diff --git a/.env.example b/.env.example index 682120f3d..06c46bcd7 100755 --- a/.env.example +++ b/.env.example @@ -2,9 +2,11 @@ NODE_ENV=dev PORT=5420 +# Kubo RPC endpoints IPFS_NODE_URL=http://host.docker.internal:5001 PUBLIC_IPFS_RESOLVER=http://host.docker.internal:5002 +# Kubo path gateway endpoint IPFS_RESOLVER_OVERRIDE=http://host.docker.internal:8089/ipfs ### Database - Postgres diff --git a/.gitignore b/.gitignore index 8977d33b5..1bb951e19 100644 --- a/.gitignore +++ b/.gitignore @@ -15,6 +15,7 @@ ipfs-data/ local-data/ **/node_modules .idea +**/*.iml .composedbRuntimeDefinition.json openalex-importer -sync-server \ No newline at end of file +sync-server diff --git a/.nvmrc b/.nvmrc index 5bacb9a1f..f812e4592 100755 --- a/.nvmrc +++ b/.nvmrc @@ -1 +1 @@ -20.8.1 \ No newline at end of file +20.18.1 \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 1c24d9a2c..b117de67c 100755 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,8 @@ -FROM node:20.8.1-bullseye-slim +FROM node:20.18.1-bullseye-slim VOLUME /root/.yarn -RUN apt-get -qy update && apt-get -qy install openssl curl - -RUN npm install -g npm@9.8.1 +RUN apt-get -qy update && apt-get -qy install openssl curl socat jq RUN mkdir /app RUN chown -R node:node /app diff --git a/Makefile b/Makefile index 958c0f944..a5ef86ecd 100644 --- a/Makefile +++ b/Makefile @@ -4,6 +4,7 @@ build: .env desci-contracts/.env $(MAKE) -C desci-contracts build $(MAKE) -C desci-server install $(MAKE) -C desci-repo install + $(MAKE) -C nodes-lib build .PHONY: sterile sterile: clean-rec diff --git a/desci-models/package-lock.json b/desci-models/package-lock.json deleted file mode 100644 index acb86cd8c..000000000 --- a/desci-models/package-lock.json +++ /dev/null @@ -1,3288 +0,0 @@ -{ - "name": "@desci-labs/desci-models", - "version": "0.2.13", - "lockfileVersion": 3, - "requires": true, - "packages": { - "": { - "name": "@desci-labs/desci-models", - "version": "0.2.13", - "license": "MIT", - "dependencies": { - "jsonld": "^8.1.1", - "schema-dts": "^1.1.2" - }, - "devDependencies": { - "@types/chai": "^4.3.4", - "@types/jsonld": "^1.5.8", - 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"dev": true, - "license": "MIT", - "engines": { - "node": ">=10" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" - } - } - } -} diff --git a/desci-models/package.json b/desci-models/package.json index ba34d9fa4..9a98cecb5 100644 --- a/desci-models/package.json +++ b/desci-models/package.json @@ -1,6 +1,6 @@ { "name": "@desci-labs/desci-models", - "version": "0.2.18", + "version": "0.2.19", "description": "Data models for DeSci Nodes", "main": "dist/index.js", "types": "dist/index.d.ts", @@ -38,4 +38,4 @@ "ts-node": "^10.9.1", "typescript": "^4.9.4" } -} +} \ No newline at end of file diff --git a/desci-models/src/ResearchObject.ts b/desci-models/src/ResearchObject.ts index 594ac8b19..8c6e5594a 100644 --- a/desci-models/src/ResearchObject.ts +++ b/desci-models/src/ResearchObject.ts @@ -404,42 +404,43 @@ export type FileExtension = string; /** A semi-complete selection of license choices */ export type License = - | 'CC-BY-4.0' - | 'CC-BY' - | 'CC-BY-SA-4.0' - | 'CC-BY-SA' - | 'CC-BY-ND-4.0' - | 'CC-BY-ND' - | 'CC-BY-NC-4.0' - | 'CC-BY-NC' - | 'CC-BY-NC-SA-4.0' - | 'CC-BY-NC-SA' - | 'CC-BY-NC-ND-4.0' - | 'CC-BY-NC-ND' - | 'CC0-1.0' + | 'AGPL-3.0' + | 'Apache 2.0' + | 'Apache License 2.0' + | 'Apache-2.0' + | 'BSD-2-Clause' + | 'BSD-3-Clause' | 'CC BY' - | 'CC BY-SA' - | 'CC BY-ND' | 'CC BY-NC' - | 'CC BY-NC-SA' | 'CC BY-NC-ND' + | 'CC BY-NC-SA' + | 'CC BY-ND' + | 'CC BY-SA' + | 'CC-BY' + | 'CC-BY-3.0' + | 'CC-BY-4.0' + | 'CC-BY-NC' + | 'CC-BY-NC-4.0' + | 'CC-BY-NC-ND' + | 'CC-BY-NC-ND-4.0' + | 'CC-BY-NC-SA' + | 'CC-BY-NC-SA-4.0' + | 'CC-BY-ND' + | 'CC-BY-ND-4.0' + | 'CC-BY-SA' + | 'CC-BY-SA-4.0' | 'CC0' + | 'CC0-1.0' + | 'CDDL-1.0' + | 'EPL-2.0' | 'GPL-3.0' + | 'LGPL-2.1' + | 'LGPL-3.0' | 'MIT License' - | 'Apache License 2.0' - | 'Apache 2.0' - | 'Mozilla Public License 2.0' - | 'MPL 2.0' | 'MIT' - | 'BSD-3-Clause' - | 'BSD-2-Clause' - | 'Apache-2.0' - | 'LGPL-3.0' - | 'LGPL-2.1' + | 'MPL 2.0' | 'MPL-2.0' - | 'CDDL-1.0' - | 'EPL-2.0' - | 'AGPL-3.0' + | 'Mozilla Public License 2.0' | 'Unlicense'; /** diff --git a/desci-models/src/automerge.ts b/desci-models/src/automerge.ts index ce9bc3a0e..58021d9c1 100644 --- a/desci-models/src/automerge.ts +++ b/desci-models/src/automerge.ts @@ -60,6 +60,7 @@ export type ManifestActions = cid: string | undefined; } | { type: 'Add Reference'; reference: ResearchObjectReference } - | { type: 'Add References'; reference: ResearchObjectReference[] } + | { type: 'Add References'; references: ResearchObjectReference[] } + | { type: 'Set References'; references: ResearchObjectReference[] } | { type: 'Delete Reference'; referenceId: string } | { type: 'Set Contributors'; contributors: ResearchObjectV1Author[] }; diff --git a/desci-models/yarn.lock b/desci-models/yarn.lock index 61b6d705e..acad7d27c 100644 --- a/desci-models/yarn.lock +++ b/desci-models/yarn.lock @@ -22,7 +22,7 @@ resolved "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.20.10.tgz" integrity sha512-sEnuDPpOJR/fcafHMjpcpGN5M2jbUGUHwmuWKM/YdPzeEDJg8bgmbcWQFUfE32MQjti1koACvoPVsDe8Uq+idg== -"@babel/core@^7.0.0", "@babel/core@^7.7.5": +"@babel/core@^7.7.5": version "7.20.12" resolved "https://registry.npmjs.org/@babel/core/-/core-7.20.12.tgz" integrity sha512-XsMfHovsUYHFMdrIHkZphTN/2Hzzi78R08NuHfDBehym2VsPDL6Zn/JAD/JQdnRvbSsbQc4mVaU1m6JgtTEElg== @@ -239,7 +239,7 @@ "@jridgewell/sourcemap-codec" "^1.4.10" "@jridgewell/trace-mapping" "^0.3.9" -"@jridgewell/resolve-uri@^3.0.3", "@jridgewell/resolve-uri@3.1.0": +"@jridgewell/resolve-uri@3.1.0", "@jridgewell/resolve-uri@^3.0.3": version "3.1.0" resolved "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.0.tgz" integrity sha512-F2msla3tad+Mfht5cJq7LSXcdudKTWCVYUgw6pLFOOHSTtZlj6SWNYAp+AhuqLmWdBO2X5hPrLcu8cVP8fy28w== @@ -249,19 +249,11 @@ resolved "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz" integrity sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw== -"@jridgewell/sourcemap-codec@^1.4.10", "@jridgewell/sourcemap-codec@1.4.14": +"@jridgewell/sourcemap-codec@1.4.14", "@jridgewell/sourcemap-codec@^1.4.10": version "1.4.14" resolved "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.14.tgz" integrity sha512-XPSJHWmi394fuUuzDnGz1wiKqWfo1yXecHQMRf2l6hztTO+nPru658AyDngaBe7isIxEkRsPR3FZh+s7iVa4Uw== -"@jridgewell/trace-mapping@^0.3.9": - 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minimatch "^3.0.4" + minimatch "^3.1.1" once "^1.3.0" path-is-absolute "^1.0.0" @@ -1022,6 +1022,13 @@ js-tokens@^4.0.0: resolved "https://registry.npmjs.org/js-tokens/-/js-tokens-4.0.0.tgz" integrity sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ== +js-yaml@4.1.0: + version "4.1.0" + resolved "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz" + integrity sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA== + dependencies: + argparse "^2.0.1" + js-yaml@^3.13.1: version "3.14.1" resolved "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.1.tgz" @@ -1030,13 +1037,6 @@ js-yaml@^3.13.1: argparse "^1.0.7" esprima "^4.0.0" -js-yaml@4.1.0: - version "4.1.0" - resolved "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz" - integrity sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA== - dependencies: - argparse "^2.0.1" - jsesc@^2.5.1: version "2.5.2" resolved "https://registry.npmjs.org/jsesc/-/jsesc-2.5.2.tgz" @@ -1072,7 +1072,7 @@ ky-universal@^0.11.0: abort-controller "^3.0.0" node-fetch "^3.2.10" -ky@^0.33.3, ky@>=0.31.4: +ky@^0.33.3: version "0.33.3" resolved "https://registry.npmjs.org/ky/-/ky-0.33.3.tgz" integrity sha512-CasD9OCEQSFIam2U8efFK81Yeg8vNMTBUqtMOHlrcWQHqUX3HeCl9Dr31u4toV7emlH8Mymk5+9p0lL6mKb/Xw== @@ -1137,13 +1137,6 @@ make-error@^1.1.1: resolved "https://registry.npmjs.org/make-error/-/make-error-1.3.6.tgz" integrity sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw== -minimatch@^3.0.4, minimatch@^3.1.1: - 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version "8.1.1" - resolved "https://registry.npmjs.org/supports-color/-/supports-color-8.1.1.tgz" - integrity sha512-MpUEN2OodtUzxvKQl72cUF7RQ5EiHsGvSsVG0ia9c5RbWGL2CI4C7EpPS8UTBIplnlzZiNuV56w+FuNxy3ty2Q== - dependencies: - has-flag "^4.0.0" - test-exclude@^6.0.0: version "6.0.0" resolved "https://registry.npmjs.org/test-exclude/-/test-exclude-6.0.0.tgz" @@ -1608,7 +1608,7 @@ typescript@^3.0.0: resolved "https://registry.npmjs.org/typescript/-/typescript-3.9.10.tgz" integrity sha512-w6fIxVE/H1PkLKcCPsFqKE7Kv7QUwhU8qQY2MueZXWx5cPZdwFupLgKK3vntcK98BtNHZtAF4LA/yl2a7k8R6Q== -typescript@^4.9.4, typescript@>=2.7, typescript@>=4.1.0: +typescript@^4.9.4: version "4.9.4" resolved "https://registry.npmjs.org/typescript/-/typescript-4.9.4.tgz" integrity sha512-Uz+dTXYzxXXbsFpM86Wh3dKCxrQqUcVMxwU54orwlJjOpO3ao8L7j5lH+dWfTwgCwIuM9GQ2kvVotzYJMXTBZg== @@ -1643,7 +1643,7 @@ v8-compile-cache-lib@^3.0.1: resolved "https://registry.npmjs.org/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz" integrity sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg== -web-streams-polyfill@^3.0.3, web-streams-polyfill@>=3.2.1: +web-streams-polyfill@^3.0.3: version "3.2.1" resolved "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.2.1.tgz" integrity sha512-e0MO3wdXWKrLbL0DgGnUV7WHVuw9OUvL4hjgnPkIeEvESk74gAITi5G606JtZPp39cd8HA9VQzCIvA49LpPN5Q== @@ -1718,6 +1718,11 @@ yallist@^4.0.0: resolved "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz" integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A== +yargs-parser@20.2.4: + version "20.2.4" + resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.4.tgz" + integrity sha512-WOkpgNhPTlE73h4VFAFsOnomJVaovO8VqLDzy5saChRBFQFBoMYirowyW+Q9HB4HFF4Z7VZTiG3iSzJJA29yRA== + yargs-parser@^18.1.2: version "18.1.3" resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-18.1.3.tgz" @@ -1731,11 +1736,6 @@ yargs-parser@^20.2.2: resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz" integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w== -yargs-parser@20.2.4: - version "20.2.4" - resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.4.tgz" - integrity sha512-WOkpgNhPTlE73h4VFAFsOnomJVaovO8VqLDzy5saChRBFQFBoMYirowyW+Q9HB4HFF4Z7VZTiG3iSzJJA29yRA== - yargs-unparser@2.0.0: version "2.0.0" resolved "https://registry.npmjs.org/yargs-unparser/-/yargs-unparser-2.0.0.tgz" @@ -1746,6 +1746,19 @@ yargs-unparser@2.0.0: flat "^5.0.2" is-plain-obj "^2.1.0" +yargs@16.2.0: + version "16.2.0" + resolved "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz" + integrity sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw== + dependencies: + cliui "^7.0.2" + escalade "^3.1.1" + get-caller-file "^2.0.5" + require-directory "^2.1.1" + string-width "^4.2.0" + y18n "^5.0.5" + yargs-parser "^20.2.2" + yargs@^15.0.2: version "15.4.1" resolved "https://registry.npmjs.org/yargs/-/yargs-15.4.1.tgz" @@ -1763,19 +1776,6 @@ yargs@^15.0.2: y18n "^4.0.0" yargs-parser "^18.1.2" -yargs@16.2.0: - version "16.2.0" - resolved "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz" - integrity sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw== - dependencies: - cliui "^7.0.2" - escalade "^3.1.1" - get-caller-file "^2.0.5" - require-directory "^2.1.1" - string-width "^4.2.0" - y18n "^5.0.5" - yargs-parser "^20.2.2" - yn@3.1.1: version "3.1.1" resolved "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz" diff --git a/desci-repo/.eslintrc.cjs b/desci-repo/.eslintrc.cjs new file mode 100755 index 000000000..3f766f768 --- /dev/null +++ b/desci-repo/.eslintrc.cjs @@ -0,0 +1,44 @@ +module.exports = { + parser: '@typescript-eslint/parser', + + extends: ['plugin:@typescript-eslint/recommended', 'prettier', 'plugin:prettier/recommended'], + + plugins: ['@typescript-eslint', 'import'], + + rules: { + // General + '@typescript-eslint/no-unused-vars': 0, + '@typescript-eslint/explicit-module-boundary-types': 0, + '@typescript-eslint/no-explicit-any': 0, + '@typescript-eslint/no-non-null-assertion': 0, + '@typescript-eslint/ban-ts-comment': 0, + '@typescript-eslint/no-empty-interface': 0, + + // Import + 'import/order': [ + 'error', + { + groups: ['builtin', 'external', 'internal', 'parent', 'sibling'], + 'newlines-between': 'always', + alphabetize: { + order: 'asc', + caseInsensitive: true, + }, + }, + ], + }, + + parserOptions: { + ecmaVersion: 2018, + sourceType: 'module', + }, + + settings: { + 'import/resolver': { + node: { + extensions: ['.js', '.jsx', '.ts', '.tsx'], + moduleDirectory: ['node_modules', 'src/', '/test'], + }, + }, + }, +}; diff --git a/desci-repo/package.json b/desci-repo/package.json index 740c5882e..5ba2d559f 100644 --- a/desci-repo/package.json +++ b/desci-repo/package.json @@ -41,13 +41,16 @@ "@automerge/automerge-repo-storage-nodefs": "^1.0.19", "@types/chai": "^4.3.11", "@types/cors": "^2.8.17", + "@types/deep-equal": "^1.0.4", "@types/express": "^4.17.21", "@types/jsonwebtoken": "^9.0.5", "@types/mocha": "^10.0.6", "@types/morgan": "^1.9.9", "@types/pg": "^8.10.9", + "@types/uuid": "^10.0.0", "@types/ws": "^8.5.10", "@typescript-eslint/eslint-plugin": "^6.13.1", + "@typescript-eslint/parser": "^8.14.0", "chai": "4.3.4", "dotenv-cli": "^7.3.0", "eslint": "^8.55.0", @@ -68,7 +71,7 @@ "typescript": "5.1.6" }, "dependencies": { - "@desci-labs/desci-models": "0.2.11", + "@desci-labs/desci-models": "^0.2.19", "@sentry/node": "8.29.0", "@sentry/profiling-node": "8.32.0", "@sentry/tracing": "^7.84.0", diff --git a/desci-repo/src/config.ts b/desci-repo/src/config.ts index 20a668d30..cb06c9b0d 100644 --- a/desci-repo/src/config.ts +++ b/desci-repo/src/config.ts @@ -3,4 +3,4 @@ export const PUBLIC_IPFS_PATH = ? `http://host.docker.internal:8089/ipfs` : process.env.NODE_ENV === 'test' ? 'http://host.docker.internal:8091/ipfs' - : 'https://ipfs.desci.com/ipfs'; \ No newline at end of file + : 'https://ipfs.desci.com/ipfs'; diff --git a/desci-repo/src/controllers/nodes/documents.ts b/desci-repo/src/controllers/nodes/documents.ts index f4f8f271c..90a8fc593 100644 --- a/desci-repo/src/controllers/nodes/documents.ts +++ b/desci-repo/src/controllers/nodes/documents.ts @@ -1,16 +1,18 @@ +import { Doc } from '@automerge/automerge'; +import { AutomergeUrl, DocumentId } from '@automerge/automerge-repo'; +import { ManifestActions } from '@desci-labs/desci-models'; import { Request, Response } from 'express'; -import { ResearchObjectDocument } from '../../types.js'; +import { ZodError } from 'zod'; + +import { findNodeByUuid } from '../../db/index.js'; import { logger as parentLogger } from '../../logger.js'; -import { AutomergeUrl, DocumentId } from '@automerge/automerge-repo'; import { RequestWithNode } from '../../middleware/guard.js'; import { backendRepo } from '../../repo.js'; import { getAutomergeUrl, getDocumentUpdater } from '../../services/manifestRepo.js'; -import { findNodeByUuid, query } from '../../db/index.js'; -import { Doc } from '@automerge/automerge'; -import { ZodError } from 'zod'; +import { ResearchObjectDocument } from '../../types.js'; import { actionsSchema } from '../../validators/schema.js'; + import { ensureUuidEndsWithDot } from './utils.js'; -import { ManifestActions } from '@desci-labs/desci-models'; export const createNodeDocument = async function (req: Request, res: Response) { const logger = parentLogger.child({ module: 'createNodeDocument', body: req.body, param: req.params }); @@ -22,7 +24,8 @@ export const createNodeDocument = async function (req: Request, res: Response) { return; } - let { uuid, manifest } = req.body; + let uuid = req.body.uuid; + const manifest = req.body.manifest; uuid = ensureUuidEndsWithDot(uuid); logger.info({ peerId: backendRepo.networkSubsystem.peerId, uuid }, '[Backend REPO]:'); const handle = backendRepo.create(); diff --git a/desci-repo/src/controllers/nodes/utils.ts b/desci-repo/src/controllers/nodes/utils.ts index f3891315d..e73cf568d 100644 --- a/desci-repo/src/controllers/nodes/utils.ts +++ b/desci-repo/src/controllers/nodes/utils.ts @@ -1,9 +1,10 @@ -import axios from 'axios'; import { ResearchObjectV1 } from '@desci-labs/desci-models'; +import axios from 'axios'; + import { PUBLIC_IPFS_PATH } from '../../config.js'; -import { logger as parentLogger } from '../../logger.js'; -import { createIpfsUnresolvableError } from '../../lib/errors.js'; import { findNodeByUuid } from '../../db/index.js'; +import { createIpfsUnresolvableError } from '../../lib/errors.js'; +import { logger as parentLogger } from '../../logger.js'; import { Node } from '../../middleware/guard.js'; export async function getLatestManifest( diff --git a/desci-repo/src/lib/PostgresStorageAdapter.ts b/desci-repo/src/lib/PostgresStorageAdapter.ts index f8c3876c4..787236617 100644 --- a/desci-repo/src/lib/PostgresStorageAdapter.ts +++ b/desci-repo/src/lib/PostgresStorageAdapter.ts @@ -2,8 +2,8 @@ import path from 'path'; import { Chunk, StorageAdapter, StorageKey } from '@automerge/automerge-repo'; -import { logger as parentLogger } from '../logger.js'; import { query } from '../db/index.js'; +import { logger as parentLogger } from '../logger.js'; const logger = parentLogger.child({ module: 'PostgresStorageAdapter' }); export class PostgresStorageAdapter extends StorageAdapter { diff --git a/desci-repo/src/logger.ts b/desci-repo/src/logger.ts index 22ede5be2..bab514035 100644 --- a/desci-repo/src/logger.ts +++ b/desci-repo/src/logger.ts @@ -1,8 +1,10 @@ -import { pino } from 'pino'; -import { fileURLToPath } from 'url'; +import { AsyncLocalStorage } from 'async_hooks'; import path from 'path'; +import { fileURLToPath } from 'url'; + +import { pino } from 'pino'; + import { pool } from './db/index.js'; -import { AsyncLocalStorage } from 'async_hooks'; export const als = new AsyncLocalStorage(); diff --git a/desci-repo/src/middleware/ensureApiKey.ts b/desci-repo/src/middleware/ensureApiKey.ts index 28433065e..b5fbfa070 100644 --- a/desci-repo/src/middleware/ensureApiKey.ts +++ b/desci-repo/src/middleware/ensureApiKey.ts @@ -1,4 +1,5 @@ import { Request, Response, NextFunction } from 'express'; + import { logger } from '../logger.js'; const REPO_SERVICE_API_KEY = process.env.REPO_SERVICE_SECRET_KEY; diff --git a/desci-repo/src/middleware/guard.ts b/desci-repo/src/middleware/guard.ts index 49665ae7b..02797acfc 100644 --- a/desci-repo/src/middleware/guard.ts +++ b/desci-repo/src/middleware/guard.ts @@ -1,10 +1,11 @@ // import { Node, User } from '@prisma/client'; import { Request, Response, NextFunction } from 'express'; -import { extractAuthToken, extractUserFromToken } from './permissions.js'; +import { query } from '../db/index.js'; import { logger as parentLogger } from '../logger.js'; import { hideEmail } from '../services/user.js'; -import { query } from '../db/index.js'; + +import { extractAuthToken, extractUserFromToken } from './permissions.js'; const logger = parentLogger.child({ module: 'MIDDLEWARE/GUARD' }); diff --git a/desci-repo/src/repo.ts b/desci-repo/src/repo.ts index fe90c1c23..48286004e 100644 --- a/desci-repo/src/repo.ts +++ b/desci-repo/src/repo.ts @@ -4,12 +4,12 @@ import { DocHandleChangePayload, DocHandleEvents, PeerId, Repo, RepoConfig } fro import { NodeWSServerAdapter } from '@automerge/automerge-repo-network-websocket'; import { WebSocketServer } from 'ws'; +import { ensureUuidEndsWithDot } from './controllers/nodes/utils.js'; +import * as db from './db/index.js'; import { PostgresStorageAdapter } from './lib/PostgresStorageAdapter.js'; import { logger as parentLogger } from './logger.js'; import { verifyNodeDocumentAccess } from './services/nodes.js'; import { ResearchObjectDocument } from './types.js'; -import * as db from './db/index.js'; -import { ensureUuidEndsWithDot } from './controllers/nodes/utils.js'; export const socket = new WebSocketServer({ port: process.env.WS_PORT ? parseInt(process.env.WS_PORT) : 5445, diff --git a/desci-repo/src/routes/v1/nodes.ts b/desci-repo/src/routes/v1/nodes.ts index 6714813db..d039cea44 100644 --- a/desci-repo/src/routes/v1/nodes.ts +++ b/desci-repo/src/routes/v1/nodes.ts @@ -1,4 +1,5 @@ import { Router } from 'express'; + import { createNodeDocument, dispatchDocumentActions, diff --git a/desci-repo/src/server.ts b/desci-repo/src/server.ts index f8b95d724..d63bffcf8 100644 --- a/desci-repo/src/server.ts +++ b/desci-repo/src/server.ts @@ -1,32 +1,27 @@ +import type { Server as HttpServer } from 'http'; +import path from 'path'; +import { fileURLToPath } from 'url'; + import * as Sentry from '@sentry/node'; import { nodeProfilingIntegration } from '@sentry/profiling-node'; - -const ENABLE_TELEMETRY = process.env.NODE_ENV === 'production'; -const IS_DEV = !ENABLE_TELEMETRY; - -// @ts-check import 'dotenv/config'; import 'reflect-metadata'; -import path from 'path'; - +import bodyParser from 'body-parser'; +import cors from 'cors'; import express from 'express'; import type { Express, Request } from 'express'; -import cors from 'cors'; -import bodyParser from 'body-parser'; - -import type { Server as HttpServer } from 'http'; +import { pinoHttp } from 'pino-http'; import { v4 } from 'uuid'; import { als, logger } from './logger.js'; +import { RequestWithUser } from './middleware/guard.js'; +import { extractAuthToken, extractUserFromToken } from './middleware/permissions.js'; +import { socket as wsSocket } from './repo.js'; import routes from './routes/index.js'; // import SocketServer from './wsServer.js'; -import { fileURLToPath } from 'url'; -import { socket as wsSocket } from './repo.js'; - -import { extractAuthToken, extractUserFromToken } from './middleware/permissions.js'; -import { pinoHttp } from 'pino-http'; -import { RequestWithUser } from './middleware/guard.js'; +const ENABLE_TELEMETRY = process.env.NODE_ENV === 'production'; +const IS_DEV = !ENABLE_TELEMETRY; const __filename = fileURLToPath(import.meta.url); const __dirname = path.dirname(__filename); diff --git a/desci-repo/src/services/manifestRepo.ts b/desci-repo/src/services/manifestRepo.ts index b82b6e1d0..a071e2794 100644 --- a/desci-repo/src/services/manifestRepo.ts +++ b/desci-repo/src/services/manifestRepo.ts @@ -196,22 +196,6 @@ export const getDocumentUpdater = (documentId: DocumentId) => { { time: Date.now(), message: action.type }, ); break; - case 'Delete Component': - handle.change( - (document) => { - deleteComponent(document, action.path); - }, - { time: Date.now(), message: action.type }, - ); - break; - case 'Update Component': - handle.change( - (document) => { - updateManifestComponent(document, action.component, action.componentIndex); - }, - { time: Date.now(), message: action.type }, - ); - break; case 'Upsert Component': handle.change( (document) => { @@ -247,7 +231,7 @@ export const getDocumentUpdater = (documentId: DocumentId) => { ); break; case 'Pin Component': - let componentIndex = latestDocument?.manifest.components.findIndex((c) => c.payload?.path === action.path); + const componentIndex = latestDocument?.manifest.components.findIndex((c) => c.payload?.path === action.path); if (componentIndex && componentIndex != -1) { handle.change( (document) => { @@ -258,7 +242,7 @@ export const getDocumentUpdater = (documentId: DocumentId) => { } break; case 'UnPin Component': - let index = latestDocument?.manifest.components.findIndex((c) => c.payload?.path === action.path); + const index = latestDocument?.manifest.components.findIndex((c) => c.payload?.path === action.path); if (index && index != -1) { handle.change( (document) => { @@ -336,18 +320,26 @@ export const getDocumentUpdater = (documentId: DocumentId) => { document.manifest.references = []; } - for (const reference of action.reference) { + for (const reference of action.references) { if (!document.manifest.references.find((ref) => ref.id === reference.id)) document.manifest.references.push(reference); } }); break; + case 'Set References': + handle.change((document) => { + if (!document.manifest.references) { + document.manifest.references = []; + } + document.manifest.references = action.references; + }); + break; case 'Delete Reference': if (!action.referenceId) return; const deletedIdx = latestDocument.manifest.references?.findIndex((ref) => ref.id === action.referenceId); - if (deletedIdx !== -1) { + if (deletedIdx !== undefined && deletedIdx !== -1) { handle.change((document) => { - document.manifest.references?.splice(deleteIdx, 1); + document.manifest.references?.splice(deletedIdx, 1); }); } break; @@ -494,6 +486,7 @@ const upsertManifestComponent = (doc: Doc, component: Re } }; +// eslint-disable-next-line @typescript-eslint/ban-types type TypeInitialisers = {} | '' | 0 | []; const getTypeDefault = (value: unknown): TypeInitialisers => { diff --git a/desci-repo/src/services/nodes.ts b/desci-repo/src/services/nodes.ts index 6da88e2e9..6af9f294b 100644 --- a/desci-repo/src/services/nodes.ts +++ b/desci-repo/src/services/nodes.ts @@ -1,4 +1,5 @@ import { DocumentId } from '@automerge/automerge-repo'; + import { query } from '../db/index.js'; import { logger } from '../logger.js'; diff --git a/desci-repo/src/services/user.ts b/desci-repo/src/services/user.ts index 3f8e40d99..6d88dddf1 100644 --- a/desci-repo/src/services/user.ts +++ b/desci-repo/src/services/user.ts @@ -1,5 +1,5 @@ -import { logger as parentLogger } from '../logger.js'; import { query } from '../db/index.js'; +import { logger as parentLogger } from '../logger.js'; export const hideEmail = (email: string) => { return email.replace(/(.{1,1})(.*)(@.*)/, '$1...$3'); diff --git a/desci-repo/src/types.ts b/desci-repo/src/types.ts index 79d6062c8..56f660a18 100644 --- a/desci-repo/src/types.ts +++ b/desci-repo/src/types.ts @@ -4,4 +4,4 @@ export interface ResearchObjectDocument { manifest: ResearchObjectV1; uuid: string; driveClock: string; -} \ No newline at end of file +} diff --git a/desci-repo/src/validators/schema.ts b/desci-repo/src/validators/schema.ts index a93669e47..a5596561e 100644 --- a/desci-repo/src/validators/schema.ts +++ b/desci-repo/src/validators/schema.ts @@ -1,4 +1,3 @@ -import { z } from 'zod'; import { ResearchObjectComponentType, ResearchObjectV1AuthorRole, @@ -8,6 +7,7 @@ import { ManifestActions, ResearchObjectReference, } from '@desci-labs/desci-models'; +import { z } from 'zod'; const researchObject = z .object({ @@ -64,7 +64,7 @@ const componentSchema: z.ZodType = z export const DPID_PATH_REGEX = /^https:\/\/(?dev-beta|beta)\.dpid\.org(?\/\d+)(?\/v\d+)?(?\/root.*)?/m; -export const DOI_REGEX = /(https:\/\/doi.org\/)?(?10.\d{4,9}\/[-._;()/:A-Z0-9]+$)/i; +export const DOI_REGEX = /(https:\/\/doi.org\/)?(?10.\d{4,9}\/[-+<>._;()/:A-Z0-9]+$)/i; const referenceSchema: z.ZodType = z .object({ @@ -98,6 +98,7 @@ export const actionsSchema = z.array( z.object({ type: z.literal('Update CoverImage'), cid: z.string().optional() }), z.object({ type: z.literal('Add Reference'), reference: referenceSchema }), z.object({ type: z.literal('Add References'), references: z.array(referenceSchema) }), + z.object({ type: z.literal('Set References'), references: z.array(referenceSchema) }), z.object({ type: z.literal('Delete Reference'), referenceId: z.string() }), ]), ); diff --git a/desci-repo/src/validators/test/schema.spec.ts b/desci-repo/src/validators/test/schema.spec.ts index fbb4e24f5..590e57224 100644 --- a/desci-repo/src/validators/test/schema.spec.ts +++ b/desci-repo/src/validators/test/schema.spec.ts @@ -1,7 +1,4 @@ import 'mocha'; -import { expect } from 'chai'; -import { actionsSchema } from '../../validators/schema.js'; -import { ZodError } from 'zod'; import { CodeComponent, ExternalLinkComponent, @@ -11,6 +8,10 @@ import { ResearchObjectV1AuthorRole, ResearchObjectV1Component, } from '@desci-labs/desci-models'; +import { expect } from 'chai'; +import { ZodError } from 'zod'; + +import { actionsSchema } from '../../validators/schema.js'; describe('ManifestActions Schema', () => { describe('Valid Actions', () => { @@ -312,8 +313,9 @@ describe('ManifestActions Schema', () => { console.log('error' in validated && validated.error); expect(validated.success).to.be.true; }); + it('should validate add new references', () => { - let validated = actionsSchema.safeParse([ + const validated = actionsSchema.safeParse([ { type: 'Add References', references: [ @@ -325,8 +327,21 @@ describe('ManifestActions Schema', () => { expect(validated.success).to.be.true; }); + it('should validate ovewriting references', () => { + const validated = actionsSchema.safeParse([ + { + type: 'Set References', + references: [ + { id: 'https://doi.org/10.1111/af325', type: 'doi' }, + { id: 'https://beta.dpid.org/165/v6', type: 'dpid' }, + ], + }, + ]); + expect(validated.success).to.be.true; + }); + it('should reject invalid references', () => { - let validated = actionsSchema.safeParse([ + const validated = actionsSchema.safeParse([ { type: 'Add References', references: [ @@ -339,7 +354,7 @@ describe('ManifestActions Schema', () => { }); it('should reject reference Id/type mismatch', () => { - let validated = actionsSchema.safeParse([ + const validated = actionsSchema.safeParse([ { type: 'Add References', references: [ @@ -370,7 +385,7 @@ describe('ManifestActions Schema', () => { }); it('should validate delete existing reference', () => { - let validated = actionsSchema.safeParse([ + const validated = actionsSchema.safeParse([ { type: 'Delete Reference', referenceId: 'https://doi.org/10.111/af325' }, ]); expect(validated.success).to.be.true; diff --git a/desci-repo/yarn.lock b/desci-repo/yarn.lock index e6744e445..0f924b725 100644 --- a/desci-repo/yarn.lock +++ b/desci-repo/yarn.lock @@ -131,10 +131,10 @@ dependencies: "@jridgewell/trace-mapping" "0.3.9" -"@desci-labs/desci-models@0.2.11": - version "0.2.11" - resolved "https://registry.yarnpkg.com/@desci-labs/desci-models/-/desci-models-0.2.11.tgz#3dabeeb606ce34f98597c36a92bb1235ebd88265" - integrity sha512-U+Svmqn2vzK967zoHek2oxNkELowKL87JSplh41V7eMjZMUeaDvnkWS5FCbn4YtjDaMOYVHBVV9CpDUWO+dAvQ== +"@desci-labs/desci-models@^0.2.19": + version "0.2.19" + resolved "https://registry.yarnpkg.com/@desci-labs/desci-models/-/desci-models-0.2.19.tgz#430f8e6b6a1967d6b06fc8a36e6c32536e1a4a42" + integrity sha512-XaZyLom2z4vi+A47qS5G1ecc65fw3MxfAKutH1iXrb92AXmxQG7TcH313O3qv4206pIDdNfmJNfgjo4h78cVJw== dependencies: jsonld "^8.1.1" schema-dts "^1.1.2" @@ -808,6 +808,11 @@ dependencies: "@types/node" "*" +"@types/deep-equal@^1.0.4": + version "1.0.4" + resolved "https://registry.yarnpkg.com/@types/deep-equal/-/deep-equal-1.0.4.tgz#c0a854be62d6b9fae665137a6639aab53389a147" + integrity sha512-tqdiS4otQP4KmY0PR3u6KbZ5EWvhNdUoS/jc93UuK23C220lOZ/9TvjfxdPcKvqwwDVtmtSCrnr0p/2dirAxkA== + "@types/express-serve-static-core@^4.17.33": version "4.17.42" resolved "https://registry.npmjs.org/@types/express-serve-static-core/-/express-serve-static-core-4.17.42.tgz" @@ -972,6 +977,11 @@ resolved "https://registry.npmjs.org/@types/strip-json-comments/-/strip-json-comments-0.0.30.tgz" integrity sha512-7NQmHra/JILCd1QqpSzl8+mJRc8ZHz3uDm8YV1Ks9IhK0epEiTw8aIErbvH9PI+6XbqhyIQy3462nEsn7UVzjQ== +"@types/uuid@^10.0.0": + version "10.0.0" + resolved "https://registry.yarnpkg.com/@types/uuid/-/uuid-10.0.0.tgz#e9c07fe50da0f53dc24970cca94d619ff03f6f6d" + integrity sha512-7gqG38EyHgyP1S+7+xomFtL+ZNHcKv6DwNaCZmJmo1vgMugyF3TCnXVg4t1uk89mLNwnLtnY3TpOpCOyp1/xHQ== + "@types/ws@^8.5.10": version "8.5.10" resolved "https://registry.npmjs.org/@types/ws/-/ws-8.5.10.tgz" @@ -996,6 +1006,17 @@ semver "^7.5.4" ts-api-utils "^1.0.1" +"@typescript-eslint/parser@^8.14.0": + version "8.14.0" + resolved "https://registry.yarnpkg.com/@typescript-eslint/parser/-/parser-8.14.0.tgz#0a7e9dbc11bc07716ab2d7b1226217e9f6b51fc8" + integrity sha512-2p82Yn9juUJq0XynBXtFCyrBDb6/dJombnz6vbo6mgQEtWHfvHbQuEa9kAOVIt1c9YFwi7H6WxtPj1kg+80+RA== + dependencies: + "@typescript-eslint/scope-manager" "8.14.0" + "@typescript-eslint/types" "8.14.0" + "@typescript-eslint/typescript-estree" "8.14.0" + "@typescript-eslint/visitor-keys" "8.14.0" + debug "^4.3.4" + "@typescript-eslint/scope-manager@6.20.0": version "6.20.0" resolved "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-6.20.0.tgz" @@ -1004,6 +1025,14 @@ "@typescript-eslint/types" "6.20.0" "@typescript-eslint/visitor-keys" "6.20.0" +"@typescript-eslint/scope-manager@8.14.0": + version "8.14.0" + resolved "https://registry.yarnpkg.com/@typescript-eslint/scope-manager/-/scope-manager-8.14.0.tgz#01f37c147a735cd78f0ff355e033b9457da1f373" + integrity sha512-aBbBrnW9ARIDn92Zbo7rguLnqQ/pOrUguVpbUwzOhkFg2npFDwTgPGqFqE0H5feXcOoJOfX3SxlJaKEVtq54dw== + dependencies: + "@typescript-eslint/types" "8.14.0" + "@typescript-eslint/visitor-keys" "8.14.0" + "@typescript-eslint/type-utils@6.20.0": version "6.20.0" resolved "https://registry.npmjs.org/@typescript-eslint/type-utils/-/type-utils-6.20.0.tgz" @@ -1019,6 +1048,11 @@ resolved "https://registry.npmjs.org/@typescript-eslint/types/-/types-6.20.0.tgz" integrity sha512-MM9mfZMAhiN4cOEcUOEx+0HmuaW3WBfukBZPCfwSqFnQy0grXYtngKCqpQN339X3RrwtzspWJrpbrupKYUSBXQ== +"@typescript-eslint/types@8.14.0": + version "8.14.0" + resolved "https://registry.yarnpkg.com/@typescript-eslint/types/-/types-8.14.0.tgz#0d33d8d0b08479c424e7d654855fddf2c71e4021" + integrity sha512-yjeB9fnO/opvLJFAsPNYlKPnEM8+z4og09Pk504dkqonT02AyL5Z9SSqlE0XqezS93v6CXn49VHvB2G7XSsl0g== + "@typescript-eslint/typescript-estree@6.20.0": version "6.20.0" resolved "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-6.20.0.tgz" @@ -1033,6 +1067,20 @@ semver "^7.5.4" ts-api-utils "^1.0.1" +"@typescript-eslint/typescript-estree@8.14.0": + version "8.14.0" + resolved "https://registry.yarnpkg.com/@typescript-eslint/typescript-estree/-/typescript-estree-8.14.0.tgz#a7a3a5a53a6c09313e12fb4531d4ff582ee3c312" + integrity sha512-OPXPLYKGZi9XS/49rdaCbR5j/S14HazviBlUQFvSKz3npr3NikF+mrgK7CFVur6XEt95DZp/cmke9d5i3vtVnQ== + dependencies: + "@typescript-eslint/types" "8.14.0" + "@typescript-eslint/visitor-keys" "8.14.0" + debug "^4.3.4" + fast-glob "^3.3.2" + is-glob "^4.0.3" + minimatch "^9.0.4" + semver "^7.6.0" + ts-api-utils "^1.3.0" + "@typescript-eslint/utils@6.20.0": version "6.20.0" resolved "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-6.20.0.tgz" @@ -1054,6 +1102,14 @@ "@typescript-eslint/types" "6.20.0" eslint-visitor-keys "^3.4.1" +"@typescript-eslint/visitor-keys@8.14.0": + version "8.14.0" + resolved "https://registry.yarnpkg.com/@typescript-eslint/visitor-keys/-/visitor-keys-8.14.0.tgz#2418d5a54669af9658986ade4e6cfb7767d815ad" + integrity sha512-vG0XZo8AdTH9OE6VFRwAZldNc7qtJ/6NLGWak+BtENuEUXGZgFpihILPiBvKXvJ2nFu27XNGC6rKiwuaoMbYzQ== + dependencies: + "@typescript-eslint/types" "8.14.0" + eslint-visitor-keys "^3.4.3" + "@ungap/structured-clone@^1.2.0": version "1.2.0" resolved "https://registry.npmjs.org/@ungap/structured-clone/-/structured-clone-1.2.0.tgz" @@ -2243,7 +2299,7 @@ fast-diff@^1.1.2: resolved "https://registry.npmjs.org/fast-diff/-/fast-diff-1.3.0.tgz" integrity sha512-VxPP4NqbUjj6MaAOafWeUn2cXWLcCtljklUtZf0Ind4XQ+QPtmA0b18zZy0jIQx+ExRVCR/ZQpBmik5lXshNsw== -fast-glob@^3.2.9: +fast-glob@^3.2.9, fast-glob@^3.3.2: version "3.3.2" resolved "https://registry.npmjs.org/fast-glob/-/fast-glob-3.3.2.tgz" integrity sha512-oX2ruAFQwf/Orj8m737Y5adxDQO0LAB7/S5MnxCdTNDd4p6BsyIVsv9JQsATbTSq8KHRpLwIHbVlUNatxd+1Ow== @@ -3294,6 +3350,13 @@ minimatch@^3.0.4, minimatch@^3.0.5, minimatch@^3.1.1, minimatch@^3.1.2: dependencies: brace-expansion "^1.1.7" +minimatch@^9.0.4: + version "9.0.5" + resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-9.0.5.tgz#d74f9dd6b57d83d8e98cfb82133b03978bc929e5" + integrity sha512-G6T0ZX48xgozx7587koeX9Ys2NYy6Gmv//P89sEte9V9whIapMNF4idKxnW2QtCcLiTWlb/wfCabAtAFWhhBow== + dependencies: + brace-expansion "^2.0.1" + minimist@^1.2.0, minimist@^1.2.6: version "1.2.8" resolved "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz" @@ -4264,7 +4327,7 @@ semver@^6.3.1: resolved "https://registry.npmjs.org/semver/-/semver-6.3.1.tgz" integrity sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA== -semver@^7.3.5, semver@^7.5.2: +semver@^7.3.5, semver@^7.5.2, semver@^7.6.0: version "7.6.3" resolved "https://registry.yarnpkg.com/semver/-/semver-7.6.3.tgz#980f7b5550bc175fb4dc09403085627f9eb33143" integrity 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"signal": "SIGINT" } diff --git a/desci-server/package.json b/desci-server/package.json index a75b83a23..fea5187b0 100755 --- a/desci-server/package.json +++ b/desci-server/package.json @@ -61,7 +61,7 @@ "@aws-sdk/client-s3": "^3.537.0", "@desci-labs/desci-codex-lib": "^1.1.7", "@desci-labs/desci-contracts": "^0.2.7", - "@desci-labs/desci-models": "0.2.18", + "@desci-labs/desci-models": "^0.2.19", "@elastic/elasticsearch": "^8.14.0", "@honeycombio/opentelemetry-node": "^0.3.2", "@ipld/dag-pb": "^4.0.0", @@ -178,4 +178,4 @@ "prisma": { "seed": "node --no-warnings=ExperimentalWarning --loader ts-node/esm prisma/seed.ts" } -} +} \ No newline at end of file diff --git a/desci-server/src/services/data/externalCidProcessing.ts b/desci-server/src/services/data/externalCidProcessing.ts index c4e69b045..fab924cc4 100644 --- a/desci-server/src/services/data/externalCidProcessing.ts +++ b/desci-server/src/services/data/externalCidProcessing.ts @@ -13,20 +13,10 @@ import { prisma } from '../../client.js'; import { ExternalCid } from '../../controllers/data/updateExternalCid.js'; import { persistManifest } from '../../controllers/data/utils.js'; import { logger as parentLogger } from '../../logger.js'; -import { ensureUniquePathsDraftTree, getLatestDriveTime } from '../../services/draftTrees.js'; -import { - GetExternalSizeAndTypeResult, - convertToCidV1, - getExternalCidSizeAndType, - pubRecursiveLs, -} from '../../services/ipfs.js'; import { DRAFT_CID } from '../../utils/draftTreeUtils.js'; -import { - FirstNestingComponent, - addComponentsToDraftManifest, - getTreeAndFill, - prepareFirstNestingComponents, -} from '../../utils/driveUtils.js'; +import { getTreeAndFill, prepareFirstNestingComponents } from '../../utils/driveUtils.js'; +import { ensureUniquePathsDraftTree, getLatestDriveTime } from '../draftTrees.js'; +import { GetExternalSizeAndTypeResult, convertToCidV1, getExternalCidSizeAndType, pubRecursiveLs } from '../ipfs.js'; import { NodeUuid, getLatestManifestFromNode } from '../manifestRepo.js'; import repoService from '../repoService.js'; @@ -50,6 +40,7 @@ interface ProcessExternalCidDataToIpfsParams { externalCids: ExternalCid[]; user: User; node: Node; + /** * @type {string} path to the directory to be updated */ @@ -71,6 +62,17 @@ export async function processExternalCidDataToIpfs({ componentSubtype, autoStar, }: ProcessExternalCidDataToIpfsParams) { + logger.debug({ + fn: 'processExternalCidDataToIpfs', + externalCids, + user, + node, + contextPath, + componentType, + componentSubtype, + autoStar, + }); + try { /** * Prepare the CIDs for addition, see if they're resolvable and get their sizes and types @@ -189,25 +191,6 @@ export async function processExternalCidDataToIpfs({ const componentTypeMap: ResearchObjectComponentTypeMap = constructComponentTypeMapFromFiles(entriesDiscovered); - // Predefine components with their types, only happens if a predefined component type is passed - // if (componentType) { - // const firstNestingComponents: FirstNestingComponent[] = extCidsBeingAdded.map((file) => { - // const neutralFullPath = contextPath + '/' + file.name; - // return { - // name: file.name, - // path: neutralFullPath, - // cid: file.cid, - // componentType, - // componentSubtype, - // star: autoStar, - // }; - // }); - - // if (firstNestingComponents.length > 0) { - // await addComponentsToDraftManifest(node, firstNestingComponents); - // } - // } - let updatedManifest = await getLatestManifestFromNode(ltsNode); if (componentTypeMap) { @@ -231,6 +214,8 @@ export async function processExternalCidDataToIpfs({ pinnedFirstNestingFiles: firstNestingFiles, contextPath, componentTypeMap, + componentType, + componentSubtype, star: true, }); const preparedComponents = prepareFirstNestingComponents(firstNestingComponents); diff --git a/desci-server/src/services/data/processing.ts b/desci-server/src/services/data/processing.ts index 42a18f14f..61d3d7fc0 100644 --- a/desci-server/src/services/data/processing.ts +++ b/desci-server/src/services/data/processing.ts @@ -505,7 +505,9 @@ export function predefineComponentsForPinnedFiles({ star, }: PredefineComponentsForPinnedFilesParams): FirstNestingComponent[] { const firstNestingComponents: FirstNestingComponent[] = pinnedFirstNestingFiles.map((file) => { - const neutralFullPath = contextPath + '/' + file.path; + const neutralFullPath = file.path.startsWith(contextPath) + ? file.path + : contextPath + '/' + file.path; const pathSplit = file.path.split('/'); const name = pathSplit.pop(); return { diff --git a/desci-server/src/services/ipfs.ts b/desci-server/src/services/ipfs.ts index 3fadd2d55..8c1aeeed5 100644 --- a/desci-server/src/services/ipfs.ts +++ b/desci-server/src/services/ipfs.ts @@ -1,6 +1,5 @@ import fs from 'fs'; import https from 'https'; -import path from 'path'; import { Readable } from 'stream'; import { @@ -30,9 +29,6 @@ import { DRIVE_NODE_ROOT_PATH, type ExternalCidMap, type newCid, type oldCid } f import { getGithubExternalUrl, processGithubUrl } from '../utils/githubUtils.js'; import { createManifest, getUrlsFromParam, makePublic } from '../utils/manifestDraftUtils.js'; -// eslint-disable-next-line @typescript-eslint/no-var-requires -export const IPFS_PATH_TMP = '/tmp/ipfs'; - const logger = parentLogger.child({ module: 'Services::Ipfs', }); @@ -59,8 +55,9 @@ export const readerClient = create({ url: PUBLIC_IPFS_PATH }); export const publicIpfs = create({ url: process.env.PUBLIC_IPFS_RESOLVER + '/api/v0', options: { agent: httpsAgent } }); // Timeouts for resolution on internal and external IPFS nodes, to prevent server hanging, in ms. -const INTERNAL_IPFS_TIMEOUT = 30000; -const EXTERNAL_IPFS_TIMEOUT = 120000; +const INTERNAL_IPFS_TIMEOUT = 30_000; +// We mostly fetch single blocks, so this does not limit transfers +const EXTERNAL_IPFS_TIMEOUT = 30_000; export const updateManifestAndAddToIpfs = async ( manifest: ResearchObjectV1, @@ -94,15 +91,16 @@ export const updateManifestAndAddToIpfs = async ( return { cid: result.cid.toString(), size: result.size, ref, nodeVersion: version }; }; -export const addBufferToIpfs = (buf: Buffer, key: string) => { - return client.add(buf, { cidVersion: 1 }).then((res) => { - return { cid: res.cid.toString(), size: res.size, key }; - }); +export const addBufferToIpfs = async ( + buf: Buffer, + key: string, +): Promise<{ cid: string; size: number; key: string }> => { + const { cid, size } = await client.add(buf, { cidVersion: 1 }); + return { cid: cid.toString(), size: Number(size), key }; }; export const getSizeForCid = async (cid: string, asDirectory: boolean | undefined): Promise => { - const size = await getSize(client, cid, asDirectory); - return size; + return await getSize(client, cid, asDirectory); }; export const downloadFilesAndMakeManifest = async ({ title, defaultLicense, pdf, code, researchFields }) => { @@ -182,7 +180,7 @@ interface CodeComponentSingle { const processUrls = (key: string, data: Array): Array> => { logger.trace({ fn: 'processUrls' }, `processUrls key: ${key}, data: ${data}`); - return data.map(async (e, i) => { + return data.map(async (e) => { // if our payload points to github, download a zip of the main branch if (key === 'code') { if (e.indexOf('github.com') > -1) { @@ -205,10 +203,10 @@ export const downloadFile = async (url: string, key: string): Promise { + return new Promise(async (resolve, _reject) => { try { logger.info({ fn: 'downloadFile' }, `start download ${url.substring(0, 256)}`); - const { data, headers } = await axios({ + const { data } = await axios({ method: 'get', url: url, responseType: 'stream', @@ -322,12 +320,9 @@ export interface RecursiveLsResult extends IpfsPinnedResult { export const convertToCidV1 = (cid: string | multiformats.CID): string => { if (typeof cid === 'string') { - const c = multiformats.CID.parse(cid); - return c.toV1().toString(); - } else { - const cV1 = cid.toV1().toString(); - return cV1; + cid = multiformats.CID.parse(cid); } + return cid.toV1().toString(); }; export const resolveIpfsData = async (cid: string): Promise => { @@ -361,8 +356,7 @@ export const resolveIpfsData = async (cid: string): Promise => { targetValue = (targetValue as Uint8Array).buffer; } - const buffer = Buffer.from(targetValue); - return buffer; + return Buffer.from(targetValue); } }; @@ -407,32 +401,20 @@ export const getDirectoryTree = async ( { fn: 'getDirectoryTree', cid, returnFiles, returnExternalFiles }, `[getDirectoryTree]retrieving tree for cid: ${cid}, ipfs online: ${isOnline}`, ); - try { - // const tree = await getOrCache( - // `full-tree-${cid}${!returnFiles ? '-no-files' : ''}${cid}${!returnExternalFiles ? '-no-ext-files' : ''}`, - // getTree, - // ); - const tree = null; - if (tree) return tree; - throw new Error('[getDirectoryTree] Failed to retrieve tree from cache'); - } catch (err) { - logger.warn({ fn: 'getDirectoryTree', err }, '[getDirectoryTree] error'); - logger.info('[getDirectoryTree] Falling back on uncached tree retrieval'); - const startTime = process.hrtime(); - const treeRes = await getTree(); - // return getTree(); - const endTime = process.hrtime(startTime); - logger.info(`[getDirectoryTree] Execution time: ${endTime[0]}s ${endTime[1] / 1000000}ms`); - return treeRes; - } + + const startTime = process.hrtime(); + const treeRes = await getTree(); + const endTime = process.hrtime(startTime); + logger.info(`[getDirectoryTree] Execution time: ${endTime[0]}s ${endTime[1] / 1000000}ms`); + return treeRes; + async function getTree() { if (Object.keys(externalCidMap).length === 0) { logger.info({ fn: 'getDirectoryTree' }, `[getDirectoryTree] using standard ls, dagCid: ${cid}`); return await recursiveLs(cid); } else { logger.info({ fn: 'getDirectoryTree' }, `[getDirectoryTree] using mixed ls, dagCid: ${cid}`); - const tree = await mixedLs(cid, externalCidMap, returnFiles, returnExternalFiles); - return tree; + return await mixedLs(cid, externalCidMap, returnFiles, returnExternalFiles); } } }; @@ -445,7 +427,7 @@ export const recursiveLs = async (cid: string, carryPath?: string) => { const lsOp = client.ls(cid, { timeout: INTERNAL_IPFS_TIMEOUT }); for await (const filedir of lsOp) { - const promise = new Promise(async (resolve, reject) => { + const promise = new Promise(async (resolve, _reject) => { const res: any = filedir; // if (parent) { // res.parent = parent; @@ -486,7 +468,7 @@ export async function mixedLs( carryPath = carryPath || convertToCidV1(dagCid); const tree: RecursiveLsResult[] = []; const cidObject = multiformats.CID.parse(dagCid); - let block; + let block: Uint8Array; try { block = await client.block.get(cidObject, { timeout: INTERNAL_IPFS_TIMEOUT }); //instead of throwing, catch and print cid } catch (err) { @@ -518,7 +500,7 @@ export async function mixedLs( if (linkCidObject.code === rawCode || isFile) { result.size = link.Tsize; } else { - let linkBlock; + let linkBlock: Uint8Array; try { linkBlock = await client.block.get(linkCidObject, { timeout: INTERNAL_IPFS_TIMEOUT }); //instead of throwing, catch and print cid } catch (err) { @@ -596,12 +578,18 @@ export async function discoveryLs(dagCid: string, externalCidMap: ExternalCidMap const tree: RecursiveLsResult[] = []; const cidObject = multiformats.CID.parse(dagCid); let block = await client.block.get(cidObject, { timeout: INTERNAL_IPFS_TIMEOUT }); - if (!block) block = await publicIpfs.block.get(cidObject, { timeout: INTERNAL_IPFS_TIMEOUT }); - if (!block) throw new Error('Could not find block for cid: ' + dagCid); + if (!block) { + block = await publicIpfs.block.get(cidObject, { timeout: INTERNAL_IPFS_TIMEOUT }); + } + if (!block) { + throw new Error('Could not find block for cid: ' + dagCid); + } const { Data, Links } = dagPb.decode(block); const unixFs = UnixFS.unmarshal(Data); const isDir = dirTypes.includes(unixFs?.type); - if (!isDir) return null; + if (!isDir) { + return null; + } for (const link of Links) { const result: RecursiveLsResult = { name: link.Name, @@ -611,15 +599,21 @@ export async function discoveryLs(dagCid: string, externalCidMap: ExternalCidMap type: 'file', }; const externalCidMapEntry = externalCidMap[result.cid]; - if (externalCidMapEntry) result.external = true; + if (externalCidMapEntry) { + result.external = true; + } const isExternalFile = externalCidMapEntry && externalCidMapEntry.directory == false; const linkCidObject = multiformats.CID.parse(result.cid); if (linkCidObject.code === rawCode || isExternalFile) { result.size = link.Tsize; } else { let linkBlock = await client.block.get(linkCidObject, { timeout: INTERNAL_IPFS_TIMEOUT }); - if (!linkBlock) linkBlock = await publicIpfs.block.get(cidObject, { timeout: EXTERNAL_IPFS_TIMEOUT }); - if (!linkBlock) throw new Error('Could not find block for cid: ' + dagCid); + if (!linkBlock) { + linkBlock = await publicIpfs.block.get(cidObject, { timeout: EXTERNAL_IPFS_TIMEOUT }); + } + if (!linkBlock) { + throw new Error('Could not find block for cid: ' + dagCid); + } const { Data: linkData } = dagPb.decode(linkBlock); const unixFsLink = UnixFS.unmarshal(linkData); const isLinkDir = dirTypes.includes(unixFsLink?.type); @@ -646,16 +640,14 @@ export async function discoveryLs(dagCid: string, externalCidMap: ExternalCidMap } export const getDag = async (cid: CID) => { - const dag = await client.dag.get(cid); - return dag; + return await client.dag.get(cid); }; -export const getDatasetTar = async (cid) => { - const files = await client.get(cid, { archive: true }); - return files; +export const getDatasetTar = async (cid: CID | string): Promise> => { + return client.get(cid, { archive: true }); }; -export const getDataset = async (cid: CID) => { +export const getDataset = async (cid: CID | string) => { const files = []; for await (const file of client.get(cid)) { files.push(file); @@ -702,7 +694,7 @@ type FileInfo = { cid: string; size?: number }; export type FilesToAddToDag = Record; export const addFilesToDag = async (rootCid: string, contextPath: string, filesToAddToDag: FilesToAddToDag) => { - const dagCidsToBeReset = []; + const dagCidsToBeReset: CID[] = []; // CID(String): DAGNode - cached to prevent duplicate calls const dagsLoaded: Record = {}; dagCidsToBeReset.push(CID.parse(rootCid)); @@ -711,8 +703,7 @@ export const addFilesToDag = async (rootCid: string, contextPath: string, filesT for (let i = 0; i < stagingDagNames.length; i++) { const dagLinkName = stagingDagNames[i]; const containingDagCid = dagCidsToBeReset[i]; - //FIXME containingDag is of type PBNode - const containingDag: any = await client.object.get(containingDagCid); + const containingDag: PBNode = await client.object.get(containingDagCid); if (!containingDag) { throw Error('Failed updating dataset, existing DAG not found'); } @@ -727,9 +718,7 @@ export const addFilesToDag = async (rootCid: string, contextPath: string, filesT //if context path doesn't exist(update add at DAG root level), the dag won't be cached yet. if (!dagsLoaded.length) { - //FIXME rootDag is of type PBNode - const rootDag = await client.object.get(dagCidsToBeReset[0]); - dagsLoaded[rootCid] = rootDag; + dagsLoaded[rootCid] = await client.object.get(dagCidsToBeReset[0]); } //establishing the tail dag that's being updated @@ -748,8 +737,7 @@ export const addFilesToDag = async (rootCid: string, contextPath: string, filesT while (dagCidsToBeReset.length) { const currentNodeCid = dagCidsToBeReset.pop(); - //FIXME should be PBLink - const currentNode: any = dagsLoaded[currentNodeCid.toString()] + const currentNode: PBNode = dagsLoaded[currentNodeCid.toString()] ? dagsLoaded[currentNodeCid.toString()] : await client.object.get(currentNodeCid); const linkName = stagingDagNames.pop(); @@ -771,7 +759,7 @@ export const addFilesToDag = async (rootCid: string, contextPath: string, filesT }; export const removeFileFromDag = async (rootCid: string, contextPath: string, fileNameToRemove: string) => { - const dagCidsToBeReset = []; + const dagCidsToBeReset: CID[] = []; // CID(String): DAGNode - cached to prevent duplicate calls const dagsLoaded: Record = {}; dagCidsToBeReset.push(CID.parse(rootCid)); @@ -780,8 +768,7 @@ export const removeFileFromDag = async (rootCid: string, contextPath: string, fi for (let i = 0; i < stagingDagNames.length; i++) { const dagLinkName = stagingDagNames[i]; const containingDagCid = dagCidsToBeReset[i]; - //FIXME containingDag is of type PBNode - const containingDag: any = await client.object.get(containingDagCid); + const containingDag: PBNode = await client.object.get(containingDagCid); if (!containingDag) { throw Error('Failed updating dataset, existing DAG not found'); } @@ -796,9 +783,7 @@ export const removeFileFromDag = async (rootCid: string, contextPath: string, fi //if context path doesn't exist(update add at DAG root level), the dag won't be cached yet. if (!dagsLoaded.length) { - //FIXME rootDag is of type PBNode - const rootDag = await client.object.get(dagCidsToBeReset[0]); - dagsLoaded[rootCid] = rootDag; + dagsLoaded[rootCid] = await client.object.get(dagCidsToBeReset[0]); } //establishing the tail dag that's being updated @@ -814,8 +799,7 @@ export const removeFileFromDag = async (rootCid: string, contextPath: string, fi let lastUpdatedCid = updatedTailNodeCid; while (dagCidsToBeReset.length) { const currentNodeCid = dagCidsToBeReset.pop(); - //FIXME should be PBLink - const currentNode: any = dagsLoaded[currentNodeCid.toString()] + const currentNode: PBNode = dagsLoaded[currentNodeCid.toString()] ? dagsLoaded[currentNodeCid.toString()] : await client.object.get(currentNodeCid); const linkName = stagingDagNames.pop(); @@ -830,7 +814,9 @@ export const removeFileFromDag = async (rootCid: string, contextPath: string, fi }; export async function removeDagLink(dagCid: string | multiformats.CID, linkName: string) { - if (typeof dagCid === 'string') dagCid = multiformats.CID.parse(dagCid); + if (typeof dagCid === 'string') { + dagCid = multiformats.CID.parse(dagCid); + } if (dagCid.code == rawCode) { throw new Error('raw cid -- not a directory'); @@ -860,7 +846,7 @@ export async function removeDagLink(dagCid: string | multiformats.CID, linkName: } export const renameFileInDag = async (rootCid: string, contextPath: string, linkToRename: string, newName: string) => { - const dagCidsToBeReset = []; + const dagCidsToBeReset: CID[] = []; // CID(String): DAGNode - cached to prevent duplicate calls const dagsLoaded: Record = {}; dagCidsToBeReset.push(CID.parse(rootCid)); @@ -869,8 +855,7 @@ export const renameFileInDag = async (rootCid: string, contextPath: string, link for (let i = 0; i < stagingDagNames.length; i++) { const dagLinkName = stagingDagNames[i]; const containingDagCid = dagCidsToBeReset[i]; - //FIXME containingDag is of type PBNode - const containingDag: any = await client.object.get(containingDagCid); + const containingDag: PBNode = await client.object.get(containingDagCid); if (!containingDag) { throw Error('Failed updating dataset, existing DAG not found'); } @@ -885,9 +870,7 @@ export const renameFileInDag = async (rootCid: string, contextPath: string, link //if context path doesn't exist(update add at DAG root level), the dag won't be cached yet. if (!dagsLoaded.length) { - //FIXME rootDag is of type PBNode - const rootDag = await client.object.get(dagCidsToBeReset[0]); - dagsLoaded[rootCid] = rootDag; + dagsLoaded[rootCid] = await client.object.get(dagCidsToBeReset[0]); } //establishing the tail dag that's being updated @@ -903,8 +886,7 @@ export const renameFileInDag = async (rootCid: string, contextPath: string, link let lastUpdatedCid = updatedTailNodeCid; while (dagCidsToBeReset.length) { const currentNodeCid = dagCidsToBeReset.pop(); - //FIXME should be PBLink - const currentNode: any = dagsLoaded[currentNodeCid.toString()] + const currentNode: PBNode = dagsLoaded[currentNodeCid.toString()] ? dagsLoaded[currentNodeCid.toString()] : await client.object.get(currentNodeCid); const linkName = stagingDagNames.pop(); @@ -946,7 +928,9 @@ export const moveFileInDag = async (rootCid: string, contextPath: string, fileTo }; export async function renameDagLink(dagCid: string | multiformats.CID, linkName: string, newName: string) { - if (typeof dagCid === 'string') dagCid = multiformats.CID.parse(dagCid); + if (typeof dagCid === 'string') { + dagCid = multiformats.CID.parse(dagCid); + } if (dagCid.code == rawCode) { throw new Error('raw cid -- not a directory'); @@ -999,8 +983,8 @@ export async function getExternalCidSizeAndType(cid: string) { const { Data } = dagPb.decode(block); const unixFs = UnixFS.unmarshal(Data); - let isDirectory; - let size; + let isDirectory: boolean; + let size: number; const isDir = dirTypes.includes(unixFs?.type); if (code === 0x70 && isDir) { //0x70 === dag-pb @@ -1010,12 +994,14 @@ export async function getExternalCidSizeAndType(cid: string) { isDirectory = false; const fSize = unixFs.fileSize(); if (fSize) { - size = fSize; + size = Number(fSize); } else { - size = unixFs.blockSizes.reduce((a, b) => a + b, BigInt(0)); + size = unixFs.blockSizes.map(Number).reduce((a, b) => a + b, 0); } } - if (isDirectory !== undefined && size !== undefined) return { isDirectory, size }; + if (size !== undefined) { + return { isDirectory, size }; + } throw new Error(`Failed to resolve CID or determine file size/type for cid: ${cid}`); } catch (error) { logger.error({ fn: 'getExternalCidSizeAndType', error }, `[getExternalCidSizeAndType]Error: ${error.message}`); @@ -1048,8 +1034,7 @@ export function strIsCid(cid: string) { const cidObj = multiformats.CID.parse(cid); const validCid = multiformats.CID.asCID(cidObj); - if (!!validCid) return true; - return false; + return !!validCid; } catch (e) { return false; } @@ -1113,16 +1098,14 @@ export type BlockMetadata = { CumulativeSize: number; }; export async function getCidMetadata(cid: string, external?: boolean): Promise { - /* - ** External handling should be added once our pub node is properly configured - */ try { - // const metadata: BlockMetadata = await client.block.stat(CID.parse(cid), { timeout: INTERNAL_IPFS_TIMEOUT }); - const metadata: BlockMetadata = await client.object.stat(CID.parse(cid), { timeout: INTERNAL_IPFS_TIMEOUT }); - // let localResolver = process.env.IPFS_RESOLVER_OVERRIDE; - // if (localResolver.endsWith('/ipfs')) localResolver = localResolver.slice(0, -5); - // const url = `${localResolver}/api/v0/object/stat?arg=${cid}`; - // const metadata = await axios.get(url).then((res) => res.data); + let metadata: BlockMetadata; + if (external) { + metadata = await publicIpfs.object.stat(CID.parse(cid), { timeout: EXTERNAL_IPFS_TIMEOUT }); + } else { + metadata = await client.object.stat(CID.parse(cid), { timeout: INTERNAL_IPFS_TIMEOUT }); + } + return metadata; } catch (e) { logger.trace({ fn: 'getCidMetadata', cid, e }, 'Failed to get CID metadata'); diff --git a/desci-server/src/utils/dagConcat.ts b/desci-server/src/utils/dagConcat.ts index 2f3aa4a5d..7cf56e310 100644 --- a/desci-server/src/utils/dagConcat.ts +++ b/desci-server/src/utils/dagConcat.ts @@ -8,7 +8,7 @@ import { code as rawCode } from 'multiformats/codecs/raw'; // const { default: UnixFS } = IpfsUnixFS; // =========================================================================== -export async function getSize(ipfs, cid, allowDir = false) { +export async function getSize(ipfs, cid, allowDir = false): Promise { const block = await ipfs.block.get(cid); // console.log('cid: ', cid); if (typeof cid === 'string') cid = CID.parse(cid); @@ -30,9 +30,9 @@ export async function getSize(ipfs, cid, allowDir = false) { if (unixfs.data) { return unixfs.data.length; } else if (!unixfs.isDirectory()) { - return unixfs.fileSize(); + return Number(unixfs.fileSize()); } else { - return unixfs.blockSizes.reduce((a, b) => a + b, BigInt(0)); + return unixfs.blockSizes.map(Number).reduce((a, b) => a + b, 0); } } diff --git a/desci-server/src/utils/dataRefTools.ts b/desci-server/src/utils/dataRefTools.ts index ffed38cb4..2d41e2d45 100644 --- a/desci-server/src/utils/dataRefTools.ts +++ b/desci-server/src/utils/dataRefTools.ts @@ -1,11 +1,11 @@ import { FileType, ResearchObjectV1, isNodeRoot, neutralizePath, recursiveFlattenTree } from '@desci-labs/desci-models'; -import { DataReference, DataType, NodeVersion, Prisma, Node } from '@prisma/client'; +import { DataReference, DataType, Prisma, Node } from '@prisma/client'; import axios from 'axios'; import { prisma } from '../client.js'; import { PUBLIC_IPFS_PATH } from '../config/index.js'; import { logger as parentLogger } from '../logger.js'; -import { discoveryLs, getDirectoryTree, getSizeForCid } from '../services/ipfs.js'; +import { discoveryLs, getDirectoryTree, getSizeForCid, RecursiveLsResult } from '../services/ipfs.js'; import { ensureUuidEndsWithDot, objectPropertyXor, omitKeys } from '../utils.js'; import { DRAFT_CID, TimestampMap, draftNodeTreeEntriesToFlatIpfsTree } from './draftTreeUtils.js'; @@ -97,7 +97,7 @@ export async function generateDataReferences({ const externalCidMap = workingTreeUrl ? await extractExternalCidMapFromTreeUrl(workingTreeUrl) : await generateExternalCidMap(node.uuid); - let dataTree; + let dataTree: RecursiveLsResult[]; if (isPublished) { if (markExternals) { dataTree = recursiveFlattenTree(await discoveryLs(dataBucketCid, externalCidMap)); @@ -106,7 +106,7 @@ export async function generateDataReferences({ } } else { const dbTree = await prisma.draftNodeTree.findMany({ where: { nodeId: node.id } }); - dataTree = await draftNodeTreeEntriesToFlatIpfsTree(dbTree); + dataTree = draftNodeTreeEntriesToFlatIpfsTree(dbTree); } const manifestPathsToDbTypes = generateManifestPathsToDbTypeMap(manifestEntry); @@ -135,7 +135,11 @@ export async function generateDataReferences({ return [...(isPublished ? [dataRootEntry, ...manifestRefIncluded] : [...manifestRefIncluded]), ...dataTreeToPubRef]; } -// used to prepare data refs for a given dag and manifest (differs from generateDataReferences in that you don't need the updated manifestCid ahead of time) +/** + * used to prepare data refs for a given dag and manifest. Differs from generateDataReferences in that you don't + * need the updated manifestCid ahead of time. + * @deprecated - unused + */ export async function prepareDataRefs( nodeUuid: string, manifest: ResearchObjectV1, @@ -207,7 +211,7 @@ export async function prepareDataRefsForDraftTrees( const manifestEntry: ResearchObjectV1 = manifest; const dbTree = await prisma.draftNodeTree.findMany({ where: { nodeId: node.id } }); - const dataTree = await draftNodeTreeEntriesToFlatIpfsTree(dbTree); + const dataTree = draftNodeTreeEntriesToFlatIpfsTree(dbTree); const manifestPathsToDbTypes = generateManifestPathsToDbTypeMap(manifestEntry); // debugger; @@ -223,6 +227,7 @@ export async function prepareDataRefsForDraftTrees( size: entry.size, type: dbType, nodeId: node.id, + external: entry.external || null, }; }); @@ -283,6 +288,9 @@ export async function prepareDataRefsForDagSkeleton({ return [dataRootEntry, ...dataTreeToPubRef]; } +/** + * @deprecated - unused + */ export async function prepareDataRefsExternalCids( nodeUuid: string, manifest: ResearchObjectV1, diff --git a/desci-server/src/utils/draftTreeUtils.ts b/desci-server/src/utils/draftTreeUtils.ts index c99e7184b..b1b638c79 100644 --- a/desci-server/src/utils/draftTreeUtils.ts +++ b/desci-server/src/utils/draftTreeUtils.ts @@ -35,7 +35,10 @@ interface IpfsDagToDraftNodeTreeEntriesParams { /** * Converts an IPFS tree to an array of DraftNodeTree entries ready to be added to the DraftNodeTree table + * @param ipfsTree + * @param node * @param timestampMap - Optional map that maps drive paths to their created/last modified timestamps, if not provided then they'll be generated automatically by the DB. + * @param contextPath */ export function ipfsDagToDraftNodeTreeEntries({ ipfsTree, @@ -69,7 +72,7 @@ export function ipfsDagToDraftNodeTreeEntries({ * Converts a draftNodeTree to a flat IPFS tree, ready to be consumed by functions that take a flat IPFS tree. * More efficient than converting to an IPFS tree and then flattening it, when unflatenned variant is unnecessary. */ -export function draftNodeTreeEntriesToFlatIpfsTree(draftNodeTree: DraftNodeTree[]) { +export function draftNodeTreeEntriesToFlatIpfsTree(draftNodeTree: DraftNodeTree[]): RecursiveLsResult[] { const flatIpfsTree: RecursiveLsResult[] = []; draftNodeTree.forEach((entry) => { const { cid, size, directory, path, external } = entry; @@ -117,14 +120,12 @@ export function flatTreeToHierarchicalTree(flatTree: RecursiveLsResult[]): Recur /* * Function to add a DAGNode to IPFS and return its CID */ -async function addDagNodeToIpfs(dagNode) { - const cid = await client.block.put(encode(prepare(dagNode)), { +async function addDagNodeToIpfs(dagNode: unknown): Promise { + return await client.block.put(encode(prepare(dagNode)), { version: 1, format: 'dag-pb', // pin: true, }); - // logger.debug(`Added DAGNode to IPFS: ${cid.toString()}`); - return cid; } /* diff --git a/desci-server/yarn.lock b/desci-server/yarn.lock index b1955f279..669b34ac2 100644 --- a/desci-server/yarn.lock +++ b/desci-server/yarn.lock @@ -2021,10 +2021,10 @@ resolved "https://registry.yarnpkg.com/@desci-labs/desci-contracts/-/desci-contracts-0.2.7.tgz#4047e52e405c361f0c1723bb966364ccc2dfb865" integrity sha512-T5XhH0qn7z93jb9MlGd68i4mf0tJP+ppfyWKfFBjp+dCUC4GeTMM3Z/6eqaD8QXsBpvRfi+cvb0or3BY47MR2A== -"@desci-labs/desci-models@0.2.18": - version "0.2.18" - resolved "https://registry.yarnpkg.com/@desci-labs/desci-models/-/desci-models-0.2.18.tgz#d4873db35fdeaa5133beb75ebcb263587d7e2e4b" - integrity sha512-VypYv1gtN7ttSnfsqrTZf9EzXl50fCaYmg+3qOnZ2x+yNPIZPEhTY4YGmTLXvPqspG8kVlCtX+zG2NTUcu8fTg== +"@desci-labs/desci-models@^0.2.19": + version "0.2.19" + resolved "https://registry.yarnpkg.com/@desci-labs/desci-models/-/desci-models-0.2.19.tgz#430f8e6b6a1967d6b06fc8a36e6c32536e1a4a42" + integrity sha512-XaZyLom2z4vi+A47qS5G1ecc65fw3MxfAKutH1iXrb92AXmxQG7TcH313O3qv4206pIDdNfmJNfgjo4h78cVJw== dependencies: jsonld "^8.1.1" schema-dts "^1.1.2" diff --git a/nodes-lib/Makefile b/nodes-lib/Makefile new file mode 100644 index 000000000..9dec79d52 --- /dev/null +++ b/nodes-lib/Makefile @@ -0,0 +1,11 @@ +.PHONY: install build + +build: install + npm run build + +install: + npm ci --no-fund --no-audit + +clean: + rm -rf node_modules + rm -rf dist diff --git a/nodes-lib/package-lock.json b/nodes-lib/package-lock.json index d9292655e..f0f6cf6a4 100644 --- a/nodes-lib/package-lock.json +++ b/nodes-lib/package-lock.json @@ -1,17 +1,17 @@ { "name": "@desci-labs/nodes-lib", - "version": "0.1.3", + "version": "0.1.4", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "@desci-labs/nodes-lib", - "version": "0.1.3", + "version": "0.1.4", "license": "MIT", "dependencies": { "@desci-labs/desci-codex-lib": "^1.1.7", "@desci-labs/desci-contracts": "^0.2.7", - "@desci-labs/desci-models": "^0.2.3-rc1", + "@desci-labs/desci-models": "^0.2.19", "@didtools/cacao": "^3.0.1", "@didtools/pkh-ethereum": "^0.5.0", "@stablelib/random": "^1.0.2", @@ -1016,9 +1016,10 @@ "integrity": "sha512-T5XhH0qn7z93jb9MlGd68i4mf0tJP+ppfyWKfFBjp+dCUC4GeTMM3Z/6eqaD8QXsBpvRfi+cvb0or3BY47MR2A==" }, "node_modules/@desci-labs/desci-models": { - "version": "0.2.3-rc1", - "resolved": "https://registry.npmjs.org/@desci-labs/desci-models/-/desci-models-0.2.3-rc1.tgz", - "integrity": "sha512-FW74CkgfZTNhky0Q6Sk3lCoBZ+Yl5D4KVTTLBv/NG+e8qH9jyT6DVbiXvaThQWZQNulFXJg2UFZm73AVInu3wA==", + "version": "0.2.19", + "resolved": "https://registry.npmjs.org/@desci-labs/desci-models/-/desci-models-0.2.19.tgz", + "integrity": "sha512-XaZyLom2z4vi+A47qS5G1ecc65fw3MxfAKutH1iXrb92AXmxQG7TcH313O3qv4206pIDdNfmJNfgjo4h78cVJw==", + "license": "MIT", "dependencies": { "jsonld": "^8.1.1", "schema-dts": "^1.1.2" @@ -10851,9 +10852,9 @@ "integrity": "sha512-T5XhH0qn7z93jb9MlGd68i4mf0tJP+ppfyWKfFBjp+dCUC4GeTMM3Z/6eqaD8QXsBpvRfi+cvb0or3BY47MR2A==" }, "@desci-labs/desci-models": { - "version": "0.2.3-rc1", - "resolved": "https://registry.npmjs.org/@desci-labs/desci-models/-/desci-models-0.2.3-rc1.tgz", - "integrity": "sha512-FW74CkgfZTNhky0Q6Sk3lCoBZ+Yl5D4KVTTLBv/NG+e8qH9jyT6DVbiXvaThQWZQNulFXJg2UFZm73AVInu3wA==", + "version": "0.2.19", + "resolved": "https://registry.npmjs.org/@desci-labs/desci-models/-/desci-models-0.2.19.tgz", + "integrity": "sha512-XaZyLom2z4vi+A47qS5G1ecc65fw3MxfAKutH1iXrb92AXmxQG7TcH313O3qv4206pIDdNfmJNfgjo4h78cVJw==", "requires": { "jsonld": "^8.1.1", "schema-dts": "^1.1.2" diff --git a/nodes-lib/package.json b/nodes-lib/package.json index 502cb6943..4d62d66c9 100644 --- a/nodes-lib/package.json +++ b/nodes-lib/package.json @@ -1,6 +1,6 @@ { "name": "@desci-labs/nodes-lib", - "version": "0.1.3", + "version": "0.1.4", "homepage": "https://github.com/desci-labs/nodes#readme", "description": "Stand-alone client library for interacting with desci-server", "repository": { @@ -28,7 +28,7 @@ "dependencies": { "@desci-labs/desci-codex-lib": "^1.1.7", "@desci-labs/desci-contracts": "^0.2.7", - "@desci-labs/desci-models": "^0.2.3-rc1", + "@desci-labs/desci-models": "^0.2.19", "@didtools/cacao": "^3.0.1", "@didtools/pkh-ethereum": "^0.5.0", "@stablelib/random": "^1.0.2", diff --git a/nodes-lib/src/api.ts b/nodes-lib/src/api.ts index 04f7a20fc..79c67f05e 100644 --- a/nodes-lib/src/api.ts +++ b/nodes-lib/src/api.ts @@ -1,37 +1,37 @@ -import { AxiosError } from "axios"; +import {AxiosError} from "axios"; import { - ResearchObjectComponentType, type CodeComponent, type DataComponent, type DriveObject, type ExternalLinkComponent, + type License, + type ManifestActions, type PdfComponent, - type ResearchObjectV1, + type ResearchField, + ResearchObjectComponentCodeSubtype, ResearchObjectComponentDocumentSubtype, ResearchObjectComponentLinkSubtype, - ResearchObjectComponentCodeSubtype, - type ManifestActions, - type ResearchObjectV1Component, - type License, - type ResearchObjectV1Author, - type ResearchField, type ResearchObjectComponentSubtypes, + ResearchObjectComponentType, + type ResearchObjectV1, + type ResearchObjectV1Author, + type ResearchObjectV1Component, } from "@desci-labs/desci-models"; import FormData from "form-data"; -import { createReadStream } from "fs"; -import type { NodeIDs } from "@desci-labs/desci-codex-lib"; -import { legacyPublish, publish } from "./publish.js"; -import type { ResearchObjectDocument } from "./automerge.js"; -import { randomUUID } from "crypto"; -import { getNodesLibInternalConfig } from "./config/index.js"; -import { makeRequest } from "./routes.js"; -import { Signer } from "ethers"; -import { type DID } from "dids"; -import { getFullState } from "./codex.js"; -import { bnToString, convertUUIDToDecimal } from "./util/converting.js"; -import { lookupLegacyDpid } from "./chain.js"; -import { PublishError } from "./errors.js"; -import { errWithCause } from "pino-std-serializers"; +import {createReadStream} from "fs"; +import type {NodeIDs} from "@desci-labs/desci-codex-lib"; +import {legacyPublish, publish} from "./publish.js"; +import type {ResearchObjectDocument} from "./automerge.js"; +import {randomUUID} from "crypto"; +import {makeRequest} from "./routes.js"; +import {Signer} from "ethers"; +import {type DID} from "dids"; +import {getFullState} from "./codex.js"; +import {bnToString, convertUUIDToDecimal} from "./util/converting.js"; +import {lookupLegacyDpid} from "./chain.js"; +import {PublishError} from "./errors.js"; +import {errWithCause} from "pino-std-serializers"; +import {getHeaders} from "./util/headers.js"; export const ENDPOINTS = { deleteData: { @@ -144,6 +144,12 @@ export const ENDPOINTS = { _payloadT: undefined, _responseT: {}, }, + claimAttestation: { + method: "post", + route: `/v1/attestations/claim`, + _payloadT: {}, + _responseT: {}, + }, } as const; const LOG_CTX = "[nodes-lib::api]"; @@ -704,6 +710,8 @@ export type AddExternalTreeParams = { componentType: ResearchObjectComponentType; /** The subtype of the imported data */ componentSubtype: ResearchObjectComponentSubtypes; + /** Mark the content as particularly important for the node */ + autoStar?: boolean; }; /** @@ -1085,13 +1093,30 @@ export const updateCoverImage = async ( ): Promise => await changeManifest(uuid, [{ type: "Update CoverImage", cid }]); -const getHeaders = (isFormData: boolean = false) => { - const headers = { - "api-key": getNodesLibInternalConfig().apiKey, - ...(isFormData ? { "content-type": "multipart/form-data" } : {}), - }; - return headers; -}; +export type ClaimAttestationParams = { + attestationId: number; + nodeVersion: number; + nodeUuid: string; + nodeDpid: string; + claimerId: number; +} +type NodeAttestation = { + id: number,attestationId: number, + attestationVersionId: number, + desciCommunityId: number, + claimedById: number, + nodeDpid10: string | null, + nodeUuid: string, + nodeVersion: number, + claimedAt: Date, + revoked: boolean, + revokedAt: Date | null +} + +export const claimAttestation = async ( + params: ClaimAttestationParams +): Promise => + await makeRequest(ENDPOINTS.claimAttestation, getHeaders(), params); /** * Best-effort way of ensuring reasonable representations of absolute paths diff --git a/nodes-lib/src/index.ts b/nodes-lib/src/index.ts index c50b1f285..dcbea420a 100644 --- a/nodes-lib/src/index.ts +++ b/nodes-lib/src/index.ts @@ -1,3 +1,4 @@ export * from "./api.js" export * from "./config/index.js"; export * from "./errors.js"; +export {getHeaders} from "./util/headers.js"; diff --git a/nodes-lib/src/util/headers.ts b/nodes-lib/src/util/headers.ts new file mode 100644 index 000000000..b0d220e76 --- /dev/null +++ b/nodes-lib/src/util/headers.ts @@ -0,0 +1,8 @@ +import {getNodesLibInternalConfig} from "../config/index.js"; + +export const getHeaders = (isFormData: boolean = false) => { + return { + "api-key": getNodesLibInternalConfig().apiKey, + ...(isFormData ? {"content-type": "multipart/form-data"} : {}), + }; +}; \ No newline at end of file diff --git a/toolshed/insight-import/.env.example b/toolshed/insight-import/.env.example new file mode 100644 index 000000000..51b0a23f9 --- /dev/null +++ b/toolshed/insight-import/.env.example @@ -0,0 +1,16 @@ +# API token from nodes user profile +NODES_API_TOKEN= +# Private key used to make publishes +PUBLISH_PKEY= +# Select target env: local, dev, prod +ENV= +# ID of creating user +USER_ID= + +# IJ attestation ID, differs in DB between envs +## local: +IJ_ATT_ID= +OC_ATT_ID= +## dev: +#IJ_ATT_ID=298 +#OC_ATT_ID=102 diff --git a/toolshed/insight-import/.gitignore b/toolshed/insight-import/.gitignore new file mode 100644 index 000000000..f876eb73a --- /dev/null +++ b/toolshed/insight-import/.gitignore @@ -0,0 +1,7 @@ +data +.insight-journal-clone +test +cids_*.log +missing*.txt +.credentials +existingNodes_local.json diff --git a/toolshed/insight-import/README.md b/toolshed/insight-import/README.md new file mode 100644 index 000000000..02d03a60a --- /dev/null +++ b/toolshed/insight-import/README.md @@ -0,0 +1,285 @@ +# Insight Importer +This project contains tools for importing publications from Insight Journal to Nodes. The method might be useful for other imports, where there is static data for publication history that should be reflected in the history of new nodes. + +## Method +An external git repo contains a metadata manifest, and optionally a cover image, for each publication. This _roughly_ corresponds to the ResearchoObject schema, but needs transforming. `sync.sh` grabs information from this repo, grabs referenced CIDs to articles, code and/or data, and the node scripts wrangles them into functional nodes with `nodes-lib`. + +### Data fetching +These `metadata.json` files contain CIDs for article PDFs and code/data, per version, so the data necessary isn't contained in the repo. [`sync.sh`](./sync.sh) tries its best to filter out these CIDs and find them with `lassie`. Each parsed CID is saved as a CAR file in `local-data/cars/[cid].car`. + +The output format looks like this: + +``` +ο„• local-data +β”œβ”€β”€ ο„• cars +β”‚ β”œβ”€β”€ ο€– bafkreia2c64uqq226j3ion6muy75pvm6ayomqrgpqrmvuq2tyrsfcr6jpm.car +β”‚ β”œβ”€β”€ ο€– bafkreia3kapmuip4p42wrs7yrc4ykop75vfjgpyi2dnmyuttpz45zqmsxu.car +β”‚ β”œβ”€β”€ ο€– bafkreia4bjka5wovgbnvftxe55chrbk7urkp5lkmdj2av4k7qdff3xiyty.car +β”‚ β”œβ”€β”€ ο€– bafkreia4l6rrso2u53224wmps5ak6z4c4lczruzkolqtmjnn3ul5p7ffw4.car +β”‚ ┆ +β”‚ +β”œβ”€β”€ ο„• issues +β”‚ β”œβ”€β”€ ξ˜‹ 1.json +β”‚ β”œβ”€β”€ ξ˜‹ 156.json +β”‚ β”œβ”€β”€ ξ˜‹ 157.json +β”‚ β”œβ”€β”€ ξ˜‹ 162.json +β”‚ β”œβ”€β”€ ξ˜‹ 166.json +β”‚ ┆ +β”‚ +└── ο„• publications + β”œβ”€β”€ ο„• 10 + β”‚ β”œβ”€β”€ ο„• data + β”‚ └── ξ˜‹ metadata.json + β”œβ”€β”€ ο„• 101 + β”‚ └── ξ˜‹ metadata.json + β”œβ”€β”€ ο„• 102 + β”‚ β”œβ”€β”€ ο‡… cover.jpeg + β”‚ └── ξ˜‹ metadata.json + ┆ +``` + +Some notes: +- Not all publications have associated files (55, 424, ...) +- Not all have cover images (321, ) + +Some CIDs pare particulary elusive, but `sync.sh` will only retry failed fetches on re-runs. So, run sync a couple of times, checking the output and/or the `cids_[date].log` files to see how much is still left to find. It defaults to using https://nftstorage.link, which races multiple public gateways, because this is much faster in 95% of the cases, but falls back to dynamic peer discovery when it fails to resolve content that way. Some of the peers will be eeeextremely slow, but the next run will probably try a new one so don't lose hope. 🌞 + +#### Manually get missing article CIDs +Some article CIDs not resolvable at all, but could be found in a bundle DAG holding article PDFs, found by sniffing the network requests made when loading them on insight-journal.org. + +After `sync.sh` runs have stabilised, there are probably a bunch of persistent failure. Mainly articles, it seems. Run this script on your sync logfile to list context for the missing CIDs: + +```bash +❯ ./analyseMissing.sh cids_2024-11-05T12:10:42Z.log +10 article bafybeifrq6agqtqbhhmfjve7we4wglgkce7gpexdxhltj7zyumhk3yjc7u +107 source_code bafybeiej3rxpc4gdy5lwtqapysrpov6g3jwmyq44d34lghynbsfeh7lnu4 +110 source_code bafybeihooy64tij5yxald5lgcuzudnip3q3x6nehezaciupekr2shzizbe +116 source_code bafybeifka4mgty7d6inxfmloxcd2phad7sowx3vvkevveraqimsgkg2z2e +12 article bafybeidbie4scd6d5ku7b4dnyw5owhaxafmovawxrfocvzlbx2qexzyfa4 +``` + +For articles, we can try rechunking the data found in the article DAG to arrive at the original CID. To do this, put the analysis results in a file and invoke `rebuildRawArticles.sh`. It's cool if there are non-articles in there too, they will be skipped: + +```bash +❯ ./analyseMissing.sh cids_2024-11-05T12:10:42Z.log > missing.txt +❯ ./rebuildRawArticles.sh missing.txt +πŸš— Article bafybeifrq6agqtqbhhmfjve7we4wglgkce7gpexdxhltj7zyumhk3yjc7u reconstructed for pub 10 +πŸƒ Skipping non-article CID bafybeiej3rxpc4gdy5lwtqapysrpov6g3jwmyq44d34lghynbsfeh7lnu4 for pub 107 +πŸš— Article bafybeidbie4scd6d5ku7b4dnyw5owhaxafmovawxrfocvzlbx2qexzyfa4 reconstructed for pub 12 +πŸƒ Skipping non-article CID bafybeiet5egbeltbu5nsr2i3nmd57c4prcfrzenbmzmkujj5trpwuayodq for pub 129 +``` + +Try running `sync.sh` again and see if that fixed all the remaining CIDs! + +#### Remote DAG imports +Many of these CIDs weren't resolvable over the DHT or IPNS, so to help their availability we import the DAGs to our public node. The `dag import` command pins the CAR root, which by default works recursively. Hence, all subgraphs will be pinned as well. + +```bash +# Pins to the CF R2 public kubo node +./remoteDagImport.sh local-data/cars s3-public-ipfs-prod-8547f975ff-5sftc +``` + +This takes 20ish minutes to run, depending on your connection. + +#### Export cover images +Run `covers.sh` to generate a CAR file for each cover photo, and send them to the public node as well: + +```bash +./covers.sh +./remoteDagImport.sh local-data/covers s3-public-ipfs-prod-8547f975ff-5sftc +``` + +The `covers.sh` script writes the cover image CID to a new top-level field `coverImage`, that can be used to connect them when creating the manifest later. + +### Node creation + +#### Type generation +We use `quicktype` to generate types and parsers that match all of the IJ metadata files, so we can leverage type system to detect incompatabilities with `ResearchObject`. E.g., `null` instead of `undefined`, optionals, data shapes, etc. + +This is checked in as [src/ijTypes.ts](src/ijTypes.ts), and can be regenerated with `npm run generate-types`. + +#### Create nodes +If running locally, first do these steps: +1. Tunnel to the `pub.desci.com` RPC service: `kubectl port-forward --address 0.0.0.0 s3-public-ipfs-prod-xx-yy 5005:5001` +2. Configure the backend to run locally, but with `PUBLIC_IPFS_RESOLVER=http://host.docker.internal:5005` so it can find content via `pub.desci.com` + +Regardless, do these steps: +1. Run `cp .env.example .env` and fill it in according to the instructions. You need to setup an account, generate an API key, etc. +2. Run `npm start`, which will start creating nodes using nodes-lib against the configured API. + +## Noteworthy fields +Some IJ metadata fields are a bit different than what we're used to in `desci-models`. + +### `abstract` +Suitable to use as `description`, but contains some HTML tags, `\r\n` line feeds, and raw unicode characters: + +``` +An Insight Toolkit (ITK) processing framework for segmentation using active contours without edges \r\nis presented in this paper. Our algorithm is based on the work of Chan and Vese [1] that uses level- \r\nsets to accomplish region segmentation in images with poor or no gradient information. The basic idea \r\nis to partion the image into two piecewise constant intensity regions. This work is in contrast to the \r\nlevel-set methods currently available in ITK which necessarily require gradient information. Similar to \r\nthose methods, the methods presented in this paper are also made ef\ufb01cient using a sparse implementation \r\nstrategy that solves the contour evolution PDE at the level-set boundary. The framework consists of 6 \r\nnew ITK \ufb01lters that inherit in succession from itk::SegmentationFilter. We include 2D/3D example \r\ncode, parameter settings and show the results generated on a 2D cardiac image. +``` + +The raw unicode is removed automatically when we copy it into `local-data`, but the others stay for now. + +### `authors` +- No attached `role`, assume co-author? +- Ordering: in a bunch of cases this array isn't sorted, so rely on the `author_place` key for ordering +- Unclear what the `author[i].persona_id` maps to + +### `reviews` +Peer-review entries. Unclear what the `reviews[i].author.author_id` field maps to. + +Not sure what to do with these. + +### `comments` +Public (?) correspondence on the publication. Some is sort-of peer review-y, but some is very generic. Not sure what to do with these atm. + +View pubs with comments: +```bash +cat local-data/publications/**/metadata.json | jq 'select(.publication.comments[] | length > 0)' +``` + +### `categories` +Similar to `ResearchField`, and much lower dimension than `tags` below. 1868 uses, but only 82 distinct categories. They do seem a bit more specific than research field though, as many of the categories does't have a dito `ResearchField`. + +List tags: +```bash +cat local-data/publications/**/metadata.json | jq '.publication.categories[]' +``` + +### `tags` +Some overlap with our `ResearchField`, but leaning more toward free-form SEO keywords. It seems to be freetext because there are many similar entries, some have the "list" in a single entry, etc. Not sure how/if we should try to match with research fields, because it probably won't be super straight-forward. We have listed the component `keywords` as deprecated, which is kinda what this would be (on the article). + +List all unique tags: +```bash +❯ cat local-data/publications/**/metadata.json | jq --raw-output 'select(.publication.tags != null) | .publication.tags[]' | sort --unique +``` + +
+ All tags (click to expand) + + ``` + Active appearance models + Anisotropic blurring filters + Atlas-based segmentation + Bayesian Decision Theory + Blurring filters + CMake + Classification + Code memory optimization + Code speed optimization + Component Analysis and Discriminants + DART + DICOM + Data + Data Representation + Decision trees and non-metric classification + Deformable registration + Density Estimation + Density Functions + Derivatives and Integrals + Diffusion Tensor Imaging + Discriminant Functions + Distance maps + Distributed computation + Edge Detection + Error Estimation + Extreme Programming + Feature extraction + Filtering + Generic Programming + Geometric transforms + Groupwise registration + Higher order derivatives + Hypothesis Testing + IO + Image + Image pyramids + Images + Information Theory + Iterative clustering + Iterators + Language binding + Level sets + Linear Algebra + Mathematical Morphology + Mathematics + Mesh + Missing and Noisy Features + Mixture of densities + Model-to-image registration + Multi-classifier decision fusion + Multi-modality registration + Neighborhood filters + Neural networks + Non-parametric Techniques + Objects + Optimization + Parallelization, SMP + Parameter Techniques + Path + Point distribution models + PointSet + Probability + Programming + Reformating and tensor reorientation + Region growing + Registration + Registration metrics + Registration optimizers + Regularization and filtering + Resampling + Segmentation + Spatial Objects + Statistical shape models + Statistics on tensors + Streaming + Surface extraction + Tensor image reconstruction + Thresholding + Tractography + Transforms + Unsupervised learning and clustering + Watersheds + ``` + +
+ +One indicator of things being a bit crazy is that there are 2167 tags used in total, and a whopping 1567 unique ones. +```bash +cat local-data/publications/**/metadata.json | jq --raw-output 'select(.publication.tags != null) | .publication.tags[]' | wc -l +2167 + +cat local-data/publications/**/metadata.json | jq --raw-output 'select(.publication.tags != null) | .publication.tags[]' | sort --unique | wc -l +1567 +``` + +### `handle` +A handle.net reference alongside the DOIs, something we don't have support for atm. Example from the IJ webside: + +``` +Please use this identifier to cite or link to this publication: http://hdl.handle.net/1926/53 +New: Prefer using the following doi: https://doi.org/10.54294/o48iej +``` + +### `citation_list` +There is a list of references parsed from latex `\cite` or PDF, which is matched against a CrossRef `query.bibliographic` request. If this has a good match (> 60), the corresponding DOI is included in the struct, but otherwise it isn't. + +More info here: +- https://github.com/InsightSoftwareConsortium/InsightJournal/issues/70 +- https://github.com/InsightSoftwareConsortium/InsightJournal/pull/74 + +Observations: +1. The citation isn't _necessarily_ to the right thing? +2. The `unstructured` key contains more stuff than the title +3. + +### `license` +Holds the full license instead of its code/identifier, but they all seem to be `CC-BY-3.0` so this is used as a constant in the import: + +```bash +❯ cat local-data/publications/*/metadata.json | jq ".publication.license" | sort --unique +"You are licensing your work to Kitware Inc. under the\nCreative Commons Attribution License Version 3.0.\n\nKitware Inc. agrees to the following:\n\nKitware is free\n * to copy, distribute, display, and perform the work\n * to make derivative works\n * to make commercial use of the work\n\nUnder the following conditions:\n\\\"by Attribution\\\" - Kitware must attribute the work in the manner specified by the author or licensor.\n\n * For any reuse or distribution, they must make clear to others the license terms of this work.\n * Any of these conditions can be waived if they get permission from the copyright holder.\n\nYour fair use and other rights are in no way affected by the above.\n\nThis is a human-readable summary of the Legal Code (the full license) available at\nhttp://creativecommons.org/licenses/by/3.0/legalcode" +``` + ### Cover photo +Not in the metadata file, and not on IPFS. How should we handle this? +1. Pin and set in manifest? +2. Something else? diff --git a/toolshed/insight-import/analyseMissing.sh b/toolshed/insight-import/analyseMissing.sh new file mode 100755 index 000000000..ce76320c4 --- /dev/null +++ b/toolshed/insight-import/analyseMissing.sh @@ -0,0 +1,17 @@ +#! /bin/env bash + +set -euo pipefail + +logfile=$1 + +if [ -z "$logfile" ]; then + echo "❌ expected a sync log file as \$1" + exit 1 +fi + +grep ERR "$logfile" | cut -d" " -f2 | while read -r cid; do + grep "$cid" local-data/publications/*/metadata.json \ + | sed -E 's|^.*/([0-9]*)/metadata.json|\1|' \ + | sed -E 's| +| |' \ + | tr -d '":,{}' +done diff --git a/toolshed/insight-import/covers.sh b/toolshed/insight-import/covers.sh new file mode 100755 index 000000000..d60112058 --- /dev/null +++ b/toolshed/insight-import/covers.sh @@ -0,0 +1,20 @@ +#! /bin/env bash + +coverCarDir=local-data/covers +mkdir -p $coverCarDir + +find local-data/publications -name cover.jpeg | while read -r cover; do + echo "πŸ“” Publication $(grep -Eo '[0-9]+' <<< "$cover")" + cid=$(ipfs add --quieter --cid-version=1 "$cover") + echo "- Cover CID: $cid" + echo "- Exporting DAG to $coverCarDir/$cid.car..." + ipfs dag export "$cid" > "$coverCarDir/$cid.car" 2> /dev/null + + echo "- Writing to metadata file: coverImage = $cid" + metadataFile=$(dirname "$cover")/metadata.json + json=$(cat "$metadataFile") + jq ".coverImage = \"$cid\"" <<<"$json" > "$metadataFile" + echo "- Done!" +done + +echo "🏁 All done! Check $coverCarDir and see README for remote ingestion." diff --git a/toolshed/insight-import/generateTsTypes.sh b/toolshed/insight-import/generateTsTypes.sh new file mode 100755 index 000000000..416f7b9ba --- /dev/null +++ b/toolshed/insight-import/generateTsTypes.sh @@ -0,0 +1,18 @@ +#! /bin/env bash + +set -euo pipefail + +tmpdir=/tmp/ij_metadata/IJMetadata +mkdir -p $tmpdir + +for f in local-data/publications/*/metadata.json; do + dir_name=$(basename $(dirname "$f")) + cp "$f" "$tmpdir/${dir_name}-metadata.json" +done + +npx --yes quicktype \ + --prefer-types \ + "$(dirname $tmpdir)" \ + -o src/ijTypes.ts + +rm -r "$(dirname $tmpdir)" diff --git a/toolshed/insight-import/inspectCars.sh b/toolshed/insight-import/inspectCars.sh new file mode 100755 index 000000000..a10161877 --- /dev/null +++ b/toolshed/insight-import/inspectCars.sh @@ -0,0 +1,6 @@ +#! /bin/env bash + +find local-data -name '*.car' \ + -exec echo \; \ + -exec echo "πŸ”Ž {}" \; \ + -exec car inspect {} \; diff --git 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"main": "index.js", + "scripts": { + "generate-types": "./generateTsTypes.sh", + "start": "tsx src/index.ts" + }, + "author": "Edvard HΓΌbinette", + "license": "MIT", + "devDependencies": { + "@types/node": "^20.8.1", + "eslint-import-resolver-typescript": "^3.6.3", + "eslint-plugin-import": "^2.31.0", + "tsx": "^4.19.1", + "typescript": "^5.6.3" + }, + "dependencies": { + "@desci-labs/desci-models": "file:../../desci-models", + "@desci-labs/nodes-lib": "file:../../nodes-lib", + "axios": "^1.7.7", + "dotenv": "^16.4.7" + } +} diff --git a/toolshed/insight-import/rebuildRawArticles.sh b/toolshed/insight-import/rebuildRawArticles.sh new file mode 100755 index 000000000..b61abeb68 --- /dev/null +++ b/toolshed/insight-import/rebuildRawArticles.sh @@ -0,0 +1,51 @@ +#! /bin/env bash + +set -euo pipefail + +if ! command -v ipfs > /dev/null; then + echo 'πŸ™… ipfs is required, please install kubo!' + exit 1 +fi + +missingFile=$1 +if [ -z "$missingFile" ]; then + echo "❌ Expected a file path to the output of analyseMissing.sh as arugment" + exit 1 +fi + +ARTICLE_DAG="bafybeialgmdqikskc56dhy2xrnio2te23xdzqdm77wtqxpxybr3ys5cpli" + +if [ ! -f "$missingFile" ]; then + echo '❌ Need a file with newline separated "cid pub-id" pairs for articles' + exit 1 +fi + +while IFS=" " read -r pubId type cid; do + if [ ! "$type" = "article" ]; then + echo "πŸƒ Skipping non-article CID $cid for pub $pubId" + continue + fi + + carPath="local-data/cars/$cid.car" + if [ -f "$carPath" ]; then + echo "πŸš— Found existing CAR at $carPath, this will be clobbered!" + fi + + url="https://$ARTICLE_DAG.ipfs.dweb.link/ij-articles/$pubId/1/article.pdf" + # These files are unchunked/raw binary DAGS, so the CIDs do not match the metadata files. + # We compute the default chunked DAG, export this to a car, and we get the correct CID. + curl --silent "$url" \ + | ipfs add --quieter --cid-version=1 \ + | xargs ipfs dag export --progress=false \ + > "$carPath" + + if ! car verify "$carPath"; then + echo "πŸ’₯ CAR failed verification for pub $pubId, bad download?" + rm -f "$carPath" + elif [ ! "$(car root "$carPath")" = "$cid" ]; then + echo "😬 CAR root and CID isn't matching for pub $pubId, failed to recreate expected CID" + rm -f "$carPath" + else + echo "πŸš— Article $cid reconstructed for pub $pubId" + fi +done < missing.txt diff --git a/toolshed/insight-import/remoteDagImport.sh b/toolshed/insight-import/remoteDagImport.sh new file mode 100755 index 000000000..914962007 --- /dev/null +++ b/toolshed/insight-import/remoteDagImport.sh @@ -0,0 +1,31 @@ +#! /bin/env bash + +carPath=$1 +pod=$2 + +tmpPath=/tmp/cars_to_import.tar.gz + +if [ -z "$1" ] || [ -z "$2" ]; then + echo '❌ Expected args: path to car dir (1), target pod name (2)' + exit 1 +fi + +set -euo pipefail + +echo "πŸ“₯ Packing cars for transfer..." +find "$carPath" -name "*.car" -print0 \ + | tar --null -T - -czf $tmpPath + +echo "πŸ’Œ Yeeting the lot to pod $pod..." +kubectl cp $tmpPath "$pod:$tmpPath" + +if ! kubectl exec -it "$pod" -- tar --version | grep -q "GNU"; then + echo "✨ Installing GNU tar on pod..." + apk add tar +fi + +echo "πŸ“€ Importing cars on $pod..." +kubectl exec -it "$pod" -- bash -c \ + "tar xzf $tmpPath --to-command='ipfs dag import --stats'" + +echo "🎊 Happy clappy success, probably!" diff --git a/toolshed/insight-import/src/ijTypes.ts b/toolshed/insight-import/src/ijTypes.ts new file mode 100644 index 000000000..4c4e6dadd --- /dev/null +++ b/toolshed/insight-import/src/ijTypes.ts @@ -0,0 +1,429 @@ +// To parse this data: +// +// import { Convert, IJMetadata } from "./file"; +// +// const iJMetadata = Convert.toIJMetadata(json); +// +// These functions will throw an error if the JSON doesn't +// match the expected interface, even if the JSON is valid. + +export type IJMetadata = { + publication: Publication; + coverImage?: string; +} + +export type Publication = { + abstract: null | string; + authors: AuthorElement[]; + categories: string[]; + comments: Comment[]; + date_submitted: string; + journals: Journal[]; + license: string; + publication_id: number; + reviews: Review[]; + revisions: Revision[]; + source_code_git_repo: null | string; + submitted_by_author: SubmittedByAuthor; + tags: string[] | null; + title: string; + articles?: null[]; +} + +export type AuthorElement = { + author_fullname: string; + author_place: number; + persona_email?: string; + persona_firstname?: string; + persona_id: number | null; + persona_lastname?: string; +} + +export type Comment = { + content: string; + date: Date; + persona_email: null | string; + persona_firstname: null | string; + persona_id: number; + persona_lastname: null | string; +} + +export type Journal = { + journal_id: number; + journal_name: JournalName; +} + +export enum JournalName { + TheInsightJournal = "The Insight Journal", + TheMIDASJournal = "The MIDAS Journal", + TheVTKJournal = "The VTK Journal", +} + +export type Review = { + author: ReviewAuthor; + content: string; + date: string; + review_id: number; +} + +export type ReviewAuthor = { + author_email: null | string; + author_firstname: null | string; + author_id: number | null; + author_lastname: null | string; +} + +export type Revision = { + article: null | string; + citation_list?: CitationList[]; + dapp: null; + dataset: null; + doi: string; + handle: string; + source_code: null | string; + source_code_git_ref: null; +} + +export type CitationList = { + doi?: string; + key: Key; + score?: number; + unstructured: string; +} + +export enum Key { + Ref1 = "ref1", + Ref10 = "ref10", + Ref11 = "ref11", + Ref12 = "ref12", + Ref13 = "ref13", + Ref14 = "ref14", + Ref15 = "ref15", + Ref16 = "ref16", + Ref17 = "ref17", + Ref18 = "ref18", + Ref19 = "ref19", + Ref2 = "ref2", + Ref20 = "ref20", + Ref21 = "ref21", + Ref22 = "ref22", + Ref23 = "ref23", + Ref24 = "ref24", + Ref25 = "ref25", + Ref26 = "ref26", + Ref27 = "ref27", + Ref28 = "ref28", + Ref29 = "ref29", + Ref3 = "ref3", + Ref30 = "ref30", + Ref31 = "ref31", + Ref32 = "ref32", + Ref33 = "ref33", + Ref34 = "ref34", + Ref35 = "ref35", + Ref36 = "ref36", + Ref37 = "ref37", + Ref4 = "ref4", + Ref5 = "ref5", + Ref6 = "ref6", + Ref7 = "ref7", + Ref8 = "ref8", + Ref9 = "ref9", +} + +export type SubmittedByAuthor = { + author_email: null | string; + author_firstname: null | string; + author_fullname: string; + author_id: number | null; + author_institution: string; + author_lastname: null | string; +} + +// Converts JSON strings to/from your types +// and asserts the results of JSON.parse at runtime +export class Convert { + public static toIJMetadata(json: string): IJMetadata { + return cast(JSON.parse(json), r("IJMetadata")); + } + + public static iJMetadataToJson(value: IJMetadata): string { + return JSON.stringify(uncast(value, r("IJMetadata")), null, 2); + } +} + +function invalidValue(typ: any, val: any, key: any, parent: any = ''): never { + const prettyTyp = prettyTypeName(typ); + const parentText = parent ? ` on ${parent}` : ''; + const keyText = key ? ` for key "${key}"` : ''; + throw Error(`Invalid value${keyText}${parentText}. Expected ${prettyTyp} but got ${JSON.stringify(val)}`); +} + +function prettyTypeName(typ: any): string { + if (Array.isArray(typ)) { + if (typ.length === 2 && typ[0] === undefined) { + return `an optional ${prettyTypeName(typ[1])}`; + } else { + return `one of [${typ.map(a => { return prettyTypeName(a); }).join(", ")}]`; + } + } else if (typeof typ === "object" && typ.literal !== undefined) { + return typ.literal; + } else { + return typeof typ; + } +} + +function jsonToJSProps(typ: any): any { + if (typ.jsonToJS === undefined) { + const map: any = {}; + typ.props.forEach((p: any) => map[p.json] = { key: p.js, typ: p.typ }); + typ.jsonToJS = map; + } + return typ.jsonToJS; +} + +function jsToJSONProps(typ: any): any { + if (typ.jsToJSON === undefined) { + const map: any = {}; + typ.props.forEach((p: any) => map[p.js] = { key: p.json, typ: p.typ }); + typ.jsToJSON = map; + } + return typ.jsToJSON; +} + +function transform(val: any, typ: any, getProps: any, key: any = '', parent: any = ''): any { + function transformPrimitive(typ: string, val: any): any { + if (typeof typ === typeof val) return val; + return invalidValue(typ, val, key, parent); + } + + function transformUnion(typs: any[], val: any): any { + // val must validate against one typ in typs + const l = typs.length; + for (let i = 0; i < l; i++) { + const typ = typs[i]; + try { + return transform(val, typ, getProps); + } catch (_) {} + } + return invalidValue(typs, val, key, parent); + } + + function transformEnum(cases: string[], val: any): any { + if (cases.indexOf(val) !== -1) return val; + return invalidValue(cases.map(a => { return l(a); }), val, key, parent); + } + + function transformArray(typ: any, val: any): any { + // val must be an array with no invalid elements + if (!Array.isArray(val)) return invalidValue(l("array"), val, key, parent); + return val.map(el => transform(el, typ, getProps)); + } + + function transformDate(val: any): any { + if (val === null) { + return null; + } + const d = new Date(val); + if (isNaN(d.valueOf())) { + return invalidValue(l("Date"), val, key, parent); + } + return d; + } + + function transformObject(props: { [k: string]: any }, additional: any, val: any): any { + if (val === null || typeof val !== "object" || Array.isArray(val)) { + return invalidValue(l(ref || "object"), val, key, parent); + } + const result: any = {}; + Object.getOwnPropertyNames(props).forEach(key => { + const prop = props[key]; + const v = Object.prototype.hasOwnProperty.call(val, key) ? val[key] : undefined; + result[prop.key] = transform(v, prop.typ, getProps, key, ref); + }); + Object.getOwnPropertyNames(val).forEach(key => { + if (!Object.prototype.hasOwnProperty.call(props, key)) { + result[key] = transform(val[key], additional, getProps, key, ref); + } + }); + return result; + } + + if (typ === "any") return val; + if (typ === null) { + if (val === null) return val; + return invalidValue(typ, val, key, parent); + } + if (typ === false) return invalidValue(typ, val, key, parent); + let ref: any = undefined; + while (typeof typ === "object" && typ.ref !== undefined) { + ref = typ.ref; + typ = typeMap[typ.ref]; + } + if (Array.isArray(typ)) return transformEnum(typ, val); + if (typeof typ === "object") { + return typ.hasOwnProperty("unionMembers") ? transformUnion(typ.unionMembers, val) + : typ.hasOwnProperty("arrayItems") ? transformArray(typ.arrayItems, val) + : typ.hasOwnProperty("props") ? transformObject(getProps(typ), typ.additional, val) + : invalidValue(typ, val, key, parent); + } + // Numbers can be parsed by Date but shouldn't be. + if (typ === Date && typeof val !== "number") return transformDate(val); + return transformPrimitive(typ, val); +} + +function cast(val: any, typ: any): T { + return transform(val, typ, jsonToJSProps); +} + +function uncast(val: T, typ: any): any { + return transform(val, typ, jsToJSONProps); +} + +function l(typ: any) { + return { literal: typ }; +} + +function a(typ: any) { + return { arrayItems: typ }; +} + +function u(...typs: any[]) { + return { unionMembers: typs }; +} + +function o(props: any[], additional: any) { + return { props, additional }; +} + +function m(additional: any) { + return { props: [], additional }; +} + +function r(name: string) { + return { ref: name }; +} + +const typeMap: any = { + "IJMetadata": o([ + { json: "publication", js: "publication", typ: r("Publication") }, + { json: "coverImage", js: "coverImage", typ: u(undefined, "") }, + ], false), + "Publication": o([ + { json: "abstract", js: "abstract", typ: u(null, "") }, + { json: "authors", js: "authors", typ: a(r("AuthorElement")) }, + { json: "categories", js: "categories", typ: a("") }, + { json: "comments", js: "comments", typ: a(r("Comment")) }, + { json: "date_submitted", js: "date_submitted", typ: "" }, + { json: "journals", js: "journals", typ: a(r("Journal")) }, + { json: "license", js: "license", typ: "" }, + { json: "publication_id", js: "publication_id", typ: 0 }, + { json: "reviews", js: "reviews", typ: a(r("Review")) }, + { json: "revisions", js: "revisions", typ: a(r("Revision")) }, + { json: "source_code_git_repo", js: "source_code_git_repo", typ: u(null, "") }, + { json: "submitted_by_author", js: "submitted_by_author", typ: r("SubmittedByAuthor") }, + { json: "tags", js: "tags", typ: u(a(""), null) }, + { json: "title", js: "title", typ: "" }, + { json: "articles", js: "articles", typ: u(undefined, a(null)) }, + ], false), + "AuthorElement": o([ + { json: "author_fullname", js: "author_fullname", typ: "" }, + { json: "author_place", js: "author_place", typ: 0 }, + { json: "persona_email", js: "persona_email", typ: u(undefined, "") }, + { json: "persona_firstname", js: "persona_firstname", typ: u(undefined, "") }, + { json: "persona_id", js: "persona_id", typ: u(0, null) }, + { json: "persona_lastname", js: "persona_lastname", typ: u(undefined, "") }, + ], false), + "Comment": o([ + { json: "content", js: "content", typ: "" }, + { json: "date", js: "date", typ: Date }, + { json: "persona_email", js: "persona_email", typ: u(null, "") }, + { json: "persona_firstname", js: "persona_firstname", typ: u(null, "") }, + { json: "persona_id", js: "persona_id", typ: 0 }, + { json: "persona_lastname", js: "persona_lastname", typ: u(null, "") }, + ], false), + "Journal": o([ + { json: "journal_id", js: "journal_id", typ: 0 }, + { json: "journal_name", js: "journal_name", typ: r("JournalName") }, + ], false), + "Review": o([ + { json: "author", js: "author", typ: r("ReviewAuthor") }, + { json: "content", js: "content", typ: "" }, + { json: "date", js: "date", typ: "" }, + { json: "review_id", js: "review_id", typ: 0 }, + ], false), + "ReviewAuthor": o([ + { json: "author_email", js: "author_email", typ: u(null, "") }, + { json: "author_firstname", js: "author_firstname", typ: u(null, "") }, + { json: "author_id", js: "author_id", typ: u(0, null) }, + { json: "author_lastname", js: "author_lastname", typ: u(null, "") }, + ], false), + "Revision": o([ + { json: "article", js: "article", typ: u(null, "") }, + { json: "citation_list", js: "citation_list", typ: u(undefined, a(r("CitationList"))) }, + { json: "dapp", js: "dapp", typ: null }, + { json: "dataset", js: "dataset", typ: null }, + { json: "doi", js: "doi", typ: "" }, + { json: "handle", js: "handle", typ: "" }, + { json: "source_code", js: "source_code", typ: u(null, "") }, + { json: "source_code_git_ref", js: "source_code_git_ref", typ: null }, + ], false), + "CitationList": o([ + { json: "doi", js: "doi", typ: u(undefined, "") }, + { json: "key", js: "key", typ: r("Key") }, + { json: "score", js: "score", typ: u(undefined, 3.14) }, + { json: "unstructured", js: "unstructured", typ: "" }, + ], false), + "SubmittedByAuthor": o([ + { json: "author_email", js: "author_email", typ: u(null, "") }, + { json: "author_firstname", js: "author_firstname", typ: u(null, "") }, + { json: "author_fullname", js: "author_fullname", typ: "" }, + { json: "author_id", js: "author_id", typ: u(0, null) }, + { json: "author_institution", js: "author_institution", typ: "" }, + { json: "author_lastname", js: "author_lastname", typ: u(null, "") }, + ], false), + "JournalName": [ + "The Insight Journal", + "The MIDAS Journal", + "The VTK Journal", + ], + "Key": [ + "ref1", + "ref10", + "ref11", + "ref12", + "ref13", + "ref14", + "ref15", + "ref16", + "ref17", + "ref18", + "ref19", + "ref2", + "ref20", + "ref21", + "ref22", + "ref23", + "ref24", + "ref25", + "ref26", + "ref27", + "ref28", + "ref29", + "ref3", + "ref30", + "ref31", + "ref32", + "ref33", + "ref34", + "ref35", + "ref36", + "ref37", + "ref4", + "ref5", + "ref6", + "ref7", + "ref8", + "ref9", + ], +}; diff --git a/toolshed/insight-import/src/index.ts b/toolshed/insight-import/src/index.ts new file mode 100644 index 000000000..62944a8cf --- /dev/null +++ b/toolshed/insight-import/src/index.ts @@ -0,0 +1,54 @@ +import 'dotenv/config' +import { Convert, IJMetadata } from './ijTypes.js'; +import { makeNode } from './nodes.js'; +import {NODESLIB_CONFIGS, setApiKey, setNodesLibConfig} from '@desci-labs/nodes-lib'; +import {readdir, readFile} from "node:fs/promises"; +import { join } from 'path'; +import {signerFromPkey} from "@desci-labs/nodes-lib/dist/util/signing.js"; + +const PUBLISH_PKEY = process.env.PUBLISH_PKEY; +const API_TOKEN = process.env.NODES_API_TOKEN; +export const USER_ID = Number(process.env.USER_ID); + +if (![PUBLISH_PKEY, API_TOKEN, USER_ID].every(Boolean)) { + console.log('Expected PUBLISH_PKEY, API_TOKEN, USER_ID to both be set in .env'); + process.exit(1); +} +export const SIGNER = signerFromPkey(PUBLISH_PKEY); + +const ENVS = ['local', 'dev', 'prod']; +export const ENV = process.env.ENV || 'local'; +if (!ENVS.includes(ENV)) { + console.log(`Expected ENV to be in ${ENVS}, but got ${ENV}`); + process.exit(1); +} + +setNodesLibConfig(NODESLIB_CONFIGS[ENV]); +setApiKey(API_TOKEN); + +if (![process.env.IJ_ATT_ID, process.env.OC_ATT_ID].every(Boolean)) { + console.log('Attestation ID envvars not set!'); + process.exit(1); +} +export const ATTESTATION_IDS = { + ij: Number(process.env.IJ_ATT_ID), + openCode: Number(process.env.OC_ATT_ID), +}; + +const processPublications = async (rootDir: string) => { + const pubs: Record = {}; + const pubDirs = await readdir(rootDir); + + for (const pubDir of pubDirs) { + const metadataPath = join(rootDir, pubDir, 'metadata.json'); + const rawMetadata = await readFile(metadataPath, 'utf8'); + pubs[pubDir] = Convert.toIJMetadata(rawMetadata); + } + + return pubs; +} + +const pubs = await processPublications('local-data/publications'); +for (const [pub, metadata] of Object.entries(pubs).slice(0,10)) { + await makeNode(metadata) +} diff --git a/toolshed/insight-import/src/nodes.ts b/toolshed/insight-import/src/nodes.ts new file mode 100644 index 000000000..af69ec523 --- /dev/null +++ b/toolshed/insight-import/src/nodes.ts @@ -0,0 +1,354 @@ +import { + License, + ManifestActions, + ResearchObjectComponentCodeSubtype, + ResearchObjectComponentDocumentSubtype, + ResearchObjectComponentLinkSubtype, + ResearchObjectComponentType, + ResearchObjectReference, + ResearchObjectV1Author, + ResearchObjectV1AuthorRole, +} from '@desci-labs/desci-models'; +import type { AuthorElement, CitationList, IJMetadata, Revision, SubmittedByAuthor } from './ijTypes.js'; +import { + addExternalCid, + addLinkComponent, + AddLinkComponentParams, + changeManifest, + claimAttestation, + createDraftNode, + publishNode, + uploadFiles +} from '@desci-labs/nodes-lib'; +import { existsSync, readFileSync, writeFileSync } from 'fs'; +import { ATTESTATION_IDS, ENV, SIGNER, USER_ID } from "./index.js"; +import { getCodexHistory } from "@desci-labs/nodes-lib/dist/codex.js"; +import { AxiosError } from 'axios'; + +/** Whacky little DB approximation that saves pub:uuid mappings to enable re-runs to continue */ +let existingNodes: Record; +const getExistingNode = (pubId: number): string | undefined => { + if (existingNodes) { + return existingNodes[pubId]; + } else if (existsSync(`existingNodes_${ENV}.json`)) { + existingNodes = JSON.parse(readFileSync(`existingNodes_${ENV}.json`, 'utf8')); + return existingNodes[pubId]; + } else { + existingNodes = {}; + return undefined; + } +}; + +process.on('exit', () => { + console.log(`Process exits; writing uuid mappings to ${`existingNodes_${ENV}.json`}...`); + if (existingNodes) { + writeFileSync(`existingNodes_${ENV}.json`, JSON.stringify(existingNodes, undefined, 2)); + } +}); + +export const makeNode = async (ijMetadata: IJMetadata) => { + const ijPub = ijMetadata.publication; + + let uuid = getExistingNode(ijPub.publication_id); + if (uuid) { + console.log(`πŸ“— Pub ${ijPub.publication_id}: Re-using node ${uuid}`); + } else { + const draftResult = await createDraftNode({ + title: ijPub.title, + defaultLicense: parseLicense(ijPub.license) satisfies License, + // Unclear how to map categories and/or tags to this, not much overlap + researchFields: [], + }); + console.log(`πŸ“— Pub: ${ijPub.publication_id}: Created new node ${draftResult.node.uuid}`); + uuid = draftResult.node.uuid; + existingNodes[ijPub.publication_id] = uuid + } + + if (ijPub.source_code_git_repo) { + const params: AddLinkComponentParams = { + name: 'External git repo', + url: ijPub.source_code_git_repo, + subtype: ResearchObjectComponentLinkSubtype.OTHER, + starred: false, + }; + + await addLinkComponent(uuid, params); + } + + const manifestActions = renderStaticManifestActions(ijMetadata); + await changeManifest(uuid, manifestActions); + + const filePathsToUpload = [ + maybeWriteTmpFile('comments.md', renderCommentsMarkdown(ijPub)), + maybeWriteTmpFile('reviews.md', renderReviewsMarkdown(ijPub)), + maybeWriteTmpFile('insight-journal-metadata.json', JSON.stringify(ijPub, undefined, 2)), + ].filter(p => p !== undefined) + await uploadMissingFiles(uuid, filePathsToUpload); + + await publishRevisions(uuid, ijPub.revisions); +} + +const renderStaticManifestActions = (ijMetadata: IJMetadata): ManifestActions[] => { + const ijPub = ijMetadata.publication; + const manifestActions: ManifestActions[] = []; + if (ijPub.abstract) { + manifestActions.push({ type: 'Update Description', description: ijPub.abstract }); + } + + if (ijMetadata.coverImage) { + manifestActions.push({ type: 'Update CoverImage', cid: ijMetadata.coverImage }); + } + + const contributors = parseAuthors(ijPub.submitted_by_author, ijPub.authors); + manifestActions.push({ type: 'Set Contributors', contributors: contributors }); + + return manifestActions; +} + +const renderCommentsMarkdown = (ijPub: IJMetadata['publication']): string | undefined => { + if (ijPub.comments.length === 0) { + return undefined; + } + + const mdShards = ['# Correspondence']; + for (const { content, date, persona_firstname, persona_lastname, persona_email } of ijPub.comments) { + const author = `${persona_firstname} ${persona_lastname} <${persona_email}>`; + const fancyDate = formatDatetime(date); + + mdShards.push( + `## ${author}`, + `*${fancyDate}*`, + '', + content, + '', + ); + } + return mdShards.join('\n'); +} + +const renderReviewsMarkdown = (ijPub: IJMetadata['publication']): string | undefined => { + if (ijPub.reviews.length === 0) { + return undefined; + } + + const mdShards = ['# Reviews']; + for (const { author: authorObj, content, date } of ijPub.reviews) { + const { author_firstname, author_lastname, author_email } = authorObj; + const author = `${author_firstname} ${author_lastname} <${author_email}>`; + const fancyDate = formatDateStr(date); + + mdShards.push( + `## ${author}`, + `*${fancyDate}*`, + '', + content, + '', + ); + } + return mdShards.join('\n'); +} + +/** + * Iterates over revisions to perform draft updates and publishes + */ +const publishRevisions = async (uuid: string, revisions: Revision[]): Promise => { + for (const rev of revisions) { + const currentRev = revisions.indexOf(rev); + console.log('- Handling rev', currentRev, '...'); + if (rev.article) { + try { + await addExternalCid({ + uuid, + externalCids: [{ name: 'article.pdf', cid: rev.article }], + contextPath: '/', + componentType: ResearchObjectComponentType.PDF, + componentSubtype: ResearchObjectComponentDocumentSubtype.RESEARCH_ARTICLE, + autoStar: true, + }) + console.log(' - Added article CID:', rev.article); + } catch (e) { + const err = e as Error; + if (err.message.includes('409')) { + console.log(' - Skipping duplicate CID for article:', rev.article); + } else { + console.log({ err: err.name, msg: err.message }) + throw err; + } + } + } + + if (rev.source_code) { + try { + await addExternalCid({ + uuid, + externalCids: [{ name: 'code', cid: rev.source_code }], + contextPath: '/', + componentType: ResearchObjectComponentType.CODE, + componentSubtype: ResearchObjectComponentCodeSubtype.CODE_SCRIPTS, + autoStar: true, + }) + console.log(' - Added code CID:', rev.source_code); + } catch (e) { + const err = e as Error; + if (err.message.includes('409')) { + console.log(' - Skipping duplicate CID for code:', rev.source_code); + } else { + console.log({ err: err.name, msg: err.message }) + throw err; + } + } + } + + const references = parseReferences(rev?.citation_list); + if (references) { + console.log(' - Settings references...'); + await changeManifest(uuid, [{ type: 'Set References', references: references }]); + } + + console.log(' - Calling publish...'); + const { dpid } = await publishNode(uuid, SIGNER); + console.log(' - Claiming attestations...'); + await claimAttestations(uuid, dpid, !!rev.source_code); + } + +} + +// Seems to be only cc-by-3.0, so we do a safety check and write a constant instead of parsing +const parseLicense = (licenseText: string): License => { + if (licenseText.includes('licenses/by/3.0')) { + return 'CC-BY-3.0' + } else { + console.error('Unknown license:', licenseText); + throw new Error('Unknown license'); + } +} + +const BAD_INSTITUTIONS = ["", " ", "none"]; + +/** + * Metadata files not sorted, so re-order using `author_place` + * We can't set organization without a ROR, which is unavailable in the data. + */ +const parseAuthors = (submitter: SubmittedByAuthor, authors: AuthorElement[]): ResearchObjectV1Author[] => { + // const realSubInstitution = !BAD_INSTITUTIONS.includes(submitter.author_institution); + // const submitterOrg = realSubInstitution + // ? { id: "??", name: submitter.author_institution } + // : undefined; + + return authors + .sort((a1, a2) => a1.author_place - a2.author_place) + .map(a => ({ + name: a.author_fullname, + email: a.persona_email, + role: ResearchObjectV1AuthorRole.AUTHOR, + // ...(submitterOrg ? { organizations: [submitterOrg] } : {}), + })); +} + +/** Takes citations that were successfully matched to a DOI */ +const parseReferences = (citations: CitationList[] | undefined): ResearchObjectReference[] | undefined => { + if (!citations) { + return undefined; + } + const references = citations + .filter(c => c.doi) + .map(c => ({ + type: 'doi' as const, + id: c.doi! + })); + + if (references.length === 0) { + return undefined; + } else { + return references; + } +} + +const formatDateStr = (dateStr: string): string => + new Date(dateStr).toLocaleDateString('en-GB', { + weekday: 'long', + year: 'numeric', + month: 'long', + day: 'numeric', + }); + +const formatDatetime = (date: Date): string => + date.toLocaleString('en-GB', { + weekday: 'long', + year: 'numeric', + month: 'long', + day: 'numeric', + hour: '2-digit', + minute: '2-digit', + hourCycle: 'h23', + }); + +const maybeWriteTmpFile = (filename: string, content?: string): string | undefined => { + if (!content) { + return undefined; + } + const path = `/tmp/${filename}`; + writeFileSync(path, content); + return path; +} + + +const uploadMissingFiles = async (uuid: string, filePathsToUpload: string[]): Promise => { + for (const file of filePathsToUpload) { + try { + await uploadFiles({ + uuid, + contextPath: '/', + files: [file], + }); + console.log('- Uploaded file', file); + } catch (e) { + const err = e as Error; + if (err.message.includes('409')) { + console.log('- Skipping duplicate file', file); + } else { + console.log({ err: err.name, msg: err.message }) + throw err; + } + } + } +} + +const claimAttestations = async ( + nodeUuid: string, + nodeDpid: number, + openCode: boolean, +) => { + if (openCode) { + console.log(' - Claiming OpenCode...') + await tryClaimIgnoreDupeErr(() => claimAttestation({ + attestationId: ATTESTATION_IDS.openCode, + claimerId: USER_ID, + nodeDpid: String(nodeDpid), + nodeUuid, + nodeVersion: 0 + })); + } + console.log(' - Claiming Published in Insight Journal...') + await tryClaimIgnoreDupeErr(() => claimAttestation({ + attestationId: ATTESTATION_IDS.ij, + claimerId: USER_ID, + nodeDpid: String(nodeDpid), + nodeUuid, + nodeVersion: 0 + })); +} + +const tryClaimIgnoreDupeErr = async (apiCall: () => Promise) => { + try { + return await apiCall() + } catch (e) { + const err = e as Error; + if (err.message.includes('403')) { + // If it was actually an auth issue, we wouldn't get this far, so assume it's already-exists + console.log(' - Skipping duplicate claim...') + } else { + throw e; + } + } +} diff --git a/toolshed/insight-import/sync.sh b/toolshed/insight-import/sync.sh new file mode 100755 index 000000000..4874ef554 --- /dev/null +++ b/toolshed/insight-import/sync.sh @@ -0,0 +1,113 @@ +#! /bin/env bash + +set -euo pipefail + +if ! command -v lassie > /dev/null; then + echo 'πŸ™… Lassie and go-car are required, please install these tools!' + echo "πŸ‘‰ https://github.com/filecoin-project/lassie?tab=readme-ov-file#installation" + # shellcheck disable=SC2016 + echo '(psst, make sure ~/go/bin is in your $PATH !)' + exit 1 +fi + +insight_path=.insight-journal-clone +data_path=local-data +logfile="cids_$(date --iso-8601=seconds --utc | sed 's/+00:00/Z/').log" + +# Refresh cloned state +mkdir -p $data_path/{issues,publications} + +if [ -d $insight_path ]; then + cd $insight_path + git pull --ff-only --depth=1 > /dev/null + cd - +else + git clone --depth=1 \ + git@github.com:InsightSoftwareConsortium/InsightJournal.git \ + $insight_path > /dev/null +fi + +# Copy issue manifests +cp $insight_path/data/issues/*.json $data_path/issues + +verify () { + local cid=$1 + local file=$2 + + # 1. check archive is well-formed + # 2. check that the car root is the same cid we wanted + # 3. check the entire dag is included (no link leaves) + car verify "$file" && \ + car root "$file" | grep -q "$cid" && \ + car get-dag --strict "$file" /dev/null +} + +download () { + local cid=$1 + local target=$2 + + # First try nftstorage racing aggregator, fall back to IPNI discovery + if ! lassie fetch \ + --output "$target" \ + --providers='https://nftstorage.link' \ + --provider-timeout=20s \ + "$cid" + then + echo "⛑️ aggregator gateway failed, retrying with IPNI discovery..." + lassie fetch \ + --output "$target" \ + --provider-timeout=20s \ + "$cid" + fi +} + +fetch () { + local cid=$1 + local outdir=$2 + local target="$outdir/$cid.car" + + # if we have a file for this CID, verify the content + if [ -f "$target" ]; then + if verify "$cid" "$target"; then + echo "HAS $cid" | tee -a "$logfile" + return + else + # delete and retry if the car fails checks + echo "DEL $cid" | tee -a "$logfile" + rm "$target" + fi + fi + + if download "$cid" "$target" && verify "$cid" "$target"; then + echo "GOT $cid" | tee -a "$logfile" + else + # lassie exited nonzero; delete just in case it's partial + echo "ERR $cid" | tee -a "$logfile" + rm -f "$target" + fi +} + +while read -r file; do + pub_id=$(basename "$(dirname "$file")") + outdir="$data_path/publications/${pub_id}" + cardir="$data_path/cars" + + mkdir -p "$outdir" + # Write a copy with jq to replace ascii unicode escapes and convert encoding to utf-8 + jq "." "$file" > "$outdir/metadata.json" + + cover_file=$(dirname "$file")/cover.jpeg + if [ -f "$cover_file" ]; then + cp "$cover_file" "$outdir/cover.jpeg" + fi + + cids=$(grep -Eo 'b[0-9a-z]{58}' "$file" || true) + if [ -n "$cids" ]; then + while read -r cid; do + fetch "$cid" "$cardir" + done <<< "$cids" + fi +done < <(find $insight_path/data/publications -type f -name "metadata.json") + +echo "Data fetch successful 🏁" +echo "Finished at $(date --iso-8601=seconds --utc | sed 's/+00:00/Z/')" diff --git a/toolshed/insight-import/tsconfig.json b/toolshed/insight-import/tsconfig.json new file mode 100644 index 000000000..c9f989352 --- /dev/null +++ b/toolshed/insight-import/tsconfig.json @@ -0,0 +1,17 @@ +{ + /** https://www.typescriptlang.org/docs/handbook/modules/guides/choosing-compiler-options.html */ + "compilerOptions": { + /** Maximise compatibility with ESM/cjs and importer `moduleResolution: bundler` setting */ + "module": "nodenext", + "target": "es2020", + + /** Import friendliness */ + "noEmit": true, + +// "resolveJsonModule": true, + + /** Misc hygiene */ + "forceConsistentCasingInFileNames": true, + "noImplicitReturns": true + } +}