Merge pull request #228 from desci-labs/develop

promote main

.env.example

@@ -5,7 +5,7 @@ PORT=5420
 IPFS_NODE_URL=http://host.docker.internal:5001
 PUBLIC_IPFS_RESOLVER=https://ipfs.io
 
-# IPFS_RESOLVER_OVERRIDE=http://host.docker.internal:8089/ipfs
+IPFS_RESOLVER_OVERRIDE=http://host.docker.internal:8089/ipfs
 
 ### Database - Postgres
 PG_HOST=db_boilerplate
@@ -90,9 +90,13 @@ ORCID_API_DOMAIN=https://api.sandbox.orcid.org
 ORCID_CLIENT_ID=
 ORCID_CLIENT_SECRET=
 
-REPO_SERVER_URL=http://host.docker.internal:5445
+REPO_SERVER_URL=http://host.docker.internal:5484
 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=
+
+# SET TO 1 to run communities seed script
+RUN=1

.github/workflows/build-and-test.yaml

@@ -58,7 +58,6 @@ jobs:
       - name: Run tests
         run: |
           cd desci-server && export DOCKER_BUILDKIT=1 && yarn && yarn test
-          echo "exit code $?"
           if [ $? -ne 0 ]; then
             exit 1
-          fi
+          fi

.github/workflows/nodes-lib-docs.yml

@@ -0,0 +1,50 @@
+on:
+  push:
+    branches:
+      - develop
+    paths:
+      - nodes-lib/**
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  generate:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Configure GitHub Pages
+        uses: actions/configure-pages@v3
+
+      - uses: actions/setup-node@v3
+        with:
+          node-version-file: .nvmrc
+          cache: npm
+          cache-dependency-path: nodes-lib/package-lock.json
+
+      - name: Generate docs
+        run: |
+          cd nodes-lib
+          npm ci
+          npx typedoc src/index.ts
+      
+      - name: Upload GitHub Pages artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          path: nodes-lib/docs
+
+  deploy:
+    needs: generate
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.nvmrc

@@ -1 +1 @@
-16.16.0
+18.16.0

.vscode/settings.json

@@ -20,5 +20,11 @@
     "tw\\(.*?\\).*?`([^`]*)" // tw(Component)<xxx>`...`
   ],
   "editor.defaultFormatter": "esbenp.prettier-vscode",
-  "editor.formatOnSave": true
+  "editor.formatOnSave": true,
+  "[prisma]": {
+    "editor.defaultFormatter": "Prisma.prisma"
+  },
+  "[sql]": {
+    "editor.defaultFormatter": "ms-mssql.mssql"
+  }
 }

Makefile

@@ -3,6 +3,7 @@ build: .env desci-contracts/.env
 	$(MAKE) -C desci-models build
 	$(MAKE) -C desci-contracts build
 	$(MAKE) -C desci-server install
+	$(MAKE) -C desci-repo install
 
 .PHONY: sterile
 sterile: clean-rec
@@ -23,20 +24,21 @@ clean-rec:
 	$(MAKE) -C desci-contracts clean
 	$(MAKE) -C desci-models clean
 	$(MAKE) -C desci-server clean
+	$(MAKE) -C desci-repo clean
 
 .PHONY: .env
 .env: nodes-media/.env desci-repo/.env
 	# Phony target, always runs but is idempotent
 	# Copies example env if not present, and fails until MNEMONIC is set
-	cp --no-clobber .env.example .env || true
+	if [ ! -f .env ]; then cp .env.example .env; fi
 	if ! grep -q MNEMONIC .env; then echo "ERROR: set MNEMONIC in .env"; exit 1; fi
 
 desci-contracts/.env: .env
 	grep "MNEMONIC" .env > desci-contracts/.env
 
 nodes-media/.env:
-	cp nodes-media/.env.example nodes-media/.env
+	if [ ! -f nodes-media/.env ]; then cp nodes-media/.env.example nodes-media/.env; fi
 
 desci-repo/.env:
-	cp desci-repo/.env.example desci-repo/.env
+	if [ ! -f desci-repo/.env ]; then cp desci-repo/.env.example desci-repo/.env; fi
 

README.md

@@ -75,6 +75,11 @@ This is a Typescript types library that describes a spec for Research Objects. I
 This is a NodeJS backend that manages draft Nodes. It maintains a user auth, verifies wallet credentials, offers 2FA to users, and is the main system that orchestrates between microservices. It maintains version history for each update to Nodes. It interfaces with a Graph index to implement the [DPID](https://dpid.org) Resolution Scheme.
 <br><br>
 
+## **nodes-lib**
+
+A library for programmatically interacting with Nodes, basically allowing automation of actions possible in the webapp. See separate documentation in the [README](./nodes-lib/README.md)
+<br><br>
+
 ## **desci-art-viewer**
 
 Nobody knows why this is still here, but it implements a React+Three.js 3d torus that plays [Conway's Game of Life](https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life) on the surface of the torus. We were totally inspired by [this gif on Wikipedia](https://en.wikipedia.org/wiki/Conway%27s_Game_of_Life#/media/File:Trefoil_knot_conways_game_of_life.gif) and it only seems to work on Mac/Linux right now, YMMV.

bootstrapCeramic.sh

@@ -15,7 +15,7 @@ CTX="[bootstrapCeramic.sh]"
 set -euo pipefail
 trap catch ERR
 catch() {
-  echo "$CTX script failed"
+  echo "$CTX script failed (are CODEX_REPO_PATH and TOGGLE_CERAMIC set in .env?)"
   exit 1
 }
 
@@ -43,6 +43,13 @@ fi
 
 # Setup desci-codex and deploy composites
 pushd "$CODEX_REPO_PATH"
+
+# Check that the node admin secret is set up, otherwise the model ID's wont be correct
+if [ ! -f "packages/composedb/admin_seed.txt" ]; then
+  echo "$CTX Composites need to be deployed with the ceramic node admin seed for the local node, as the model IDs aren't deterministic otherwise"
+  exit 1
+fi
+
 if [[ ! -d "node_modules" ]]; then
   echo "$CTX installing deps desci-codex..."
   npm ci

desci-contracts/Dockerfile

@@ -1,4 +1,4 @@
-FROM node:16.20.0-bookworm
+FROM node:18.16.0-bookworm
 WORKDIR /app
 
 VOLUME /data

desci-contracts/package.json

@@ -41,9 +41,9 @@
     "as-base64": "^0.2.0",
     "chai": "^4.3.4",
     "ethereum-waffle": "^3.4.0",
-    "ethers": "^5.4.4",
+    "ethers": "5.5.4",
     "ganache": "^7.8.0",
-    "hardhat": "^2.19.2",
+    "hardhat": "2.19.3",
     "hardhat-deploy": "^0.8.11",
     "hardhat-deploy-ethers": "^0.3.0-beta.10",
     "hardhat-gas-reporter": "^1.0.4",

desci-contracts/yarn.lock

@@ -4914,22 +4914,7 @@ ethereumjs-wallet@0.6.5:
     utf8 "^3.0.0"
     uuid "^3.3.2"
 
-ethers@^4.0.40:
-  version "4.0.49"
-  resolved "https://registry.yarnpkg.com/ethers/-/ethers-4.0.49.tgz#0eb0e9161a0c8b4761be547396bbe2fb121a8894"
-  integrity sha512-kPltTvWiyu+OktYy1IStSO16i2e7cS9D9OxZ81q2UUaiNPVrm/RTcbxamCXF9VUSKzJIdJV68EAIhTEVBalRWg==
-  dependencies:
-    aes-js "3.0.0"
-    bn.js "^4.11.9"
-    elliptic "6.5.4"
-    hash.js "1.1.3"
-    js-sha3 "0.5.7"
-    scrypt-js "2.0.4"
-    setimmediate "1.0.4"
-    uuid "2.0.1"
-    xmlhttprequest "1.8.0"
-
-ethers@^5.0.1, ethers@^5.0.2, ethers@^5.4.4, ethers@^5.5.2:
+ethers@5.5.4, ethers@^5.0.1, ethers@^5.0.2, ethers@^5.5.2:
   version "5.5.4"
   resolved "https://registry.yarnpkg.com/ethers/-/ethers-5.5.4.tgz#e1155b73376a2f5da448e4a33351b57a885f4352"
   integrity sha512-N9IAXsF8iKhgHIC6pquzRgPBJEzc9auw3JoRkaKe+y4Wl/LFBtDDunNe7YmdomontECAcC5APaAgWZBiu1kirw==
@@ -4965,6 +4950,21 @@ ethers@^5.0.1, ethers@^5.0.2, ethers@^5.4.4, ethers@^5.5.2:
     "@ethersproject/web" "5.5.1"
     "@ethersproject/wordlists" "5.5.0"
 
+ethers@^4.0.40:
+  version "4.0.49"
+  resolved "https://registry.yarnpkg.com/ethers/-/ethers-4.0.49.tgz#0eb0e9161a0c8b4761be547396bbe2fb121a8894"
+  integrity sha512-kPltTvWiyu+OktYy1IStSO16i2e7cS9D9OxZ81q2UUaiNPVrm/RTcbxamCXF9VUSKzJIdJV68EAIhTEVBalRWg==
+  dependencies:
+    aes-js "3.0.0"
+    bn.js "^4.11.9"
+    elliptic "6.5.4"
+    hash.js "1.1.3"
+    js-sha3 "0.5.7"
+    scrypt-js "2.0.4"
+    setimmediate "1.0.4"
+    uuid "2.0.1"
+    xmlhttprequest "1.8.0"
+
 ethers@^5.7.1:
   version "5.7.2"
   resolved "https://registry.yarnpkg.com/ethers/-/ethers-5.7.2.tgz#3a7deeabbb8c030d4126b24f84e525466145872e"
@@ -5934,7 +5934,7 @@ hardhat-gas-reporter@^1.0.4:
     eth-gas-reporter "^0.2.24"
     sha1 "^1.1.1"
 
-hardhat@^2.19.2:
+hardhat@2.19.3:
   version "2.19.3"
   resolved "https://registry.yarnpkg.com/hardhat/-/hardhat-2.19.3.tgz#fe3b28b889e34a074ea5b740c227e3c8d4ce56e8"
   integrity sha512-zUvfILiu1O7W1a+t5E1nCJ6z1danRLNizQkSEQCCgDYcRx13AGXtH1MVZajKmdLmXIjKAPReTp/8JQQ4ZHaX3g==

desci-models/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@desci-labs/desci-models",
-  "version": "0.2.1",
+  "version": "0.2.3-rc1",
   "description": "Data models for DeSci Nodes",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -16,7 +16,7 @@
     "test": "mocha -r ts-node/register --inspect tests/**/*.test.ts",
     "coverage": "nyc -r lcov -e .ts -x \"*.test.ts\" npm run test",
     "build": "tsc",
-    "publish": "npm publish --access public",
+    "doPublish": "npm publish --access public",
     "generate": "ts-interface-builder src/ResearchObject.ts src/RoCrate.ts --ignore-generics"
   },
   "author": "",