds.json data.duckdb + +# pixi environments +.pixi +*.egg-info diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..7a1e6fc --- /dev/null +++ b/pixi.lock @@ -0,0 +1,260 @@ +version: 6 +environments: + default: + channels: + - 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'@azure/core-auth': 1.9.0 - abort-controller: 3.0.0 - form-data: 2.5.3 - node-fetch: 2.7.0(encoding@0.1.13) - tslib: 1.14.1 - tunnel: 0.0.6 - uuid: 8.3.2 - xml2js: 0.5.0 - transitivePeerDependencies: - - encoding - - supports-color - - '@azure/storage-blob@12.27.0': - dependencies: - '@azure/abort-controller': 2.1.2 - '@azure/core-auth': 1.9.0 - '@azure/core-client': 1.9.4 - '@azure/core-http-compat': 2.3.0 - '@azure/core-lro': 2.7.2 - '@azure/core-paging': 1.6.2 - '@azure/core-rest-pipeline': 1.20.0 - '@azure/core-tracing': 1.2.0 - '@azure/core-util': 1.12.0 - '@azure/core-xml': 1.4.5 - '@azure/logger': 1.2.0 - events: 3.3.0 - tslib: 2.8.1 - transitivePeerDependencies: - - supports-color - '@babel/runtime@7.27.1': {} '@esbuild/android-arm@0.15.18': @@ -1273,8 +808,6 @@ snapshots: '@esbuild/linux-loong64@0.15.18': optional: true - '@fastify/busboy@2.1.1': {} - '@ipld/car@5.4.0': dependencies: '@ipld/dag-cbor': 9.2.2 @@ -1362,26 +895,8 @@ snapshots: '@noble/hashes': 1.8.0 '@scure/base': 1.2.5 - '@socket.io/component-emitter@3.1.2': {} - '@storacha/one-webcrypto@https://codeload.github.com/web3-storage/one-webcrypto/tar.gz/9e029e2fd477bd95bb80abd3553bbac704ccc7a6': {} - '@thewtex/setup-micromamba@1.9.7(encoding@0.1.13)': - dependencies: - '@actions/cache': 3.3.0(encoding@0.1.13) - '@actions/core': 1.11.1 - '@actions/exec': 1.1.1 - '@actions/io': 1.1.3 - '@actions/tool-cache': 2.0.2 - fp-ts: 2.16.10 - js-yaml: 4.1.0 - untildify: 5.0.0 - which: 4.0.0 - zod: 3.24.4 - transitivePeerDependencies: - - encoding - - supports-color - '@types/minimatch@3.0.5': {} '@types/node@22.15.15': @@ -1390,14 +905,6 @@ snapshots: '@types/retry@0.12.1': {} - '@typespec/ts-http-runtime@0.2.2': - dependencies: - http-proxy-agent: 7.0.2 - https-proxy-agent: 7.0.6 - tslib: 2.8.1 - transitivePeerDependencies: - - supports-color - '@ucanto/client@9.0.1': dependencies: '@ucanto/core': 10.3.1 @@ -1561,14 +1068,8 @@ snapshots: transitivePeerDependencies: - encoding - abort-controller@3.0.0: - dependencies: - event-target-shim: 5.0.1 - actor@2.3.1: {} - agent-base@7.1.3: {} - ajv-formats@2.1.1(ajv@8.17.1): optionalDependencies: ajv: 8.17.1 @@ -1588,10 +1089,6 @@ snapshots: any-signal@3.0.1: {} - argparse@2.0.1: {} - - asynckit@0.4.0: {} - atomically@2.0.3: dependencies: stubborn-fs: 1.2.5 @@ -1615,11 +1112,6 @@ snapshots: base64-js: 1.5.1 ieee754: 1.2.1 - call-bind-apply-helpers@1.0.2: - dependencies: - es-errors: 1.3.0 - function-bind: 1.1.2 - cborg@4.2.10: {} chalk@4.1.2: @@ -1639,10 +1131,6 @@ snapshots: color-name@1.1.4: {} - combined-stream@1.0.8: - dependencies: - delayed-stream: 1.0.0 - commander@11.1.0: {} concat-map@0.0.1: {} @@ -1678,28 +1166,12 @@ snapshots: dependencies: mimic-fn: 4.0.0 - debug@4.3.7: - dependencies: - ms: 2.1.3 - - debug@4.4.0: - dependencies: - ms: 2.1.3 - - delayed-stream@1.0.0: {} - dot-prop@7.2.0: dependencies: type-fest: 2.19.0 dotenv@16.5.0: {} - dunder-proto@1.0.1: - dependencies: - call-bind-apply-helpers: 1.0.2 - es-errors: 1.3.0 - gopd: 1.2.0 - electron-fetch@1.9.1: dependencies: encoding: 0.1.13 @@ -1710,39 +1182,10 @@ snapshots: dependencies: iconv-lite: 0.6.3 - engine.io-client@6.6.3: - dependencies: - '@socket.io/component-emitter': 3.1.2 - debug: 4.3.7 - engine.io-parser: 5.2.3 - ws: 8.17.1 - xmlhttprequest-ssl: 2.1.2 - transitivePeerDependencies: - - bufferutil - - supports-color - - utf-8-validate - - engine.io-parser@5.2.3: {} - env-paths@3.0.0: {} err-code@3.0.1: {} - es-define-property@1.0.1: {} - - es-errors@1.3.0: {} - - es-object-atoms@1.1.1: - dependencies: - es-errors: 1.3.0 - - es-set-tostringtag@2.1.0: - dependencies: - es-errors: 1.3.0 - get-intrinsic: 1.3.0 - has-tostringtag: 1.0.2 - hasown: 2.0.2 - esbuild-android-64@0.15.18: optional: true @@ -1830,34 +1273,16 @@ snapshots: escalade@3.2.0: {} - event-target-shim@5.0.1: {} - - events@3.3.0: {} - fast-deep-equal@3.1.3: {} fast-fifo@1.3.2: {} fast-uri@3.0.6: {} - fast-xml-parser@5.2.2: - dependencies: - strnum: 2.1.0 - files-from-path@1.1.4: dependencies: graceful-fs: 4.2.11 - form-data@2.5.3: - dependencies: - asynckit: 0.4.0 - combined-stream: 1.0.8 - es-set-tostringtag: 2.1.0 - mime-types: 2.1.35 - safe-buffer: 5.2.1 - - fp-ts@2.16.10: {} - fsevents@2.3.3: optional: true @@ -1865,55 +1290,19 @@ snapshots: get-caller-file@2.0.5: {} - get-intrinsic@1.3.0: - dependencies: - call-bind-apply-helpers: 1.0.2 - es-define-property: 1.0.1 - es-errors: 1.3.0 - es-object-atoms: 1.1.1 - function-bind: 1.1.2 - get-proto: 1.0.1 - gopd: 1.2.0 - has-symbols: 1.1.0 - hasown: 2.0.2 - math-intrinsics: 1.1.0 - get-iterator@1.0.2: {} - get-proto@1.0.1: - dependencies: - dunder-proto: 1.0.1 - es-object-atoms: 1.1.1 - - gopd@1.2.0: {} - graceful-fs@4.2.11: {} has-flag@4.0.0: {} - has-symbols@1.1.0: {} - - has-tostringtag@1.0.2: - dependencies: - has-symbols: 1.1.0 - hasown@2.0.2: dependencies: function-bind: 1.1.2 - http-proxy-agent@7.0.2: - dependencies: - agent-base: 7.1.3 - debug: 4.4.0 - transitivePeerDependencies: - - supports-color - - https-proxy-agent@7.0.6: + hypha-rpc@0.20.53-post-1: dependencies: - agent-base: 7.1.3 - debug: 4.4.0 - transitivePeerDependencies: - - supports-color + '@msgpack/msgpack': 2.8.0 iconv-lite@0.6.3: dependencies: @@ -1921,15 +1310,6 @@ snapshots: ieee754@1.2.1: {} - imjoy-rpc@0.5.59: - dependencies: - '@msgpack/msgpack': 2.8.0 - socket.io-client: 4.8.1 - transitivePeerDependencies: - - bufferutil - - supports-color - - utf-8-validate - inherits@2.0.4: {} ipfs-utils@9.0.14(encoding@0.1.13): @@ -1963,8 +1343,6 @@ snapshots: is-plain-obj@2.1.0: {} - isexe@3.1.1: {} - iso-url@1.2.1: {} it-all@1.0.6: {} @@ -1983,10 +1361,6 @@ snapshots: p-fifo: 1.0.0 readable-stream: 3.6.2 - js-yaml@4.1.0: - dependencies: - argparse: 2.0.1 - json-schema-traverse@1.0.0: {} json-schema-typed@8.0.1: {} @@ -1995,26 +1369,16 @@ snapshots: long@5.3.2: {} - math-intrinsics@1.1.0: {} - merge-options@3.0.4: dependencies: is-plain-obj: 2.1.0 - mime-db@1.52.0: {} - - mime-types@2.1.35: - dependencies: - mime-db: 1.52.0 - mimic-fn@4.0.0: {} minimatch@3.1.2: dependencies: brace-expansion: 1.1.11 - ms@2.1.3: {} - multiformats@11.0.2: {} multiformats@12.1.3: {} @@ -2112,32 +1476,10 @@ snapshots: safer-buffer@2.1.2: {} - sax@1.4.1: {} - - semver@6.3.1: {} - semver@7.7.1: {} shell-quote@1.8.2: {} - socket.io-client@4.8.1: - dependencies: - '@socket.io/component-emitter': 3.1.2 - debug: 4.3.7 - engine.io-client: 6.6.3 - socket.io-parser: 4.2.4 - transitivePeerDependencies: - - bufferutil - - supports-color - - utf-8-validate - - socket.io-parser@4.2.4: - dependencies: - '@socket.io/component-emitter': 3.1.2 - debug: 4.3.7 - transitivePeerDependencies: - - supports-color - source-map-js@1.2.1: {} spawn-command@0.0.2: {} @@ -2160,8 +1502,6 @@ snapshots: dependencies: ansi-regex: 5.0.1 - strnum@2.1.0: {} - stubborn-fs@1.2.5: {} supports-color@7.2.0: @@ -2182,12 +1522,8 @@ snapshots: tree-kill@1.2.2: {} - tslib@1.14.1: {} - tslib@2.8.1: {} - tunnel@0.0.6: {} - type-fest@2.19.0: {} type-fest@4.41.0: {} @@ -2202,16 +1538,8 @@ snapshots: undici-types@6.21.0: {} - undici@5.29.0: - dependencies: - '@fastify/busboy': 2.1.1 - - untildify@5.0.0: {} - util-deprecate@1.0.2: {} - uuid@8.3.2: {} - varint@6.0.0: {} vite@3.2.11(@types/node@22.15.15): @@ -2233,27 +1561,12 @@ snapshots: when-exit@2.1.4: {} - which@4.0.0: - dependencies: - isexe: 3.1.1 - wrap-ansi@7.0.0: dependencies: ansi-styles: 4.3.0 string-width: 4.2.3 strip-ansi: 6.0.1 - ws@8.17.1: {} - - xml2js@0.5.0: - dependencies: - sax: 1.4.1 - xmlbuilder: 11.0.1 - - xmlbuilder@11.0.1: {} - - xmlhttprequest-ssl@2.1.2: {} - y18n@5.0.8: {} yargs-parser@21.1.1: {} @@ -2267,5 +1580,3 @@ snapshots: string-width: 4.2.3 y18n: 5.0.8 yargs-parser: 21.1.1 - - zod@3.24.4: {} From 32bac5b92e2a07694f6623c9213463237f8c5245 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 8 May 2025 14:34:18 -0400 Subject: [PATCH 06/18] COMP: Update hypha-rpc build Re: https://docs.amun.ai/#/migration-guide?id=_1-use-hypha-rpc-instead-of-imjoy-rpc-1 --- pixi.toml | 1 + src/hypha.js | 91 +++++++++++++++++++++++++++++----------------------- 2 files changed, 51 insertions(+), 41 deletions(-) diff --git a/pixi.toml b/pixi.toml index 24f9b2d..c7f4dc4 100644 --- a/pixi.toml +++ b/pixi.toml @@ -7,6 +7,7 @@ version = "0.1.0" [tasks] pnpm-install = { cmd="pnpm install", description="Install JavaScript dependencies", outputs=["node_modules/.pnpm-workspace-state.json"] } +build = { cmd="pnpm build", description="Build JavaScript code", depends-on=["pnpm-install"], outputs=["dist"] } [dependencies] python = "3.13.*" diff --git a/src/hypha.js b/src/hypha.js index 78f3ce8..9f92b84 100644 --- a/src/hypha.js +++ b/src/hypha.js @@ -1,49 +1,58 @@ -import { hyphaWebsocketClient } from 'imjoy-rpc' +import { hyphaWebsocketClient } from "hypha-rpc"; -const SERVER_URL = import.meta.env.VITE_HYPHA_SERVER_URL || document.location.origin +const SERVER_URL = + import.meta.env.VITE_HYPHA_SERVER_URL || document.location.origin; const SELECTORS = { - loginIframe: '#login-iframe', -} + loginIframe: "#login-iframe", +}; class HyphaUploader { - constructor() { - this.token = null - this.server = null - this.loginIframe$ = document.querySelector(SELECTORS.loginIframe) - this.loginIframe$.src = `${document.location.origin}${import.meta.env.BASE_URL}hypha-loading.html` - } - - async loginCallback(context) { - this.login_url = context.login_url - this.key = context.key - - this.loginIframe$.src = context.login_url - } - - async login(uiLoginCallback) { - this.token = await hyphaWebsocketClient.login({ 'server_url': SERVER_URL, login_callback: this.loginCallback.bind(this) }) - const server = await hyphaWebsocketClient.connectToServer({'server_url': SERVER_URL, "token": this.token}) - this.server = server - this.uploader = await server.getService('cmake-w3-externaldata-upload') - uiLoginCallback() - } - - logout() { - const logoutUrl = `${this.login_url}/?key=${this.key}&logout=true` - window.open(logoutUrl, '_blank') - } - - async email() { - const email = await this.uploader.email() - return email - } - - async uploadFile(file, callbacks) { - await this.uploader.uploadFile(file, callbacks) - } + constructor() { + this.token = null; + this.server = null; + this.loginIframe$ = document.querySelector(SELECTORS.loginIframe); + this.loginIframe$.src = `${document.location.origin}${ + import.meta.env.BASE_URL + }hypha-loading.html`; + } + + async loginCallback(context) { + this.login_url = context.login_url; + this.key = context.key; + + this.loginIframe$.src = context.login_url; + } + + async login(uiLoginCallback) { + this.token = await hyphaWebsocketClient.login({ + server_url: SERVER_URL, + login_callback: this.loginCallback.bind(this), + }); + const server = await hyphaWebsocketClient.connectToServer({ + server_url: SERVER_URL, + token: this.token, + }); + this.server = server; + this.uploader = await server.getService("cmake-w3-externaldata-upload"); + uiLoginCallback(); + } + + logout() { + const logoutUrl = `${this.login_url}/?key=${this.key}&logout=true`; + window.open(logoutUrl, "_blank"); + } + + async email() { + const email = await this.uploader.email(); + return email; + } + + async uploadFile(file, callbacks) { + await this.uploader.uploadFile(file, callbacks); + } } -const hypha = new HyphaUploader() +const hypha = new HyphaUploader(); -export default hypha +export default hypha; From 67a04dce99c8f865c582f14e053b411e0eb21cf0 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 8 May 2025 14:39:47 -0400 Subject: [PATCH 07/18] COMP: Bump vite to 6.3.5 --- package.json | 2 +- pnpm-lock.yaml | 762 +++++++++++++++++++++++++++++++------------------ 2 files changed, 491 insertions(+), 273 deletions(-) diff --git a/package.json b/package.json index 3979317..9a0809f 100644 --- a/package.json +++ b/package.json @@ -21,6 +21,6 @@ }, "devDependencies": { "concurrently": "^8.2.2", - "vite": "^3.1.4" + "vite": "^6.3.5" } } diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 78d3fe7..321e840 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+ cpu: [arm64] + os: [android] + + '@esbuild/android-arm@0.25.4': + resolution: {integrity: sha512-QNdQEps7DfFwE3hXiU4BZeOV68HHzYwGd0Nthhd3uCkkEKK7/R6MTgM0P7H7FAs5pU/DIWsviMmEGxEoxIZ+ZQ==} + engines: {node: '>=18'} cpu: [arm] os: [android] - '@esbuild/linux-loong64@0.15.18': - resolution: {integrity: sha512-L4jVKS82XVhw2nvzLg/19ClLWg0y27ulRwuP7lcyL6AbUWB5aPglXY3M21mauDQMDfRLs8cQmeT03r/+X3cZYQ==} - engines: {node: '>=12'} + '@esbuild/android-x64@0.25.4': + resolution: {integrity: sha512-TVhdVtQIFuVpIIR282btcGC2oGQoSfZfmBdTip2anCaVYcqWlZXGcdcKIUklfX2wj0JklNYgz39OBqh2cqXvcQ==} + engines: {node: '>=18'} + cpu: [x64] + os: [android] + + '@esbuild/darwin-arm64@0.25.4': + resolution: {integrity: sha512-Y1giCfM4nlHDWEfSckMzeWNdQS31BQGs9/rouw6Ub91tkK79aIMTH3q9xHvzH8d0wDru5Ci0kWB8b3up/nl16g==} + engines: {node: '>=18'} + cpu: [arm64] + os: [darwin] + + '@esbuild/darwin-x64@0.25.4': + resolution: {integrity: 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optional: true sugarss: optional: true terser: optional: true + tsx: + optional: true + yaml: + optional: true webidl-conversions@3.0.1: resolution: {integrity: sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ==} @@ -802,10 +931,79 @@ snapshots: '@babel/runtime@7.27.1': {} - '@esbuild/android-arm@0.15.18': + '@esbuild/aix-ppc64@0.25.4': + optional: true + + '@esbuild/android-arm64@0.25.4': + optional: true + + '@esbuild/android-arm@0.25.4': + optional: true + + '@esbuild/android-x64@0.25.4': + optional: true + + '@esbuild/darwin-arm64@0.25.4': + optional: true + + '@esbuild/darwin-x64@0.25.4': + optional: true + + '@esbuild/freebsd-arm64@0.25.4': + optional: true + + '@esbuild/freebsd-x64@0.25.4': + optional: true + + '@esbuild/linux-arm64@0.25.4': + optional: true + + '@esbuild/linux-arm@0.25.4': + optional: true + + '@esbuild/linux-ia32@0.25.4': + optional: true + + '@esbuild/linux-loong64@0.25.4': + optional: true + + 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true + + '@rollup/rollup-win32-x64-msvc@4.40.2': + optional: true + '@scure/base@1.2.5': {} '@scure/bip39@1.6.0': @@ -897,6 +1155,8 @@ snapshots: '@storacha/one-webcrypto@https://codeload.github.com/web3-storage/one-webcrypto/tar.gz/9e029e2fd477bd95bb80abd3553bbac704ccc7a6': {} + '@types/estree@1.0.7': {} + '@types/minimatch@3.0.5': {} '@types/node@22.15.15': @@ -1186,90 +1446,33 @@ snapshots: err-code@3.0.1: {} - esbuild-android-64@0.15.18: - optional: true - - esbuild-android-arm64@0.15.18: - optional: true - - esbuild-darwin-64@0.15.18: - optional: true - - esbuild-darwin-arm64@0.15.18: - optional: true - - esbuild-freebsd-64@0.15.18: - optional: true - - esbuild-freebsd-arm64@0.15.18: - optional: true - - esbuild-linux-32@0.15.18: - optional: true - - esbuild-linux-64@0.15.18: - optional: true - - esbuild-linux-arm64@0.15.18: - optional: true - - esbuild-linux-arm@0.15.18: - optional: true - - esbuild-linux-mips64le@0.15.18: - optional: true - - esbuild-linux-ppc64le@0.15.18: - 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{} @@ -1279,6 +1482,10 @@ snapshots: fast-uri@3.0.6: {} + fdir@6.4.4(picomatch@4.0.2): + optionalDependencies: + picomatch: 4.0.2 + files-from-path@1.1.4: dependencies: graceful-fs: 4.2.11 @@ -1286,8 +1493,6 @@ snapshots: fsevents@2.3.3: optional: true - function-bind@1.1.2: {} - get-caller-file@2.0.5: {} get-iterator@1.0.2: {} @@ -1296,10 +1501,6 @@ snapshots: has-flag@4.0.0: {} - hasown@2.0.2: - dependencies: - function-bind: 1.1.2 - hypha-rpc@0.20.53-post-1: dependencies: '@msgpack/msgpack': 2.8.0 @@ -1333,10 +1534,6 @@ snapshots: transitivePeerDependencies: - encoding - is-core-module@2.16.1: - dependencies: - hasown: 2.0.2 - is-electron@2.2.2: {} is-fullwidth-code-point@3.0.0: {} @@ -1415,10 +1612,10 @@ snapshots: '@types/retry': 0.12.1 retry: 0.13.1 - path-parse@1.0.7: {} - picocolors@1.1.1: {} + picomatch@4.0.2: {} + postcss@8.5.3: dependencies: nanoid: 3.3.11 @@ -1456,16 +1653,32 @@ snapshots: require-from-string@2.0.2: {} - resolve@1.22.10: - dependencies: - is-core-module: 2.16.1 - path-parse: 1.0.7 - supports-preserve-symlinks-flag: 1.0.0 - retry@0.13.1: {} - rollup@2.79.2: + rollup@4.40.2: + dependencies: + '@types/estree': 1.0.7 optionalDependencies: + '@rollup/rollup-android-arm-eabi': 4.40.2 + '@rollup/rollup-android-arm64': 4.40.2 + '@rollup/rollup-darwin-arm64': 4.40.2 + '@rollup/rollup-darwin-x64': 4.40.2 + '@rollup/rollup-freebsd-arm64': 4.40.2 + '@rollup/rollup-freebsd-x64': 4.40.2 + '@rollup/rollup-linux-arm-gnueabihf': 4.40.2 + '@rollup/rollup-linux-arm-musleabihf': 4.40.2 + '@rollup/rollup-linux-arm64-gnu': 4.40.2 + '@rollup/rollup-linux-arm64-musl': 4.40.2 + '@rollup/rollup-linux-loongarch64-gnu': 4.40.2 + '@rollup/rollup-linux-powerpc64le-gnu': 4.40.2 + '@rollup/rollup-linux-riscv64-gnu': 4.40.2 + '@rollup/rollup-linux-riscv64-musl': 4.40.2 + '@rollup/rollup-linux-s390x-gnu': 4.40.2 + '@rollup/rollup-linux-x64-gnu': 4.40.2 + '@rollup/rollup-linux-x64-musl': 4.40.2 + '@rollup/rollup-win32-arm64-msvc': 4.40.2 + '@rollup/rollup-win32-ia32-msvc': 4.40.2 + '@rollup/rollup-win32-x64-msvc': 4.40.2 fsevents: 2.3.3 rxjs@7.8.2: @@ -1512,12 +1725,15 @@ snapshots: dependencies: has-flag: 4.0.0 - supports-preserve-symlinks-flag@1.0.0: {} - sync-multihash-sha2@1.0.0: dependencies: '@noble/hashes': 1.8.0 + tinyglobby@0.2.13: + dependencies: + fdir: 6.4.4(picomatch@4.0.2) + picomatch: 4.0.2 + tr46@0.0.3: {} tree-kill@1.2.2: {} @@ -1542,12 +1758,14 @@ snapshots: varint@6.0.0: {} - vite@3.2.11(@types/node@22.15.15): + vite@6.3.5(@types/node@22.15.15): dependencies: - esbuild: 0.15.18 + esbuild: 0.25.4 + fdir: 6.4.4(picomatch@4.0.2) + picomatch: 4.0.2 postcss: 8.5.3 - resolve: 1.22.10 - rollup: 2.79.2 + rollup: 4.40.2 + tinyglobby: 0.2.13 optionalDependencies: '@types/node': 22.15.15 fsevents: 2.3.3 From 8dea826e9a9209876cc2bae5c00283d1e26df993 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 8 May 2025 14:49:20 -0400 Subject: [PATCH 08/18] COMP: Use hypha_rpc instead of imjoy_rpc.hypha Per: https://docs.amun.ai/#/migration-guide?id=_1-use-hypha-rpc-instead-of-imjoy-rpc --- src/register-hypha-uploader-service.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/register-hypha-uploader-service.py b/src/register-hypha-uploader-service.py index 9bbc219..72c5234 100644 --- a/src/register-hypha-uploader-service.py +++ b/src/register-hypha-uploader-service.py @@ -1,6 +1,6 @@ import os import asyncio -from imjoy_rpc.hypha import connect_to_server +from hypha_rpc import connect_to_server from dotenv import load_dotenv load_dotenv() From 539dd8b88a9801d2638ca53c1cb3ffc5c680c0ac Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 8 May 2025 15:33:07 -0400 Subject: [PATCH 09/18] COMP: Update start-hypha Need async-retrying-ng instead of retrying-async for Python 3.10+. --- pixi.lock | 206 ++++++++++++++++----------------- pixi.toml | 5 +- src/hypha-startup-functions.py | 2 +- 3 files changed, 106 insertions(+), 107 deletions(-) diff --git a/pixi.lock 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multidict>=4.0 diff --git a/pixi.toml b/pixi.toml index c7f4dc4..6e747fc 100644 --- a/pixi.toml +++ b/pixi.toml @@ -8,16 +8,17 @@ version = "0.1.0" [tasks] pnpm-install = { cmd="pnpm install", description="Install JavaScript dependencies", outputs=["node_modules/.pnpm-workspace-state.json"] } build = { cmd="pnpm build", description="Build JavaScript code", depends-on=["pnpm-install"], outputs=["dist"] } +start-hypha = { cmd="pnpm start-hypha", description="Start the Hypha server", depends-on=["build"] } [dependencies] -python = "3.13.*" +python = "3.11.*" pnpm = ">=10.10.0,<11" [pypi-dependencies] duckdb = ">=1.2.2, <2" mailjet-rest = ">=1.4.0, <2" python-dotenv = ">=1.1.0, <2" -retrying-async = ">=2.0.0, <3" hypha = { version=">=0.20.51.post4, <0.21", extras=["server-apps"] } hypha-rpc = ">=0.20.53, <0.21" redis = "==5.2.0" +async-retrying-ng = ">=0.1.3, <0.2" diff --git a/src/hypha-startup-functions.py b/src/hypha-startup-functions.py index c1b944b..441bce2 100644 --- a/src/hypha-startup-functions.py +++ b/src/hypha-startup-functions.py @@ -1,6 +1,6 @@ """Startup function file for Hypha.""" -from retrying_async import retry +from async_retrying_ng import retry from uploader import uploader From 7d0ad23bdca8cba5fa9a48cc5879e6d556fd1af3 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 8 May 2025 15:36:23 -0400 Subject: [PATCH 10/18] DOC: remove Kitware's HTTP server as the list of providers No longer used. --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index c4385e0..8139f66 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,6 @@ the following: - Peer [IPFS](https://ipfs.io/) nodes - [web3.storage](https://web3.storage/) - [pinata.cloud](https://pinata.cloud) -- Kitware\'s HTTP Server *Note: This currently requires an extended version of the ExternalData.cmake module developed in the [CMakeIPFSExternalData repository](https://github.com/InsightSoftwareConsortium/CMakeIPFSExternalData). This has not been integrated into upstream CMake due to the availability of C++ CID verification code to complete the feature set in a portable way.* From 46177ef3348ffc9f1f92b74cb1ab97e0c18e8a52 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Thu, 8 May 2025 15:47:50 -0400 Subject: [PATCH 11/18] ENH: Add pixi start task Start the development server. --- pixi.toml | 1 + vite.config.js | 10 ++++++---- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/pixi.toml b/pixi.toml index 6e747fc..6335d5f 100644 --- a/pixi.toml +++ b/pixi.toml @@ -9,6 +9,7 @@ version = "0.1.0" pnpm-install = { cmd="pnpm install", description="Install JavaScript dependencies", outputs=["node_modules/.pnpm-workspace-state.json"] } build = { cmd="pnpm build", description="Build JavaScript code", depends-on=["pnpm-install"], outputs=["dist"] } start-hypha = { cmd="pnpm start-hypha", description="Start the Hypha server", depends-on=["build"] } +start = { cmd="pnpm start", description="Start the application", depends-on=["build"] } [dependencies] python = "3.11.*" diff --git a/vite.config.js b/vite.config.js index bea5b61..d23706d 100644 --- a/vite.config.js +++ b/vite.config.js @@ -1,11 +1,13 @@ -import { defineConfig } from 'vite' +import { defineConfig } from "vite"; -import 'dotenv/config' +import "dotenv/config"; -const base = process.env.VITE_HYPHA_SERVER_URL?.includes('https') ? '/' : '/app/' +const base = process.env.VITE_HYPHA_SERVER_URL?.includes("https") + ? 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python >=3.9 + license: MIT + license_family: MIT + purls: + - pkg:pypi/six?source=hash-mapping + size: 16385 + timestamp: 1733381032766 - pypi: https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl name: sniffio version: 1.3.1 diff --git a/pixi.toml b/pixi.toml index 6335d5f..86fb6be 100644 --- a/pixi.toml +++ b/pixi.toml @@ -14,6 +14,7 @@ start = { cmd="pnpm start", description="Start the application", depends-on=["bu [dependencies] python = "3.11.*" pnpm = ">=10.10.0,<11" +pandas = ">=2.2.3,<3" [pypi-dependencies] duckdb = ">=1.2.2, <2" From 8e55debd6bd2fa52ca4d33532ce98b82fb1b3946 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Mon, 12 May 2025 16:30:38 -0400 Subject: [PATCH 14/18] DOC: Update dependency installation for pixi --- README.md | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 8139f66..b42b023 100644 --- a/README.md +++ b/README.md @@ -70,13 +70,16 @@ git clone https://github.com/InsightSoftwareConsortium/cmake-w3-externaldata-upl cd cmake-w3-externaldata-upload ``` -Change to this directory and install dependencies +Install [pixi](https://pixi.sh/) if not already installed: ```sh -cd cmake-w3-externaldata-upload -npm install --location=global pnpm -pnpm install -pnpm setup-micromamba +curl -fsSL https://pixi.sh/install.sh | sh +``` + +Start with an empty database: + +```sh +cp data.duckdb.empty data.duckdb ``` ### Populate .env @@ -94,11 +97,13 @@ For monitor emails, set the [MailJet](https://mailjet.com) keys `MJ_APIKEY_PUBLI ### Run the dev server ```sh -pnpm dev +pixi run start ``` This starts, a [hypha server](https://ha.amun.ai/#/), a hypha Python service, and the client side build, and serves them locally. +Visit [http://localhost:9000/app/index.html](http://localhost:9000/app/index.html) to view the application. + To test production builds instead, run ```sh From b71b6417bddbba8f49a5549d3b2d56f4cd1e0112 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Mon, 12 May 2025 16:31:17 -0400 Subject: [PATCH 15/18] ENH: Add start-hypha-service and preview tasks to pixi config --- pixi.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pixi.toml b/pixi.toml index 86fb6be..d9d41dd 100644 --- a/pixi.toml +++ b/pixi.toml @@ -10,6 +10,8 @@ pnpm-install = { cmd="pnpm install", description="Install JavaScript dependencie build = { cmd="pnpm build", description="Build JavaScript code", depends-on=["pnpm-install"], outputs=["dist"] } start-hypha = { cmd="pnpm start-hypha", description="Start the Hypha server", depends-on=["build"] } start = { cmd="pnpm start", description="Start the application", depends-on=["build"] } +start-hypha-service = { cmd="pnpm start-hypha-service", description="Start the production Hypha service", depends-on=["build"] } +preview = { cmd="pnpm preview", description="Preview the production web page", depends-on=["build"] } [dependencies] python = "3.11.*" From f1a7a49ad81b1e2f926b4c4b43f26eb77e2d835c Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Mon, 12 May 2025 16:37:30 -0400 Subject: [PATCH 16/18] ENH: Update hypha server url We host hypha.service, and we can explicitly update versions. --- package.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index 9a0809f..65fd17d 100644 --- a/package.json +++ b/package.json @@ -4,10 +4,10 @@ "scripts": { "start": "concurrently -n \"hypha,vite\" --success first -k \"pnpm start-hypha\" \"vite build --sourcemap true --watch\"", "dev": "pnpm start", - "build": "VITE_HYPHA_SERVER_URL=https://hypha.aicell.io vite build", + "build": "VITE_HYPHA_SERVER_URL=https://hypha.website vite build", "start-hypha": "VITE_HYPHA_SERVER_URL=http://localhost:9000 PYTHONPATH=./src hypha --host=0.0.0.0 --port=9000 --startup-functions=./src/hypha-startup-functions.py:hypha_startup --static-mounts=/app/:./dist/", - "start-hypha-service": "VITE_HYPHA_SERVER_URL=https://hypha.aicell.io -e PYTHONPATH=./src python ./src/register-hypha-uploader-service.py", - "preview": "VITE_HYPHA_SERVER_URL=https://hypha.aicell.io vite preview --port 4173" + "start-hypha-service": "VITE_HYPHA_SERVER_URL=https://hypha.website PYTHONPATH=./src python ./src/register-hypha-uploader-service.py", + "preview": "VITE_HYPHA_SERVER_URL=https://hypha.website vite preview --port 4173" }, "dependencies": { "@ipld/car": "^5.2.6", From df35750d4ddac93f3c87fc22153462ba0ee9418d Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 13 May 2025 15:29:38 -0400 Subject: [PATCH 17/18] COMP: Make base directory more explicit And only set to "/" for the "build" script, used for the netlify deployment. --- .gitignore | 3 +++ package.json | 2 +- vite.config.js | 4 +--- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index f959b6d..fbc9c77 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,6 @@ data.duckdb # pixi environments .pixi *.egg-info + +# Local Netlify folder +.netlify diff --git a/package.json b/package.json index 65fd17d..d89819a 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,7 @@ "scripts": { "start": "concurrently -n \"hypha,vite\" --success first -k \"pnpm start-hypha\" \"vite build --sourcemap true --watch\"", "dev": "pnpm start", - "build": "VITE_HYPHA_SERVER_URL=https://hypha.website vite build", + "build": "VITE_HYPHA_SERVER_URL=https://hypha.website BASE_DIR=/ vite build", "start-hypha": "VITE_HYPHA_SERVER_URL=http://localhost:9000 PYTHONPATH=./src hypha --host=0.0.0.0 --port=9000 --startup-functions=./src/hypha-startup-functions.py:hypha_startup --static-mounts=/app/:./dist/", "start-hypha-service": "VITE_HYPHA_SERVER_URL=https://hypha.website PYTHONPATH=./src python ./src/register-hypha-uploader-service.py", "preview": "VITE_HYPHA_SERVER_URL=https://hypha.website vite preview --port 4173" diff --git a/vite.config.js b/vite.config.js index d23706d..4f69b7a 100644 --- a/vite.config.js +++ b/vite.config.js @@ -2,9 +2,7 @@ import { defineConfig } from "vite"; import "dotenv/config"; -const base = process.env.VITE_HYPHA_SERVER_URL?.includes("https") - ? "/" - : "/app/"; +const base = process.env.BASE_DIR || "/app/"; // https://vitejs.dev/config/ export default defineConfig({ From 6c9a81046f599cfee8f1a2db159062bb8d8b03b4 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 13 May 2025 15:38:06 -0400 Subject: [PATCH 18/18] DOC: Add more details on the production service --- README.md | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index b42b023..027d1c4 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # cmake-w3-externaldata-upload -[![screenshot](./screenshot.png)](https://cmake-w3-externaldata-upload.on.fleek.co/) +[![screenshot](./screenshot.png)](https://content-link-upload.netlify.app) -[CMake Web3 ExternalData Upload UI](https://cmake-w3-externaldata-upload.on.fleek.co/) +[CMake Web3 ExternalData Upload UI](https://content-link-upload.netlify.app) Based on [the web3.storage browser client](https://web3.storage/docs/reference/js-client-library/#store-files) and [w3ui](https://github.com/web3-storage/w3ui). @@ -104,17 +104,15 @@ This starts, a [hypha server](https://ha.amun.ai/#/), a hypha Python service, an Visit [http://localhost:9000/app/index.html](http://localhost:9000/app/index.html) to view the application. -To test production builds instead, run +### Production service -```sh -pnpm start-hypha-service -``` - -in one terminal and +The production server currently runs on a cloud VM with ```sh -pnpm build -pnpm preview +pixi run start-hypha-service ``` -in another. \ No newline at end of file +Running under [supervisord](https://supervisord.org/). + +The content-link-upload.itk.org is served on +https://content-link-upload.netlify.app and built via `pnpm run build`.