Merge branch 'develop' of https://github.com/desci-labs/nodes into re…

…po-service

.ceramicDev.config.json

@@ -0,0 +1,35 @@
+{
+  "anchor": { },
+  "http-api": {
+    "cors-allowed-origins": [
+      ".*"
+    ],
+    "admin-dids": [
+      "did:key:z6MktbKJrMnhVJ37QFTo12911ycm2juKDUzWHDVETu9s5a9T"
+    ]
+  },
+  "ipfs": {
+    "mode": "remote",
+    "host": "http://host.docker.internal:5001"
+  },
+  "logger": {
+    "log-level": 2
+  },
+  "metrics": {
+    "metrics-exporter-enabled": false,
+    "metrics-port": 9090
+  },
+  "network": {
+    "name": "inmemory"
+  },
+  "node": {},
+  "state-store": {
+    "mode": "fs",
+    "local-directory": "/root/.ceramic/statestore"
+  },
+  "indexing": {
+    "db": "postgres://walter:white@db_postgres:5432/postgres",
+    "allow-queries-before-historical-sync": true,
+    "models": []
+  }
+}

.env.example

@@ -91,4 +91,8 @@ ORCID_CLIENT_ID=
 ORCID_CLIENT_SECRET=
 
 REPO_SERVER_URL=http://host.docker.internal:5445
-REPO_SERVICE_SECRET_KEY=secretrepo
+REPO_SERVICE_SECRET_KEY=secretrepo
+# Ceramic publish feature toggle, set to 1 for active
+TOGGLE_CERAMIC=
+# If above is set, clone `@desci-labs/desci-codex` and put the path to it here
+CODEX_REPO_PATH=

README.md

@@ -112,6 +112,9 @@ This starts:
 4. expedition explorer for local dev (http://localhost:3001)
 5. graph index pointing to latest deployed contract (http://localhost:8080)
 6. Local IPFS node (private, swarm key enabled) (http://localhost:5001 or http://localhost:8089)
+7. Local Ceramic node, run `bootstrapCeramic.sh` to initialize (http://localhost:7007)
+
+**Note:** The Ceramic publish functionality needs to be activated by setting the corresponding environment variable, see `.env.example` for instructions.
 
 **Note:** nodes-media (http://localhost:5454, responsible for DOI / PDF downloads, and for media transcoding) is disabled in the dev cluster by default, but can be uncommented in `docker-compose.dev.yml` for local development
 <br>

bootstrapCeramic.sh

@@ -0,0 +1,60 @@
+#! /usr/bin/env bash
+
+# This script will try to find the `desci-codex` repo and run the
+# model deployments. This yields a runtime definition file, which is
+# necessary to instantiate the composeDB client used for publishing.
+#
+# This needs to be re-run when local-data is cleaned, as the models will
+# get new streamIDs, and hence the runtime definition file is changed.
+#
+# There is no damage trying to run this multiple times in a row; it's
+# idempotent.
+
+CTX="[bootstrapCeramic.sh]"
+
+set -euo pipefail
+trap catch ERR
+catch() {
+  echo "$CTX script failed"
+  exit 1
+}
+
+# Assert running from repo root
+if [[ ! -f .env ]]; then
+  echo "$CTX Must run from repo root, aborting!"
+  exit 1
+fi
+
+# Assert desci-codex repo available
+CODEX_REPO_PATH=$(grep "CODEX_REPO_PATH" .env | cut -d"=" -f2)
+if [[ -z "$CODEX_REPO_PATH" ]]; then
+  echo "$CTX CODEX_REPO_PATH not set in .env, aborting!"
+  exit 1
+else
+  echo "$CTX Found codex repo path: $CODEX_REPO_PATH"
+fi
+
+# Assert ceramic service is running
+RUNNING_SERVICES=$(docker compose --project-name desci ps --services)
+if ! grep -q ceramic <<<"$RUNNING_SERVICES"; then
+  echo "$CTX the ceramic compose service doesn't seem to be running, aborting!"
+  exit 1
+fi
+
+# Setup desci-codex and deploy composites
+pushd "$CODEX_REPO_PATH"
+if [[ ! -d "node_modules" ]]; then
+  echo "$CTX installing deps desci-codex..."
+  npm ci
+fi
+
+echo "$CTX deploying composites..."
+npm run --workspace packages/composedb deployComposites
+popd
+
+echo "$CTX composites deployed! Copying composite runtime definition to local-data/ceramic..."
+cp \
+  "$CODEX_REPO_PATH/packages/composedb/src/__generated__/definition.js" \
+  local-data/ceramic/definition.js
+
+echo "$CTX Done! Re-run this script if local state is cleaned."

desci-contracts/scripts/seed.sh

@@ -28,7 +28,7 @@ check() {
   done
 
   echo "[seed:$CONTRACT_NAME] deployment found, killing ganache..."
-  ps aux | grep ganache-cli | grep -v grep | awk '{print $2}' | xargs -r -t kill || echo "[seed:$CONTRACT_NAME] ganache not running"
+  pkill -f "npm exec ganache" || echo "[seed:$CONTRACT_NAME] ganache not running"
   echo "[seed:$CONTRACT_NAME] ganache killed"
 }
 

desci-models/.prettierignore

@@ -0,0 +1 @@
+dist

desci-models/.prettierrc

@@ -0,0 +1,6 @@
+{
+  "printWidth": 120,
+  "semi": true,
+  "singleQuote": true,
+  "trailingComma": "all"
+}

desci-models/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@desci-labs/desci-models",
-  "version": "0.1.22",
+  "version": "0.2.1",
   "description": "Data models for DeSci Nodes",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

desci-models/src/ResearchObject.ts

@@ -12,11 +12,11 @@ export interface ResearchObjectPreviewResult {
 }
 
 export interface IpldUrl {
-  ["/"]: string;
+  ['/']: string;
 }
 
 export interface ResearchObjectV1 extends ResearchObject {
-  version: "desci-nodes-0.1.0" | "desci-nodes-0.2.0" | 1;
+  version: 'desci-nodes-0.1.0' | 'desci-nodes-0.2.0' | 1;
   title?: string;
   description?: string;
   defaultLicense?: string;
@@ -80,12 +80,12 @@ export interface ResearchObjectTransaction {
 }
 
 export enum ResearchObjectValidationType {
-  GRANT = "grant",
-  REVIEW = "review",
-  CONFERENCE = "conference",
-  AUDIT = "audit",
-  CERTIFICATION = "certification",
-  CERTIFICATION_ARC = "certification-arc",
+  GRANT = 'grant',
+  REVIEW = 'review',
+  CONFERENCE = 'conference',
+  AUDIT = 'audit',
+  CERTIFICATION = 'certification',
+  CERTIFICATION_ARC = 'certification-arc',
 }
 export interface ResearchObjectValidationDeposit {
   token: string;
@@ -105,13 +105,13 @@ export interface ResearchObjectV1Validation {
 }
 
 export enum ResearchObjectAttributeKey {
-  ACM_AVAILABLE = "available",
-  ACM_FUNCTIONAL = "functional",
-  ACM_REUSABLE = "reusable",
-  ACM_REPRODUCED = "reproduced",
-  ACM_REPLICATED = "replicated",
-  AUTHORSHIP_VERIFIED = "authorship-verified",
-  COMPUTATIONAL_REPRODUCIBILITY = "computational-reproducibility",
+  ACM_AVAILABLE = 'available',
+  ACM_FUNCTIONAL = 'functional',
+  ACM_REUSABLE = 'reusable',
+  ACM_REPRODUCED = 'reproduced',
+  ACM_REPLICATED = 'replicated',
+  AUTHORSHIP_VERIFIED = 'authorship-verified',
+  COMPUTATIONAL_REPRODUCIBILITY = 'computational-reproducibility',
 }
 
 export interface ResearchObjectV1Attributes {
@@ -120,36 +120,55 @@ export interface ResearchObjectV1Attributes {
 }
 
 export enum ResearchObjectComponentType {
-  DATA_BUCKET = "data-bucket",
-  UNKNOWN = "unknown",
-  PDF = "pdf",
-  CODE = "code",
-  VIDEO = "video",
-  TERMINAL = "terminal", // not used, TODO: remove
-  DATA = "data",
-  LINK = "link", // external link
+  DATA_BUCKET = 'data-bucket',
+  UNKNOWN = 'unknown',
+  PDF = 'pdf',
+  CODE = 'code',
+  VIDEO = 'video',
+  TERMINAL = 'terminal', // not used, TODO: remove
+  DATA = 'data',
+  LINK = 'link', // external link
 }
 
 export enum ResearchObjectComponentDocumentSubtype {
-  RESEARCH_ARTICLE = "research-article",
-  PREREGISTERED_REPORT = "preregistered-report",
-  PREREGISTERED_ANALYSIS_PLAN = "preregistered-analysis-plan",
-  SUPPLEMENTARY_INFORMATION = "supplementary-information",
-  PRESENTATION_DECK = "presentation-deck",
-  OTHER = "other",
+  RESEARCH_ARTICLE = 'research-article',
+  PREREGISTERED_REPORT = 'preregistered-report',
+  PREREGISTERED_ANALYSIS_PLAN = 'preregistered-analysis-plan',
+  SUPPLEMENTARY_INFORMATION = 'supplementary-information',
+  PRESENTATION_DECK = 'presentation-deck',
+  AUTHOR_ACCEPTED = 'author-accepted',
+  PREPRINT = 'preprint',
+  REVIEW_REPORT = 'review-report',
+  MANUSCRIPT = 'manuscript',
+  OTHER = 'other',
+}
+
+export enum ResearchObjectComponentDataSubtype {
+  PROCESSED_DATA = 'processed-data',
+  RAW_DATA = 'raw-data',
+  IMAGE = 'image',
+  OTHER = 'other',
+}
+
+export enum ResearchObjectComponentCodeSubtype {
+  CODE_SCRIPTS = 'code-scripts',
+  SOFTWARE_PACKAGE = 'software-package',
+  OTHER = 'other',
 }
 
 export enum ResearchObjectComponentLinkSubtype {
-  COMMUNITY_DISCUSSION = "community-discussion",
-  VIDEO_RESOURCE = "video-resource",
-  EXTERNAL_API = "external-api",
-  RESTRICTED_DATA = "restricted",
-  PRESENTATION_DECK = "presentation-deck",
-  OTHER = "other",
+  COMMUNITY_DISCUSSION = 'community-discussion',
+  VIDEO_RESOURCE = 'video-resource',
+  EXTERNAL_API = 'external-api',
+  RESTRICTED_DATA = 'restricted',
+  PRESENTATION_DECK = 'presentation-deck',
+  OTHER = 'other',
 }
 
 export type ResearchObjectComponentSubtypes =
   | ResearchObjectComponentDocumentSubtype
+  | ResearchObjectComponentDataSubtype
+  | ResearchObjectComponentCodeSubtype
   | ResearchObjectComponentLinkSubtype;
 
 export interface CommonComponentPayload {
@@ -189,8 +208,8 @@ export interface DataComponentPayload {
 
 export interface DataBucketComponent extends ResearchObjectV1Component {
   type: ResearchObjectComponentType.DATA_BUCKET;
-  id: "root";
-  name: "root";
+  id: 'root';
+  name: 'root';
   payload: DataBucketComponentPayload;
 }
 export interface DataBucketComponentPayload {
@@ -211,11 +230,13 @@ export interface ExternalLinkComponent extends ResearchObjectV1Component {
 
 export interface DataComponent extends ResearchObjectV1Component {
   type: ResearchObjectComponentType.DATA;
+  subtype?: ResearchObjectComponentDataSubtype;
   payload: DataComponentPayload & DataComponentMetadata;
 }
 
 export interface CodeComponent extends ResearchObjectV1Component {
   type: ResearchObjectComponentType.CODE;
+  subtype?: ResearchObjectComponentCodeSubtype;
   payload: {
     language?: string;
     code?: string;
@@ -247,9 +268,7 @@ export interface Scaled {
   pageIndex?: number;
 }
 
-export interface PdfAnnotation
-  extends ResearchObjectComponentAnnotation,
-    Scaled {
+export interface PdfAnnotation extends ResearchObjectComponentAnnotation, Scaled {
   move?: boolean;
   text?: string;
   title?: string;
@@ -264,8 +283,8 @@ export interface ResearchObjectComponentAnnotation {
 }
 
 export enum ResearchObjectV1AuthorRole {
-  AUTHOR = "Author",
-  NODE_STEWARD = "Node Steward",
+  AUTHOR = 'Author',
+  NODE_STEWARD = 'Node Steward',
 }
 
 /**
@@ -277,8 +296,5 @@ export enum ResearchObjectV1AuthorRole {
  *    '.pdf': ResearchObjectComponentType.PDF
  * }
  */
-export type ResearchObjectComponentTypeMap = Record<
-  FileExtension,
-  ResearchObjectComponentType
->;
+export type ResearchObjectComponentTypeMap = Record<FileExtension, ResearchObjectComponentType>;
 export type FileExtension = string;

desci-server/prisma/migrations/20240110092031_add_ceramic_streamid_to_node/migration.sql

@@ -0,0 +1,2 @@
+-- AlterTable
+ALTER TABLE "Node" ADD COLUMN     "ceramicStream" TEXT;

desci-server/prisma/schema.prisma

@@ -37,6 +37,7 @@ model Node {
   deletedAt           DateTime?
   UploadJobs          UploadJobs[]
   DraftNodeTree       DraftNodeTree[]
+  ceramicStream       String?
 
   @@index([ownerId])
   @@index([uuid])

desci-server/src/controllers/nodes/prepublish.ts

@@ -18,6 +18,7 @@ export interface PrepublishSuccessResponse {
   updatedManifestCid: string;
   updatedManifest: ResearchObjectV1;
   version?: NodeVersion;
+  ceramicStream?: string;
 }
 
 export interface PrepublishErrorResponse {
@@ -39,6 +40,7 @@ export const prepublish = async (req: RequestWithNode, res: Response<PrepublishR
     body: req.body,
     uuid,
     user: (req as any).user,
+    ceramicStream: node.ceramicStream,
   });
   if (!uuid) {
     return res.status(400).json({ ok: false, error: 'UUID is required.' });
@@ -89,6 +91,7 @@ export const prepublish = async (req: RequestWithNode, res: Response<PrepublishR
       updatedManifestCid: persistedManifestCid,
       updatedManifest: updatedManifest,
       version: nodeVersion,
+      ceramicStream: node.ceramicStream,
     });
   } catch (err) {
     logger.error({ err }, '[prepublish::prepublish] node-pre-publish-err');