From 8689e18e82301bda9a780f293b3499341f97d79d Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 12 Oct 2023 14:06:52 +0200
Subject: [PATCH 01/14] Add data assertions to tests, validate resolution of
 prev stream versions, make generic query fn

---
 components/ResearchObject.tsx     |    4 +-
 components/ResearchObjectForm.tsx |    4 +-
 package-lock.json                 | 1170 ++++++++++++++---------------
 pages/explore.tsx                 |    4 +-
 pages/index.tsx                   |    4 +-
 test/root.spec.ts                 |  201 +++--
 types/index.ts                    |    6 +-
 utils/populate.tsx                |    4 +-
 utils/queries.ts                  |  155 +++-
 9 files changed, 870 insertions(+), 682 deletions(-)

diff --git a/components/ResearchObject.tsx b/components/ResearchObject.tsx
index 3bb6119..300ec17 100644
--- a/components/ResearchObject.tsx
+++ b/components/ResearchObject.tsx
@@ -2,7 +2,7 @@
 import Link from "next/link";
 import styles from "@/styles/Home.module.scss";
 
-import { ROProps } from "@/types";
+import { ResearchObject } from "@/types";
 import { PropsWithChildren } from "react";
 
 const ResearchObject = ({
@@ -10,7 +10,7 @@ const ResearchObject = ({
   title,
   manifest,
   children,
-}: PropsWithChildren<ROProps>) => {
+}: PropsWithChildren<ResearchObject>) => {
   return (
     <div className={styles.post}>
       <div><big>{title}</big></div>
diff --git a/components/ResearchObjectForm.tsx b/components/ResearchObjectForm.tsx
index 597a72f..a0a8467 100644
--- a/components/ResearchObjectForm.tsx
+++ b/components/ResearchObjectForm.tsx
@@ -1,13 +1,13 @@
 "use client";
 import { useCeramicContext } from "@/context";
-import { ROProps } from "@/types";
+import { ResearchObject } from "@/types";
 import styles from "@/styles/profile.module.scss";
 import { useState } from "react";
 import { mutationCreateResearchObject } from "@/utils/queries";
 
 export const ResearchObjectForm = (updateParent: () => void) => {
   const { ceramic, composeClient } = useCeramicContext();
-  const [object, setObject] = useState<ROProps>({
+  const [object, setObject] = useState<ResearchObject>({
     title: "",
     manifest: ""
   });
diff --git a/package-lock.json b/package-lock.json
index e94c653..ad793d5 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -58,9 +58,9 @@
       }
     },
     "node_modules/@babel/runtime": {
-      "version": "7.23.1",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.23.1.tgz",
-      "integrity": "sha512-hC2v6p8ZSI/W0HUzh3V8C5g+NwSKzKPtJwSpTjwl0o297GP9+ZLQSkdvHz46CM3LqyoXxq+5G9komY+eSqSO0g==",
+      "version": "7.23.2",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.23.2.tgz",
+      "integrity": "sha512-mM8eg4yl5D6i3lu2QKPuPH4FArvJ8KhTofbE7jwMUv9KX5mBvwPAqnV3MlyBNqdp9RyRKP6Yck8TrfYrPvX3bg==",
       "dev": true,
       "dependencies": {
         "regenerator-runtime": "^0.14.0"
@@ -70,13 +70,13 @@
       }
     },
     "node_modules/@ceramicnetwork/3id-did-resolver": {
-      "version": "2.28.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/3id-did-resolver/-/3id-did-resolver-2.28.0.tgz",
-      "integrity": "sha512-MrmpobSy+zPF1DuBvtvzhstOuoRPxTyV61at8cgVEgzqj1etrB+yCv5S9nJ7mzKLNsY59ncYMOtaKGHD5V1W2Q==",
+      "version": "2.29.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/3id-did-resolver/-/3id-did-resolver-2.29.0.tgz",
+      "integrity": "sha512-SLTQWgaLeFebURvomer2rC9IAbk1MFn6QZ7WEkWj7hJkg0ql5sy5fZ4LWXjCXYIepQ+4fUvoQoaY0fol201Ndg==",
       "dev": true,
       "dependencies": {
-        "@ceramicnetwork/common": "^2.35.0",
-        "@ceramicnetwork/stream-tile": "^2.31.0",
+        "@ceramicnetwork/common": "^2.36.0",
+        "@ceramicnetwork/stream-tile": "^2.32.0",
         "@ceramicnetwork/streamid": "^2.17.0",
         "cross-fetch": "^3.1.4",
         "least-recent": "^1.0.3",
@@ -85,32 +85,32 @@
       }
     },
     "node_modules/@ceramicnetwork/anchor-listener": {
-      "version": "1.20.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/anchor-listener/-/anchor-listener-1.20.0.tgz",
-      "integrity": "sha512-ZDL1kxicvgGtEqhXzACMJFQT6oGncpz1xc47y1T4Ina5zkSve40P8FBXaLMRRJQ2ADp9lo4Rkvr6O/yisAspiw==",
+      "version": "1.21.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/anchor-listener/-/anchor-listener-1.21.0.tgz",
+      "integrity": "sha512-epZYQ+8Qjc6DMuVUIMlan4aNXpMqvni2KnQdsmI/FoZ2mianvCfgv2LUw2kbmBi2PNfxjUq+liogWggh8WYnNg==",
       "dev": true,
       "dependencies": {
-        "@ceramicnetwork/anchor-utils": "^1.18.0",
+        "@ceramicnetwork/anchor-utils": "^1.19.0",
         "@ethersproject/providers": "^5.5.1",
         "rxjs": "^7.5.2"
       }
     },
     "node_modules/@ceramicnetwork/anchor-utils": {
-      "version": "1.18.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/anchor-utils/-/anchor-utils-1.18.0.tgz",
-      "integrity": "sha512-hVsNxLZxZDxvRqXy+ydxtKnCkCh9xGKb9Ua/osXovEuShdsVBNMqfYJorU/ael6uymBn9L52PpUMOCIrPiLmwg==",
+      "version": "1.19.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/anchor-utils/-/anchor-utils-1.19.0.tgz",
+      "integrity": "sha512-1U9hG37IGgLyai7oWBfoK9DBXudWgiuzRsLnGA/Sa28Ic7wN5Y5ycWd+EN9w2tUTVJr5KORM/aQpg1KH7knWjA==",
       "dev": true,
       "dependencies": {
-        "@ceramicnetwork/common": "^2.35.0",
+        "@ceramicnetwork/common": "^2.36.0",
         "@ethersproject/abi": "^5.7.0",
         "multiformats": "^11.0.1",
         "uint8arrays": "^4.0.3"
       }
     },
     "node_modules/@ceramicnetwork/blockchain-utils-linking": {
-      "version": "2.20.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/blockchain-utils-linking/-/blockchain-utils-linking-2.20.0.tgz",
-      "integrity": "sha512-wzo6eNGfs4jFyYDZ2Ens/NYChZn3h5J9KUa1boaIl5I+7u3HNWob/updPUYC5SKafGeiErJh//7UFZfoKqbPbA==",
+      "version": "2.21.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/blockchain-utils-linking/-/blockchain-utils-linking-2.21.0.tgz",
+      "integrity": "sha512-rW99eRynpWKcok8WDv0azNZ2ojaEF3md93WxFDn9I1CbFOj+jCuZTBbEuBB4PlFcqPc+QS6qAaBASIp79sPcQA==",
       "dev": true,
       "dependencies": {
         "@ceramicnetwork/streamid": "^2.17.0",
@@ -123,13 +123,13 @@
       }
     },
     "node_modules/@ceramicnetwork/blockchain-utils-validation": {
-      "version": "2.27.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/blockchain-utils-validation/-/blockchain-utils-validation-2.27.0.tgz",
-      "integrity": "sha512-popP5FtckqB7q2nY+MUuVfB6mdlO2dMS/puC2lZfxpQPPMEvvomyAnkiqfBZSkfkc7YNHNBR7Sbp3k4jtHYu6Q==",
+      "version": "2.28.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/blockchain-utils-validation/-/blockchain-utils-validation-2.28.0.tgz",
+      "integrity": "sha512-OLy6Y68mRDtna/8kXiDphthILjG1Ld4oCmPikIu6Zy+yfmU897r6FnNfD8NZ/K5clDWKDzgLtDr5Y6KAjiWv+Q==",
       "dev": true,
       "dependencies": {
-        "@ceramicnetwork/blockchain-utils-linking": "^2.20.0",
-        "@ceramicnetwork/common": "^2.35.0",
+        "@ceramicnetwork/blockchain-utils-linking": "^2.21.0",
+        "@ceramicnetwork/common": "^2.36.0",
         "@ethersproject/contracts": "^5.5.0",
         "@ethersproject/providers": "^5.5.1",
         "@ethersproject/wallet": "^5.5.0",
@@ -146,21 +146,21 @@
       }
     },
     "node_modules/@ceramicnetwork/cli": {
-      "version": "2.40.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/cli/-/cli-2.40.0.tgz",
-      "integrity": "sha512-HuDJZcCU45TnxVqIYJFO6TWRt5MwkL2ZWXd6k3VetaK5nd6j8Nn6AT80o9exqtNmpcUz6ZtbV+MJuPYzizGsuQ==",
+      "version": "2.41.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/cli/-/cli-2.41.0.tgz",
+      "integrity": "sha512-CCpI8lRmq87vmJuLSMzg47fgpyLdf/nU9YeTRHLwfZeDrGHshSW1YzInPsgq1XuDtmA/TlE5Z/u52Cpk5VUmiA==",
       "dev": true,
       "dependencies": {
         "@awaitjs/express": "^0.9.0",
-        "@ceramicnetwork/3id-did-resolver": "^2.28.0",
-        "@ceramicnetwork/common": "^2.35.0",
-        "@ceramicnetwork/core": "^2.42.0",
-        "@ceramicnetwork/http-client": "^2.32.0",
-        "@ceramicnetwork/indexing": "^1.1.0",
-        "@ceramicnetwork/ipfs-daemon": "^2.28.0",
+        "@ceramicnetwork/3id-did-resolver": "^2.29.0",
+        "@ceramicnetwork/common": "^2.36.0",
+        "@ceramicnetwork/core": "^2.43.0",
+        "@ceramicnetwork/http-client": "^2.33.0",
+        "@ceramicnetwork/indexing": "^1.2.0",
+        "@ceramicnetwork/ipfs-daemon": "^2.29.0",
         "@ceramicnetwork/logger": "^2.5.0",
         "@ceramicnetwork/observability": "^1.4.1",
-        "@ceramicnetwork/stream-tile": "^2.31.0",
+        "@ceramicnetwork/stream-tile": "^2.32.0",
         "@ceramicnetwork/streamid": "^2.17.0",
         "@stablelib/random": "^1.0.1",
         "aws-sdk": "^2.1049.0",
@@ -193,9 +193,9 @@
       }
     },
     "node_modules/@ceramicnetwork/codecs": {
-      "version": "1.10.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/codecs/-/codecs-1.10.0.tgz",
-      "integrity": "sha512-0/5/NCjKax2UFbvnlQuRzZ+T7sp+HKgGsBsW/fKK06E/ui0MBVMSK1eitn/ozvMFUo+nCjKPQF3ixXVpdsQl4A==",
+      "version": "1.11.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/codecs/-/codecs-1.11.0.tgz",
+      "integrity": "sha512-UEK8qveRk5f+ubAamdJ+fInmIGVKKMTXD8D4SUYa8zHXkKk4zGnYw+XwThAdh7+aClCWGN83SECR9TnaMZhIGw==",
       "dependencies": {
         "@ceramicnetwork/streamid": "^2.17.0",
         "cartonne": "^2.1.1",
@@ -206,11 +206,11 @@
       }
     },
     "node_modules/@ceramicnetwork/common": {
-      "version": "2.35.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/common/-/common-2.35.0.tgz",
-      "integrity": "sha512-1TsdVYAjTIVTBz+6dlrEJACFGqMzYZeOvwLNbpk9E5vMh6fnrgRm8q9JPeGhDyGwdGlY7l4e1yqzWAoZGnJARQ==",
+      "version": "2.36.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/common/-/common-2.36.0.tgz",
+      "integrity": "sha512-cZu3953wsTd/xKUDosC1l2tXpWKLkYA+PkkueRCXIrLRvNQrMCde8yx6xnnNcFihU3hpzux/iqkHHEihATeN1Q==",
       "dependencies": {
-        "@ceramicnetwork/codecs": "^1.10.0",
+        "@ceramicnetwork/codecs": "^1.11.0",
         "@ceramicnetwork/streamid": "^2.17.0",
         "@didtools/cacao": "^2.1.0",
         "@didtools/pkh-ethereum": "^0.1.0",
@@ -245,29 +245,29 @@
       }
     },
     "node_modules/@ceramicnetwork/core": {
-      "version": "2.42.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/core/-/core-2.42.0.tgz",
-      "integrity": "sha512-bHI0eZVanuBTeTZxpD9aNsNtYrB8ehYWA6SaUNK+eZ3x2uHLwpLwLbqE566RBuYi6UA7T6e4f4fyEsP79Se/zQ==",
-      "dev": true,
-      "dependencies": {
-        "@ceramicnetwork/anchor-listener": "^1.20.0",
-        "@ceramicnetwork/anchor-utils": "^1.18.0",
-        "@ceramicnetwork/codecs": "^1.10.0",
-        "@ceramicnetwork/common": "^2.35.0",
-        "@ceramicnetwork/indexing": "^1.1.0",
-        "@ceramicnetwork/ipfs-topology": "^2.29.0",
-        "@ceramicnetwork/job-queue": "^1.2.0",
+      "version": "2.43.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/core/-/core-2.43.0.tgz",
+      "integrity": "sha512-DKUNKf65R8clcmwjr1aEDZPzzvf0i1pmoRSRephMmGgfAuEUubC/ejWHppKpKJfv58JsQsF6E/7qAkaiWc/fMw==",
+      "dev": true,
+      "dependencies": {
+        "@ceramicnetwork/anchor-listener": "^1.21.0",
+        "@ceramicnetwork/anchor-utils": "^1.19.0",
+        "@ceramicnetwork/codecs": "^1.11.0",
+        "@ceramicnetwork/common": "^2.36.0",
+        "@ceramicnetwork/indexing": "^1.2.0",
+        "@ceramicnetwork/ipfs-topology": "^2.30.0",
+        "@ceramicnetwork/job-queue": "^1.3.0",
         "@ceramicnetwork/observability": "^1.4.1",
-        "@ceramicnetwork/pinning-aggregation": "^2.27.0",
-        "@ceramicnetwork/pinning-ipfs-backend": "^2.27.0",
-        "@ceramicnetwork/stream-caip10-link": "^2.30.0",
-        "@ceramicnetwork/stream-caip10-link-handler": "^2.28.0",
-        "@ceramicnetwork/stream-model": "^1.17.0",
-        "@ceramicnetwork/stream-model-handler": "^1.17.0",
-        "@ceramicnetwork/stream-model-instance": "^1.17.0",
-        "@ceramicnetwork/stream-model-instance-handler": "^1.17.0",
-        "@ceramicnetwork/stream-tile": "^2.31.0",
-        "@ceramicnetwork/stream-tile-handler": "^2.30.0",
+        "@ceramicnetwork/pinning-aggregation": "^2.28.0",
+        "@ceramicnetwork/pinning-ipfs-backend": "^2.28.0",
+        "@ceramicnetwork/stream-caip10-link": "^2.31.0",
+        "@ceramicnetwork/stream-caip10-link-handler": "^2.29.0",
+        "@ceramicnetwork/stream-model": "^1.18.0",
+        "@ceramicnetwork/stream-model-handler": "^1.18.0",
+        "@ceramicnetwork/stream-model-instance": "^1.18.0",
+        "@ceramicnetwork/stream-model-instance-handler": "^1.18.0",
+        "@ceramicnetwork/stream-tile": "^2.32.0",
+        "@ceramicnetwork/stream-tile-handler": "^2.31.0",
         "@ceramicnetwork/streamid": "^2.17.0",
         "@ceramicnetwork/wasm-bloom-filter": "^0.1.0",
         "@datastructures-js/priority-queue": "^6.1.0",
@@ -307,15 +307,15 @@
       "dev": true
     },
     "node_modules/@ceramicnetwork/http-client": {
-      "version": "2.32.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/http-client/-/http-client-2.32.0.tgz",
-      "integrity": "sha512-2OUp33qXg2D243N+NwuwvPJfw/F2PFj2y73XT753yjwXIdyaHAJXwsoLJ8OyK1ixFYl1Q5Yb3kshO1sXurQi4g==",
-      "dependencies": {
-        "@ceramicnetwork/common": "^2.35.0",
-        "@ceramicnetwork/stream-caip10-link": "^2.30.0",
-        "@ceramicnetwork/stream-model": "^1.17.0",
-        "@ceramicnetwork/stream-model-instance": "^1.17.0",
-        "@ceramicnetwork/stream-tile": "^2.31.0",
+      "version": "2.33.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/http-client/-/http-client-2.33.0.tgz",
+      "integrity": "sha512-rZ2NlA1NoSSyA44ZK5W7KhvdNX6i3hFPu1z4NyRA5Zvl4jwEogGboaWZF2hWDDXxfkrRZX7+J/JvzxBKp360QQ==",
+      "dependencies": {
+        "@ceramicnetwork/common": "^2.36.0",
+        "@ceramicnetwork/stream-caip10-link": "^2.31.0",
+        "@ceramicnetwork/stream-model": "^1.18.0",
+        "@ceramicnetwork/stream-model-instance": "^1.18.0",
+        "@ceramicnetwork/stream-tile": "^2.32.0",
         "@ceramicnetwork/streamid": "^2.17.0",
         "@scarf/scarf": "^1.1.1",
         "query-string": "^7.1.0",
@@ -323,16 +323,16 @@
       }
     },
     "node_modules/@ceramicnetwork/indexing": {
-      "version": "1.1.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/indexing/-/indexing-1.1.0.tgz",
-      "integrity": "sha512-mlR+UEexxMVl15bkpYeXKchbYIfVcT8LSBTK670U+UxwJu+JX5PSqmw4RTUWStHOiIER6KqIcZmQaWJWcyTd4Q==",
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/indexing/-/indexing-1.2.0.tgz",
+      "integrity": "sha512-++UIl4bMqM+5LK0hEk6kOVUil2YlkCF+wEbnxUT0gZrW2Wd0SnWjT2mQFAhjlgd+h78hGmwBVQMCk7QbsfMHvw==",
       "dev": true,
       "dependencies": {
-        "@ceramicnetwork/anchor-listener": "^1.20.0",
-        "@ceramicnetwork/anchor-utils": "^1.18.0",
-        "@ceramicnetwork/common": "^2.35.0",
-        "@ceramicnetwork/job-queue": "^1.2.0",
-        "@ceramicnetwork/stream-model": "^1.17.0",
+        "@ceramicnetwork/anchor-listener": "^1.21.0",
+        "@ceramicnetwork/anchor-utils": "^1.19.0",
+        "@ceramicnetwork/common": "^2.36.0",
+        "@ceramicnetwork/job-queue": "^1.3.0",
+        "@ceramicnetwork/stream-model": "^1.18.0",
         "@ceramicnetwork/streamid": "^2.17.0",
         "@ethersproject/providers": "^5.5.1",
         "knex": "^2.5.1",
@@ -351,9 +351,9 @@
       "dev": true
     },
     "node_modules/@ceramicnetwork/indexing/node_modules/multiformats": {
-      "version": "12.1.1",
-      "resolved": "https://registry.npmjs.org/multiformats/-/multiformats-12.1.1.tgz",
-      "integrity": "sha512-GBSToTmri2vJYs8wqcZQ8kB21dCaeTOzHTIAlr8J06C1eL6UbzqURXFZ5Fl0EYm9GAFz1IlYY8SxGOs9G9NJRg==",
+      "version": "12.1.2",
+      "resolved": "https://registry.npmjs.org/multiformats/-/multiformats-12.1.2.tgz",
+      "integrity": "sha512-6mRIsrZXyw5xNPO31IGBMmxgDXBSgCGDsBAtazkZ02ip4hMwZNrQvfxXZtytRoBSWuzSq5f9VmMnXj76fIz5FQ==",
       "dev": true,
       "engines": {
         "node": ">=16.0.0",
@@ -377,13 +377,13 @@
       }
     },
     "node_modules/@ceramicnetwork/ipfs-daemon": {
-      "version": "2.28.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/ipfs-daemon/-/ipfs-daemon-2.28.0.tgz",
-      "integrity": "sha512-GpVRxUOJ5dfHPrsngg5D0GtK8XbKdiYWYMqJ122TDDm5XtNpYmps3TUVfXSukuyCZeb8CvwVflvHM+r2HgApLQ==",
+      "version": "2.29.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/ipfs-daemon/-/ipfs-daemon-2.29.0.tgz",
+      "integrity": "sha512-BpQBGNeS5orWBwv+w5Yn853b6b+PUENmuP4GfxEp2yARtSd8q5eusQ9jyGNetoYIXqNxrV0yrDCGnv4jl1Kt8Q==",
       "dev": true,
       "dependencies": {
-        "@ceramicnetwork/common": "^2.35.0",
-        "@ceramicnetwork/ipfs-topology": "^2.29.0",
+        "@ceramicnetwork/common": "^2.36.0",
+        "@ceramicnetwork/ipfs-topology": "^2.30.0",
         "express": "^4.17.2",
         "get-port": "^6.0.0",
         "go-ipfs": "^0.18.1",
@@ -398,22 +398,22 @@
       }
     },
     "node_modules/@ceramicnetwork/ipfs-topology": {
-      "version": "2.29.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/ipfs-topology/-/ipfs-topology-2.29.0.tgz",
-      "integrity": "sha512-+AuRMWaAPLoXmKu6doDw+1tlAHB15diOdnZaQmQC8B4wfyX3Qrb42YufxdToWSO1BXPQL0AlY7R3K/4tdh4jYQ==",
+      "version": "2.30.0",
+      "resolved": "https://registry.npmjs.org/@ceramicnetwork/ipfs-topology/-/ipfs-topology-2.30.0.tgz",
+      "integrity": "sha512-gPc5gImS5SmHTEJHtz8rsAlhw0QKLKjrAw6uZ6sRuTFBsJimX6x4D1yLmwd/Qw/6J19b7U8nsyGX7gQMotWrJw==",
       "dev": true,
       "dependencies": {
-        "@ceramicnetwork/common": "^2.35.0",
+        "@ceramicnetwork/common": "^2.36.0",
         "cross-fetch": "^3.1.4"
       }
     },
     "node_modules/@ceramicnetwork/job-queue": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/@ceramicnetwork/job-queue/-/job-queue-1.2.0.tgz",
-      "integrity": "sha512-KFUPbDcTkORmVQOXdG0UDeIEQP1iV8j4TSbNdnFzhVoelimmJA1Y6ZCC0/CESQWD22V8ecYgXZ4qxLn5ltC2SQ==",
+      "version": "1.3.0",
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+      "version": "4.4.0",
+      "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-4.4.0.tgz",
+      "integrity": "sha512-HT3RRs7sTfY22KuPQJkD/XjbTbxgP2Je5HPt6H6JEGvcjHd5Lqru75EbrP3tb4FYjNJ+DjLp+MNQTFQU0mhXNw==",
       "dev": true,
       "engines": {
         "node": ">=16"
@@ -16373,9 +16411,9 @@
       "dev": true
     },
     "node_modules/ufo": {
-      "version": "1.3.0",
-      "resolved": "https://registry.npmjs.org/ufo/-/ufo-1.3.0.tgz",
-      "integrity": "sha512-bRn3CsoojyNStCZe0BG0Mt4Nr/4KF+rhFlnNXybgqt5pXHNFRlqinSoQaTrGyzE4X8aHplSb+TorH+COin9Yxw==",
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/ufo/-/ufo-1.3.1.tgz",
+      "integrity": "sha512-uY/99gMLIOlJPwATcMVYfqDSxUR9//AUcgZMzwfSTJPDKzA1S8mX4VLqa+fiAtveraQUBCz4FFcwVZBGbwBXIw==",
       "dev": true
     },
     "node_modules/uint8-varint": {
@@ -16410,9 +16448,9 @@
       }
     },
     "node_modules/uint8arrays/node_modules/multiformats": {
-      "version": "12.1.1",
-      "resolved": "https://registry.npmjs.org/multiformats/-/multiformats-12.1.1.tgz",
-      "integrity": "sha512-GBSToTmri2vJYs8wqcZQ8kB21dCaeTOzHTIAlr8J06C1eL6UbzqURXFZ5Fl0EYm9GAFz1IlYY8SxGOs9G9NJRg==",
+      "version": "12.1.2",
+      "resolved": "https://registry.npmjs.org/multiformats/-/multiformats-12.1.2.tgz",
+      "integrity": "sha512-6mRIsrZXyw5xNPO31IGBMmxgDXBSgCGDsBAtazkZ02ip4hMwZNrQvfxXZtytRoBSWuzSq5f9VmMnXj76fIz5FQ==",
       "engines": {
         "node": ">=16.0.0",
         "npm": ">=7.0.0"
@@ -16434,17 +16472,23 @@
       }
     },
     "node_modules/undici": {
-      "version": "5.25.2",
-      "resolved": "https://registry.npmjs.org/undici/-/undici-5.25.2.tgz",
-      "integrity": "sha512-tch8RbCfn1UUH1PeVCXva4V8gDpGAud/w0WubD6sHC46vYQ3KDxL+xv1A2UxK0N6jrVedutuPHxe1XIoqerwMw==",
+      "version": "5.26.3",
+      "resolved": "https://registry.npmjs.org/undici/-/undici-5.26.3.tgz",
+      "integrity": "sha512-H7n2zmKEWgOllKkIUkLvFmsJQj062lSm3uA4EYApG8gLuiOM0/go9bIoC3HVaSnfg4xunowDE2i9p8drkXuvDw==",
       "dev": true,
       "dependencies": {
-        "busboy": "^1.6.0"
+        "@fastify/busboy": "^2.0.0"
       },
       "engines": {
         "node": ">=14.0"
       }
     },
+    "node_modules/undici-types": {
+      "version": "5.25.3",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.25.3.tgz",
+      "integrity": "sha512-Ga1jfYwRn7+cP9v8auvEXN1rX3sWqlayd4HP7OKk4mZWylEmu3KzXDUGrQUN6Ol7qo1gPvB2e5gX6udnyEPgdA==",
+      "dev": true
+    },
     "node_modules/unique-filename": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/unique-filename/-/unique-filename-1.1.1.tgz",
@@ -16640,9 +16684,9 @@
       }
     },
     "node_modules/vite": {
-      "version": "4.4.9",
-      "resolved": "https://registry.npmjs.org/vite/-/vite-4.4.9.tgz",
-      "integrity": "sha512-2mbUn2LlUmNASWwSCNSJ/EG2HuSRTnVNaydp6vMCm5VIqJsjMfbIWtbH2kDuwUVW5mMUKKZvGPX/rqeqVvv1XA==",
+      "version": "4.4.11",
+      "resolved": "https://registry.npmjs.org/vite/-/vite-4.4.11.tgz",
+      "integrity": "sha512-ksNZJlkcU9b0lBwAGZGGaZHCMqHsc8OpgtoYhsQ4/I2v5cnpmmmqe5pM4nv/4Hn6G/2GhTdj0DhZh2e+Er1q5A==",
       "dev": true,
       "dependencies": {
         "esbuild": "^0.18.10",
@@ -16695,9 +16739,9 @@
       }
     },
     "node_modules/vite-node": {
-      "version": "0.34.5",
-      "resolved": "https://registry.npmjs.org/vite-node/-/vite-node-0.34.5.tgz",
-      "integrity": "sha512-RNZ+DwbCvDoI5CbCSQSyRyzDTfFvFauvMs6Yq4ObJROKlIKuat1KgSX/Ako5rlDMfVCyMcpMRMTkJBxd6z8YRA==",
+      "version": "0.34.6",
+      "resolved": "https://registry.npmjs.org/vite-node/-/vite-node-0.34.6.tgz",
+      "integrity": "sha512-nlBMJ9x6n7/Amaz6F3zJ97EBwR2FkzhBRxF5e+jE6LA3yi6Wtc2lyTij1OnDMIr34v5g/tVQtsVAzhT0jc5ygA==",
       "dev": true,
       "dependencies": {
         "cac": "^6.7.14",
@@ -16736,70 +16780,24 @@
         }
       }
     },
-    "node_modules/vite/node_modules/nanoid": {
-      "version": "3.3.6",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.6.tgz",
-      "integrity": "sha512-BGcqMMJuToF7i1rt+2PWSNVnWIkGCU78jBG3RxO/bZlnZPK2Cmi2QaffxGO/2RvWi9sL+FAiRiXMgsyxQ1DIDA==",
-      "dev": true,
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/ai"
-        }
-      ],
-      "bin": {
-        "nanoid": "bin/nanoid.cjs"
-      },
-      "engines": {
-        "node": "^10 || ^12 || ^13.7 || ^14 || >=15.0.1"
-      }
-    },
-    "node_modules/vite/node_modules/postcss": {
-      "version": "8.4.30",
-      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.30.tgz",
-      "integrity": "sha512-7ZEao1g4kd68l97aWG/etQKPKq07us0ieSZ2TnFDk11i0ZfDW2AwKHYU8qv4MZKqN2fdBfg+7q0ES06UA73C1g==",
-      "dev": true,
-      "funding": [
-        {
-          "type": "opencollective",
-          "url": "https://opencollective.com/postcss/"
-        },
-        {
-          "type": "tidelift",
-          "url": "https://tidelift.com/funding/github/npm/postcss"
-        },
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/ai"
-        }
-      ],
-      "dependencies": {
-        "nanoid": "^3.3.6",
-        "picocolors": "^1.0.0",
-        "source-map-js": "^1.0.2"
-      },
-      "engines": {
-        "node": "^10 || ^12 || >=14"
-      }
-    },
     "node_modules/vitest": {
-      "version": "0.34.5",
-      "resolved": "https://registry.npmjs.org/vitest/-/vitest-0.34.5.tgz",
-      "integrity": "sha512-CPI68mmnr2DThSB3frSuE5RLm9wo5wU4fbDrDwWQQB1CWgq9jQVoQwnQSzYAjdoBOPoH2UtXpOgHVge/uScfZg==",
+      "version": "0.34.6",
+      "resolved": "https://registry.npmjs.org/vitest/-/vitest-0.34.6.tgz",
+      "integrity": "sha512-+5CALsOvbNKnS+ZHMXtuUC7nL8/7F1F2DnHGjSsszX8zCjWSSviphCb/NuS9Nzf4Q03KyyDRBAXhF/8lffME4Q==",
       "dev": true,
       "dependencies": {
         "@types/chai": "^4.3.5",
         "@types/chai-subset": "^1.3.3",
         "@types/node": "*",
-        "@vitest/expect": "0.34.5",
-        "@vitest/runner": "0.34.5",
-        "@vitest/snapshot": "0.34.5",
-        "@vitest/spy": "0.34.5",
-        "@vitest/utils": "0.34.5",
+        "@vitest/expect": "0.34.6",
+        "@vitest/runner": "0.34.6",
+        "@vitest/snapshot": "0.34.6",
+        "@vitest/spy": "0.34.6",
+        "@vitest/utils": "0.34.6",
         "acorn": "^8.9.0",
         "acorn-walk": "^8.2.0",
         "cac": "^6.7.14",
-        "chai": "^4.3.7",
+        "chai": "^4.3.10",
         "debug": "^4.3.4",
         "local-pkg": "^0.4.3",
         "magic-string": "^0.30.1",
@@ -16810,7 +16808,7 @@
         "tinybench": "^2.5.0",
         "tinypool": "^0.7.0",
         "vite": "^3.1.0 || ^4.0.0 || ^5.0.0-0",
-        "vite-node": "0.34.5",
+        "vite-node": "0.34.6",
         "why-is-node-running": "^2.2.2"
       },
       "bin": {
@@ -17151,14 +17149,6 @@
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"
       }
-    },
-    "node_modules/zod": {
-      "version": "3.21.4",
-      "resolved": "https://registry.npmjs.org/zod/-/zod-3.21.4.tgz",
-      "integrity": "sha512-m46AKbrzKVzOzs/DZgVnG5H55N1sv1M8qZU3A8RIKbs3mrACDNeIOeilDymVb2HdmP8uwshOCF4uJ8uM9rCqJw==",
-      "funding": {
-        "url": "https://github.com/sponsors/colinhacks"
-      }
     }
   }
 }
diff --git a/pages/explore.tsx b/pages/explore.tsx
index 36890ec..400c47a 100644
--- a/pages/explore.tsx
+++ b/pages/explore.tsx
@@ -1,7 +1,7 @@
 import type { NextPage } from "next";
 import { useCallback, useEffect, useState } from "react";
 import { useCeramicContext } from "@/context";
-import { ROProps } from "@/types";
+import { ResearchObject } from "@/types";
 import Head from "next/head";
 import styles from "@/styles/Home.module.scss";
 import React from "react";
@@ -13,7 +13,7 @@ import { AttestList } from "@/components/AttestList";
 const ExplorePage: NextPage = () => {
   const clients = useCeramicContext();
   const { composeClient } = clients;
-  const [objects, setObjects] = useState<ROProps[] | []>([]);
+  const [objects, setObjects] = useState<ResearchObject[] | []>([]);
 
   const getResearchObjects = useCallback(async () => {
     const researchObjects = await queryResearchObjects(composeClient);
diff --git a/pages/index.tsx b/pages/index.tsx
index f6be0cf..477b508 100644
--- a/pages/index.tsx
+++ b/pages/index.tsx
@@ -1,7 +1,7 @@
 import type { NextPage } from "next";
 import { useCallback, useEffect, useState } from "react";
 import { useCeramicContext } from "@/context";
-import { ROProps } from "@/types";
+import { ResearchObject } from "@/types";
 import Head from "next/head";
 import styles from "@/styles/Home.module.scss";
 import React from "react";
@@ -12,7 +12,7 @@ import { queryViewerId, queryViewerResearchObjects } from "@/utils/queries";
 const Home: NextPage = () => {
   const clients = useCeramicContext();
   const { ceramic, composeClient } = clients;
-  const [objects, setObjects] = useState<ROProps[] | []>([]);
+  const [objects, setObjects] = useState<ResearchObject[] | []>([]);
 
   const getResearchObjects = useCallback(async () => {
     if (ceramic.did !== undefined) {
diff --git a/test/root.spec.ts b/test/root.spec.ts
index 74a51d8..bab54fb 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -3,13 +3,16 @@ import { definition } from '@/src/__generated__/definition'
 import { RuntimeCompositeDefinition } from '@composedb/types'
 import { test, describe, beforeAll, expect } from 'vitest'
 import {
+  genericEntityQuery,
   mutationCreateAttestation, mutationCreateClaim, mutationCreateProfile,
-  mutationCreateResearchObject, mutationUpdateAttestation, mutationUpdateResearchObject, queryResearchObjects
+  mutationCreateResearchComponent,
+  mutationCreateResearchObject, mutationUpdateAttestation, mutationUpdateResearchComponent, mutationUpdateResearchObject, queryAttestation, queryClaim, queryProfile, queryResearchComponent, queryResearchObject, queryResearchObjects
 } from '../utils/queries'
 import { randomDID } from './util'
 import { CeramicClient } from '@ceramicnetwork/http-client'
 import { writeComposite } from 'scripts/composites.mjs'
 import { setTimeout } from "timers/promises";
+import { Attestation, Claim, Profile, ResearchObject } from '@/types'
 
 const CERAMIC_API = 'http:/localhost:7007'
 const TIMEOUT = 7000
@@ -37,39 +40,44 @@ describe('ComposeDB nodes', () => {
 
     // Create mutations error on failure and are otherwise successful
     test('can create research object', async () => {
-      mutationCreateResearchObject(
-        composeClient,
-        {
-          title: 'Test',
-          manifest: A_CID
-        }
+      const data: ResearchObject = {
+        title: 'Test',
+        manifest: A_CID,
+        metadata: '{ "key": "value" }'
+      }
+      const researchObject = await mutationCreateResearchObject(
+        composeClient, data
       );
+      const result = await queryResearchObject(
+        composeClient, researchObject.streamID,
+      );
+      expect(result).toEqual(data);
     });
 
-    test('can create profile', async () =>
-      await mutationCreateProfile(
-        composeClient,
-        {
-          displayName: 'First Lastname',
-          orcid: 'orcidHandle'
-        }
-      ),
-      // SINGLE accountRelation instances will ask the network for previous
-      // creations, which slowly times out. PR allowing setting this timeout
-      // in progress: https://github.com/ceramicstudio/js-composedb/pull/182
-      TIMEOUT
-    );
+    test('can create profile', async () => {
+      const data: Profile = {
+        displayName: 'First Lastname',
+        orcid: 'orcidHandle'
+      };
+      const profile = await mutationCreateProfile(composeClient, data);
 
-    test('can create claim', async () =>
-      await mutationCreateClaim(
-        composeClient,
-        {
-          title: 'My Claim',
-          description: 'The point of the claim',
-          badge: A_CID
-        }
-      )
-    );
+      const result = await queryProfile(
+        composeClient, profile.streamID,
+      );
+      expect(result).toEqual(data);
+    });
+
+    test('can create claim', async () => {
+      const data: Claim = {
+        title: 'My Claim',
+        description: 'The point of the claim',
+        badge: A_CID
+      };
+      const claim = await mutationCreateClaim(composeClient, data);
+
+      const result = await queryClaim(composeClient, claim.streamID);
+      expect(result).toEqual(data);
+    });
 
     test('can attest to own research object', async () => {
       const myResearchObject = await mutationCreateResearchObject(
@@ -87,16 +95,16 @@ describe('ComposeDB nodes', () => {
           badge: A_CID
         }
       );
-      await mutationCreateAttestation(
-        composeClient,
-        {
-          targetID: myResearchObject.streamID,
-          targetVersion: myResearchObject.commitID,
-          claimID: myClaim.streamID,
-          claimVersion: myClaim.commitID,
-          revoked: false
-        }
-      );
+      const data: Attestation = {
+        targetID: myResearchObject.streamID,
+        targetVersion: myResearchObject.commitID,
+        claimID: myClaim.streamID,
+        claimVersion: myClaim.commitID,
+        revoked: false
+      };
+      const attestation = await mutationCreateAttestation(composeClient, data);
+      const result = await queryAttestation(composeClient, attestation.streamID);
+      expect(result).toEqual(data);
     });
   });
 
@@ -123,7 +131,7 @@ describe('ComposeDB nodes', () => {
         }
       );
 
-      await mutationCreateAttestation(
+      const attestation = await mutationCreateAttestation(
         composeClient,
         {
           targetID: ownProfile.streamID,
@@ -133,6 +141,9 @@ describe('ComposeDB nodes', () => {
           revoked: false
         }
       );
+      const result = await queryAttestation(composeClient, attestation.streamID);
+      expect(result?.targetID).toEqual(ownProfile.streamID);
+      expect(result?.targetVersion).toEqual(ownProfile.commitID);
     })
 
     test('can be made to other users research object', async () => {
@@ -148,7 +159,7 @@ describe('ComposeDB nodes', () => {
 
       const user2 = await randomDID();
       composeClient.setDID(user2);
-      await mutationCreateAttestation(
+      const attestation = await mutationCreateAttestation(
         composeClient,
         {
           targetID: user1ResearchObject.streamID,
@@ -158,6 +169,9 @@ describe('ComposeDB nodes', () => {
           revoked: false
         }
       );
+      const result = await queryAttestation(composeClient, attestation.streamID);
+      expect(result?.targetID).toEqual(user1ResearchObject.streamID);
+      expect(result?.targetVersion).toEqual(user1ResearchObject.commitID);
     })
 
     test('can be updated with revokation', async () => {
@@ -189,17 +203,21 @@ describe('ComposeDB nodes', () => {
           revoked: true
         }
       );
+
+      await setTimeout(1000);
+      const result = await queryAttestation(composeClient, attestation.streamID);
+      expect(result?.revoked).toEqual(true)
     })
   })
 
   describe.skip('Annotations', async () => {
-    test('can comment on research component', async () => { });
+    test('can comment on research component', async () => {});
 
-    test('can comment on research object', async () => { });
+    test('can comment on research object', async () => {});
 
-    test('can suggest metadata change on research component', async () => { });
+    test('can suggest metadata change on research component', async () => {});
 
-    test('can suggest metadata changes on research object', async () => { });
+    test('can suggest metadata changes on research object', async () => {});
   });
 
   describe('User', async () => {
@@ -208,25 +226,29 @@ describe('ComposeDB nodes', () => {
     composeClient.setDID(user);
 
     test('can update research object', async () => {
-      const researchObject = await mutationCreateResearchObject(
-        composeClient,
-        {
-          title: 'Test',
-          manifest: A_CID
-        }
-      );
+      const data: ResearchObject = {
+        title: 'Test',
+        manifest: A_CID,
+        metadata: '{ "key": "value" }'
+      };
+      const researchObject = await mutationCreateResearchObject(composeClient, data);
+
+      const newMetadata = '{ "key": "value", "newKey": "value" }';
       await mutationUpdateResearchObject(
         composeClient,
         {
           id: researchObject.streamID,
-          title: 'A fancy new title',
-          manifest: "bafkreibtsll3aq2bynvlxnqh6nxafzdm4cpiovr3bcncbkzjcy32xaaaaa"
+          metadata: newMetadata
         }
       );
+
+      await setTimeout(500);
+      const result = await queryResearchObject(composeClient, researchObject.streamID);
+      expect(result).toEqual({ ...data, metadata: newMetadata });
     });
 
     test('can update profile', async () => {
-      await mutationCreateProfile(
+      const profile = await mutationCreateProfile(
         composeClient,
         {
           displayName: "My Name",
@@ -236,16 +258,17 @@ describe('ComposeDB nodes', () => {
 
       // Ceramic node takes a little while syncing this with the "network"
       // since it has the SINGLE accountRelation
-      await setTimeout(500);
+      await setTimeout(250);
+      const newProfile: Profile = {
+        displayName: "New Name",
+        orcid: "@handle"
+      };
       // Apparently create acts as an upsert on SINGLE accountRelation models
-      await mutationCreateProfile(
-        composeClient,
-        {
-          displayName: "New Name",
-          orcid: "@handle"
-        }
-      );
-    }, TIMEOUT);
+      await mutationCreateProfile(composeClient, newProfile);
+
+      const result = await queryProfile(composeClient, profile.streamID);
+      expect(result).toEqual(newProfile);
+    });
 
   });
 
@@ -281,6 +304,54 @@ describe('ComposeDB nodes', () => {
       const streamBetween = await ceramic.loadStream(streamID, { atTime: timeBetween });
       expect(streamBetween.state.content.title).toEqual('Old');
     });
+
+    test('can resolve stream refs in old versions', async () => {
+      const researchObjectV0 = await mutationCreateResearchObject(
+        composeClient,
+        {
+          title: 'Title',
+          manifest: A_CID
+        }
+      );
+      const componentV0 = await mutationCreateResearchComponent(
+        composeClient,
+        {
+          name: 'Filename',
+          mimeType: 'text/plain',
+          dagNode: A_CID,
+          researchObjectID: researchObjectV0.streamID,
+          researchObjectVersion: researchObjectV0.commitID
+        }
+      );
+      const newManifest = 'bafybeibeaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa';
+      const researchObjectV1 = await mutationUpdateResearchObject(
+        composeClient,
+        {
+          id: researchObjectV0.streamID,
+          manifest: newManifest
+        }
+      );
+      await mutationUpdateResearchComponent(
+        composeClient,
+        {
+          id: componentV0.streamID,
+          dagNode: newManifest,
+          // Set a new version indicator
+          researchObjectVersion: researchObjectV1.commitID
+        }
+      );
+
+      const roResult = await queryResearchObject(composeClient, researchObjectV0.streamID);
+      const rcResult = await queryResearchComponent(composeClient, componentV0.streamID);
+      expect(roResult?.manifest).toEqual(newManifest);
+      expect(rcResult?.researchObjectID).toEqual(researchObjectV0.streamID);
+
+      // Check that we can get the old state with the research object version at
+      // that point in time
+      const oldComponentState = await ceramic.loadStream(componentV0.commitID);
+      expect(oldComponentState.content.researchObjectVersion)
+        .toEqual(researchObjectV0.commitID);
+    });
   });
 
 
diff --git a/types/index.ts b/types/index.ts
index 01be5ea..2903c06 100644
--- a/types/index.ts
+++ b/types/index.ts
@@ -9,7 +9,7 @@ export type DID = {
   profile?: Profile
 };
 
-export type ROProps = {
+export type ResearchObject = {
   id?: string
   version?: string
   title: string
@@ -90,9 +90,9 @@ export type ResearchFieldRelation = {
   researchObjectVersion: string
 };
 
-export type MutationTarget = 
+export type ProtocolEntity = 
   Profile |
-  ROProps |
+  ResearchObject |
   ResearchComponent |
   Claim |
   Attestation |
diff --git a/utils/populate.tsx b/utils/populate.tsx
index 35455b4..79817c0 100644
--- a/utils/populate.tsx
+++ b/utils/populate.tsx
@@ -19,7 +19,7 @@ import {
 import { CeramicClient } from "@ceramicnetwork/http-client"
 import { definition } from '@/src/__generated__/definition'
 import { RuntimeCompositeDefinition } from "@composedb/types"
-import { Annotation, Attestation, NodeIDs, ROProps } from "@/types"
+import { Annotation, Attestation, NodeIDs, ResearchObject } from "@/types"
 import {
   AnnotationTemplate,
   AttestationTemplate,
@@ -173,7 +173,7 @@ const loadResearchObject = async (
   roTemplate: ResearchObjectTemplate,
   composeClient: ComposeClient
 ): Promise<ActorDataNodeIDs['researchObjects'][number]> => {
-  const roProps: ROProps = {
+  const roProps: ResearchObject = {
     title: roTemplate.title,
     manifest: roTemplate.manifest
   }
diff --git a/utils/queries.ts b/utils/queries.ts
index 3e71001..809d90f 100644
--- a/utils/queries.ts
+++ b/utils/queries.ts
@@ -1,5 +1,5 @@
 import { ComposeClient } from "@composedb/client";
-import { Attestation, Claim, ResearchComponent, Profile, ROProps, ContributorRelation, ReferenceRelation, ResearchFieldRelation, MutationTarget, Annotation, NodeIDs, ResearchField } from "../types";
+import { Attestation, Claim, ResearchComponent, Profile, ResearchObject, ContributorRelation, ReferenceRelation, ResearchFieldRelation, ProtocolEntity, Annotation, NodeIDs, ResearchField } from "../types";
 import { ExecutionResult } from "graphql";
 
 export const queryViewerId = async (
@@ -39,9 +39,9 @@ export const queryViewerProfile = async (
 
 export const queryViewerResearchObjects = async (
   composeClient: ComposeClient
-): Promise<ROProps[]> => {
+): Promise<ResearchObject[]> => {
   const response = await composeClient.executeQuery<
-    { viewer: { researchObjectList: { edges: { node: ROProps }[] } } }
+    { viewer: { researchObjectList: { edges: { node: ResearchObject }[] } } }
   >(`
     query {
       viewer {
@@ -88,9 +88,9 @@ export const queryViewerClaims = async (
 
 export const queryResearchObjects = async (
   composeClient: ComposeClient
-): Promise<ROProps[]> => {
+): Promise<ResearchObject[]> => {
   const response = await composeClient.executeQuery<
-    { researchObjectIndex: { edges: { node: ROProps }[] } }
+    { researchObjectIndex: { edges: { node: ResearchObject }[] } }
   >(`
     query {
       researchObjectIndex(first: 100) {
@@ -148,7 +148,7 @@ export const queryResearchObjectAttestations = async (
 
 export const mutationCreateResearchObject = async (
   composeClient: ComposeClient,
-  inputs: ROProps
+  inputs: ResearchObject
 ): Promise<NodeIDs> => genericCreate(
   composeClient,
   inputs,
@@ -176,9 +176,25 @@ export const mutationCreateResearchComponent = async (
   'createResearchComponent'
 );
 
+export const mutationUpdateResearchComponent = async (
+  composeClient: ComposeClient,
+  inputs: Partial<ResearchComponent> & { id: string }
+): Promise<NodeIDs> => genericUpdate(
+  composeClient,
+  inputs,
+  {
+    name: "String!",
+    mimeType: "String!",
+    dagNode: "InterPlanetaryCID!",
+    researchObjectID: "CeramicStreamID!",
+    researchObjectVersion: "CeramicCommitID!"
+  },
+  'updateResearchComponent'
+);
+
 export const mutationUpdateResearchObject = async (
   composeClient: ComposeClient,
-  inputs: Partial<ROProps> & { id: string }
+  inputs: Partial<ResearchObject> & { id: string }
 ): Promise<NodeIDs> => genericUpdate(
   composeClient,
   inputs,
@@ -200,7 +216,8 @@ export const mutationCreateProfile = async (
     displayName: "String!",
     orcid: "String"
   },
-  'createProfile'
+  'createProfile',
+  true
 );
 
 export const mutationCreateClaim = async (
@@ -321,19 +338,129 @@ export const mutationCreateResearchField = async (
   'createResearchField'
 );
 
-async function genericCreate<T extends MutationTarget>(
+export const queryResearchObject = async (
+  composeClient: ComposeClient,
+  id: string,
+  selection?: string
+): Promise<ResearchObject | undefined> => genericEntityQuery(
+  composeClient,
+  id,
+  'ResearchObject',
+  selection ?? 
+    `
+      title
+      manifest
+      metadata
+    `
+);
+
+export const queryProfile = async (
+  composeClient: ComposeClient,
+  id: string,
+  selection?: string
+): Promise<Profile | undefined> => genericEntityQuery(
+  composeClient,
+  id,
+  'Profile',
+  selection ??
+    `
+      displayName
+      orcid
+    `
+);
+
+export const queryClaim = async (
+  composeClient: ComposeClient,
+  id: string,
+  selection?: string
+): Promise<Claim| undefined> => genericEntityQuery(
+  composeClient,
+  id,
+  'Claim',
+  selection ??
+    `
+      title
+      description
+      badge
+    `
+);
+
+export const queryAttestation = async (
+  composeClient: ComposeClient,
+  id: string,
+  selection?: string
+): Promise<Attestation | undefined> => genericEntityQuery(
+  composeClient,
+  id,
+  'Attestation',
+  selection ??
+    `
+      targetID
+      targetVersion
+      claimID
+      claimVersion
+      revoked
+    `
+);
+
+export const queryResearchComponent = async (
+  composeClient: ComposeClient,
+  id: string,
+  selection?: string
+): Promise<ResearchComponent | undefined> => genericEntityQuery(
+  composeClient,
+  id,
+  'ResearchComponent',
+  selection ??
+    `
+      name
+      mimeType
+      dagNode
+      researchObjectID
+      researchObjectVersion
+    `
+);
+
+export async function genericEntityQuery<T extends ProtocolEntity>(
+  composeClient: ComposeClient,
+  id: string,
+  entityName: string,
+  // Specify the field structure to query for
+  selection: string
+): Promise<T | undefined> {
+  const query = `
+  query($id: ID!) {
+    node(id: $id) {
+      ...on ${entityName} {
+        ${selection}
+      }
+    }
+  }
+  `;
+  const result = await composeClient.executeQuery(query, { id })
+  assertQueryErrors(result, `${entityName} node`)
+  return result.data
+    ? result.data.node as T
+    : undefined // query can return null too, downscope type
+};
+
+async function genericCreate<T extends ProtocolEntity>(
   composeClient: ComposeClient,
   inputs: T,
-  // At least verify all keys exist in T, can still forget one though.
-  // Can't require it fully because some props are not allowed in the mutation.
+  /** At least verify all keys exist in T, can still forget one though.
+  * Can't require it fully because some props are not allowed in the mutation.
+  */
   gqlTypes: Partial<Record<keyof T, string>>,
-  mutationName: string
+  mutationName: string,
+  /** Skip timeout for single accountRelation entities */
+  noTimeout?: boolean
 ): Promise<NodeIDs> {
   const [params, content] = getQueryFields(gqlTypes as Record<string, string>, inputs);
   const response = await composeClient.executeQuery(`
     mutation( ${params} ) {
       ${mutationName}(input: {
         content: { ${content} }
+        ${noTimeout ? "options: { syncTimeout: 0 }" : ""}
       })
       {
         document {
@@ -351,12 +478,12 @@ async function genericCreate<T extends MutationTarget>(
   return nodeIDs;
 };
 
-async function genericUpdate<T extends MutationTarget>(
+async function genericUpdate<T extends ProtocolEntity>(
   composeClient: ComposeClient,
   inputs: Partial<T> & { id: string },
   // See note in genericCreate
   gqlTypes: Partial<Record<keyof T, string>>,
-  mutationName: string
+  mutationName: string,
 ): Promise<NodeIDs> {
   const [params, content] = getQueryFields(gqlTypes as Record<string, string>, inputs);
   const response = await composeClient.executeQuery(`

From cbb45d70ad0f73451047e13478b74927c8a371e9 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 12 Oct 2023 14:51:57 +0200
Subject: [PATCH 02/14] Fix bork after renaming ROProps

---
 components/ResearchObject.tsx | 4 ++--
 pages/explore.tsx             | 6 +++---
 pages/index.tsx               | 4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/components/ResearchObject.tsx b/components/ResearchObject.tsx
index 300ec17..f8c1eb8 100644
--- a/components/ResearchObject.tsx
+++ b/components/ResearchObject.tsx
@@ -5,7 +5,7 @@ import styles from "@/styles/Home.module.scss";
 import { ResearchObject } from "@/types";
 import { PropsWithChildren } from "react";
 
-const ResearchObject = ({
+const ResearchObjectComponent = ({
   owner,
   title,
   manifest,
@@ -22,4 +22,4 @@ const ResearchObject = ({
   );
 };
 
-export default ResearchObject;
+export default ResearchObjectComponent;
diff --git a/pages/explore.tsx b/pages/explore.tsx
index 400c47a..bfded2b 100644
--- a/pages/explore.tsx
+++ b/pages/explore.tsx
@@ -5,7 +5,7 @@ import { ResearchObject } from "@/types";
 import Head from "next/head";
 import styles from "@/styles/Home.module.scss";
 import React from "react";
-import ResearchObject from "@/components/ResearchObject";
+import ResearchObjectComponent from "@/components/ResearchObject";
 import { queryResearchObjects } from "@/utils/queries";
 import { AttestButton } from "@/components/AttestButton";
 import { AttestList } from "@/components/AttestList";
@@ -36,7 +36,7 @@ const ExplorePage: NextPage = () => {
             <big>The world of DeSci</big>
           </label>
           {objects.map((ro) => (
-            <ResearchObject
+            <ResearchObjectComponent
               key={ro.id}
               id={ro.id}
               title={ro.title}
@@ -45,7 +45,7 @@ const ExplorePage: NextPage = () => {
             >
               <AttestButton targetID={ro.id!} />
               <AttestList targetID={ro.id!} />
-            </ResearchObject>
+            </ResearchObjectComponent>
           ))}
         </div>
       </div>
diff --git a/pages/index.tsx b/pages/index.tsx
index 477b508..26b332d 100644
--- a/pages/index.tsx
+++ b/pages/index.tsx
@@ -5,7 +5,7 @@ import { ResearchObject } from "@/types";
 import Head from "next/head";
 import styles from "@/styles/Home.module.scss";
 import React from "react";
-import ResearchObject from "@/components/ResearchObject";
+import ResearchObjectComponent from "@/components/ResearchObject";
 import { ResearchObjectForm } from "@/components/ResearchObjectForm";
 import { queryViewerId, queryViewerResearchObjects } from "@/utils/queries";
 
@@ -43,7 +43,7 @@ const Home: NextPage = () => {
             <big>My research objects</big>
           </label>
           {objects.map((ro) => (
-            <ResearchObject
+            <ResearchObjectComponent
               key={ro.id}
               id={ro.id}
               title={ro.title}

From 37dbbf94756f8ac2a5b95cf7c200e9f10b86b179 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 12 Oct 2023 14:54:16 +0200
Subject: [PATCH 03/14] Run tests in PRs

---
 test/root.spec.ts | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/test/root.spec.ts b/test/root.spec.ts
index bab54fb..b0727d1 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -3,10 +3,19 @@ import { definition } from '@/src/__generated__/definition'
 import { RuntimeCompositeDefinition } from '@composedb/types'
 import { test, describe, beforeAll, expect } from 'vitest'
 import {
-  genericEntityQuery,
-  mutationCreateAttestation, mutationCreateClaim, mutationCreateProfile,
+  mutationCreateAttestation,
+  mutationCreateClaim,
+  mutationCreateProfile,
   mutationCreateResearchComponent,
-  mutationCreateResearchObject, mutationUpdateAttestation, mutationUpdateResearchComponent, mutationUpdateResearchObject, queryAttestation, queryClaim, queryProfile, queryResearchComponent, queryResearchObject, queryResearchObjects
+  mutationCreateResearchObject,
+  mutationUpdateAttestation,
+  mutationUpdateResearchComponent,
+  mutationUpdateResearchObject,
+  queryAttestation,
+  queryClaim,
+  queryProfile,
+  queryResearchComponent,
+  queryResearchObject
 } from '../utils/queries'
 import { randomDID } from './util'
 import { CeramicClient } from '@ceramicnetwork/http-client'
@@ -15,7 +24,6 @@ import { setTimeout } from "timers/promises";
 import { Attestation, Claim, Profile, ResearchObject } from '@/types'
 
 const CERAMIC_API = 'http:/localhost:7007'
-const TIMEOUT = 7000
 const A_CID = 'bafybeibeaampol2yz5xuoxex7dxri6ztqveqrybzfh5obz6jrul5gb4cf4'
 
 const ceramic = new CeramicClient(CERAMIC_API)
@@ -211,13 +219,13 @@ describe('ComposeDB nodes', () => {
   })
 
   describe.skip('Annotations', async () => {
-    test('can comment on research component', async () => {});
+    test('can comment on research component', async () => { });
 
-    test('can comment on research object', async () => {});
+    test('can comment on research object', async () => { });
 
-    test('can suggest metadata change on research component', async () => {});
+    test('can suggest metadata change on research component', async () => { });
 
-    test('can suggest metadata changes on research object', async () => {});
+    test('can suggest metadata changes on research object', async () => { });
   });
 
   describe('User', async () => {

From 1c303987d06f1a01053bbebcc382dd5002cc9bd2 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 12 Oct 2023 15:04:21 +0200
Subject: [PATCH 04/14] Fix CI test workflow

---
 .github/workflows/pr.yml | 4 +++-
 scripts/run.mjs          | 6 ++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 8098df6..13886e4 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -7,11 +7,13 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
-      - uses: setup-node@v3
+      - uses: actions/setup-node@v3
         with:
           node-version-file: ".nvmrc"
           cache: "npm"
           cache-dependency-path: "package-lock.json"
           check-latest: false
       - run: npm ci
+      - run: npm run generate
+      - run: CI=true npm run dev
       - run: make test
diff --git a/scripts/run.mjs b/scripts/run.mjs
index 742b330..f6e8469 100644
--- a/scripts/run.mjs
+++ b/scripts/run.mjs
@@ -3,6 +3,7 @@ import ora from 'ora'
 import { spawn } from "child_process"
 import { EventEmitter } from 'events'
 import { writeComposite } from './composites.mjs';
+import { setTimeout } from 'timers/promises';
 
 const events = new EventEmitter()
 const spinner = ora();
@@ -58,6 +59,11 @@ const start = async () => {
     events.on('ceramic', async (isRunning) => {
       if (isRunning) {
         await bootstrap()
+        if (process.env.CI) {
+          ceramic.kill()
+          await setTimeout(1000);
+          process.exit();
+        }
         await graphiql()
         await next()
       }

From 8111fb3a8b14ba06db62caaf38651ee76a785a8a Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 12 Oct 2023 15:31:48 +0200
Subject: [PATCH 05/14] Log ipfs/ceramic processes in CI

---
 .github/workflows/pr.yml | 1 +
 scripts/run.mjs          | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 13886e4..53d0ee6 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -16,4 +16,5 @@ jobs:
       - run: npm ci
       - run: npm run generate
       - run: CI=true npm run dev
+      - run: echo "PROCESSES"; ps aux | grep -e ceramic -e ipfs
       - run: make test
diff --git a/scripts/run.mjs b/scripts/run.mjs
index f6e8469..65513a5 100644
--- a/scripts/run.mjs
+++ b/scripts/run.mjs
@@ -60,8 +60,8 @@ const start = async () => {
       if (isRunning) {
         await bootstrap()
         if (process.env.CI) {
-          ceramic.kill()
-          await setTimeout(1000);
+          ceramic.kill();
+          await setTimeout(5000);
           process.exit();
         }
         await graphiql()

From f86556cba1240e302c1f7ed22e45e50db2d4c58c Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 12 Oct 2023 16:03:21 +0200
Subject: [PATCH 06/14] less stupid, more working

---
 .github/workflows/pr.yml | 2 --
 scripts/run.mjs          | 6 ------
 2 files changed, 8 deletions(-)

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 53d0ee6..693080e 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -15,6 +15,4 @@ jobs:
           check-latest: false
       - run: npm ci
       - run: npm run generate
-      - run: CI=true npm run dev
-      - run: echo "PROCESSES"; ps aux | grep -e ceramic -e ipfs
       - run: make test
diff --git a/scripts/run.mjs b/scripts/run.mjs
index 65513a5..742b330 100644
--- a/scripts/run.mjs
+++ b/scripts/run.mjs
@@ -3,7 +3,6 @@ import ora from 'ora'
 import { spawn } from "child_process"
 import { EventEmitter } from 'events'
 import { writeComposite } from './composites.mjs';
-import { setTimeout } from 'timers/promises';
 
 const events = new EventEmitter()
 const spinner = ora();
@@ -59,11 +58,6 @@ const start = async () => {
     events.on('ceramic', async (isRunning) => {
       if (isRunning) {
         await bootstrap()
-        if (process.env.CI) {
-          ceramic.kill();
-          await setTimeout(5000);
-          process.exit();
-        }
         await graphiql()
         await next()
       }

From 41f798ab73ea7c279dfcc0fbb43e75156dcc60ab Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 12 Oct 2023 16:11:00 +0200
Subject: [PATCH 07/14] try relative import paths in spec

---
 test/root.spec.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/root.spec.ts b/test/root.spec.ts
index b0727d1..d3f07ac 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -1,5 +1,5 @@
 import { ComposeClient } from '@composedb/client'
-import { definition } from '@/src/__generated__/definition'
+import { definition } from '../src/__generated__/definition'
 import { RuntimeCompositeDefinition } from '@composedb/types'
 import { test, describe, beforeAll, expect } from 'vitest'
 import {

From 69b78fc95a31feea11400982fe340909211285ab Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Fri, 13 Oct 2023 11:04:21 +0200
Subject: [PATCH 08/14] Fix clean key and config generation for CI

---
 Makefile               |  6 ++--
 scripts/commands.mjs   | 69 +++++++++++++++++++++++-------------------
 scripts/composites.mjs | 14 +++++++--
 3 files changed, 52 insertions(+), 37 deletions(-)

diff --git a/Makefile b/Makefile
index 2b31400..4aca2a6 100644
--- a/Makefile
+++ b/Makefile
@@ -4,8 +4,8 @@ clean-test:
 	rm -rf local-data/ceramic-test
 
 test: clean-test
-	sed 's|local-data/ceramic|local-data/ceramic-test|' composedb.config.json \
-		> test.config.json
+	sed 's|local-data/ceramic|local-data/ceramic-test|' composedb.config.json > test.config.json
 	npx ceramic daemon --config test.config.json &>/dev/null &
 	sleep 5
-	npm test; pkill --full "npm exec ceramic"
\ No newline at end of file
+	node scripts/composites.mjs
+	npm test; pkill --full "ceramic daemon|ipfs daemon"
\ No newline at end of file
diff --git a/scripts/commands.mjs b/scripts/commands.mjs
index 4ce9f3a..8eb7be9 100644
--- a/scripts/commands.mjs
+++ b/scripts/commands.mjs
@@ -1,27 +1,33 @@
-import KeyDIDResolver from "key-did-resolver";
+import { getResolver } from "key-did-resolver";
 import { randomBytes } from "crypto";
 import { toString } from "uint8arrays/to-string";
-import { writeFile } from "fs";
+import { fromString } from "uint8arrays/from-string";
+import { existsSync, readFileSync, writeFileSync } from "fs";
 import { DID } from "dids";
 import { Ed25519Provider } from "key-did-provider-ed25519";
 
+const PWD = process.cwd();
+const CONFIG_PATH = `${PWD}/composedb.config.json`;
+const SEED_PATH = `${PWD}/admin_seed.txt`;
+
 export const RunCommands = async () => {
+  const newSeed = () => {
+    const raw = new Uint8Array(randomBytes(32));
+    return toString(raw, 'base16')
+  }
+
   const generateAdminKeyDid = async () => {
-    const seed = new Uint8Array(randomBytes(32));
-    const keyResolver = KeyDIDResolver.getResolver();
+    const seed = readFileSync(SEED_PATH);
+    const key = fromString(seed, 'base16');
     const did = new DID({
-      provider: new Ed25519Provider(seed),
-      resolver: {
-        ...keyResolver,
-      },
+      provider: new Ed25519Provider(key),
+      resolver: getResolver(),
     });
     await did.authenticate();
-    return {
-      seed: toString(seed, "base16"),
-      did,
-    };
+    return did;
   };
-  const generateLocalConfig = async (adminSeed, adminDid) => {
+
+  const generateLocalConfig = async (adminDid) => {
     const configData = {
       anchor: {},
       "http-api": {
@@ -49,30 +55,31 @@ export const RunCommands = async () => {
         "local-directory": "local-data/ceramic/statestore",
       },
       indexing: {
-        db: `sqlite://${process.cwd()}/local-data/ceramic/indexing.sqlite`,
+        db: `sqlite://${PWD}/local-data/ceramic/indexing.sqlite`,
         "allow-queries-before-historical-sync": true,
         // Cannot be enabled on inmemory, but activate for proper networks
         // "enable-historical-sync": "true"
         models: [],
       },
     };
-    writeFile(
-      `${process.cwd()}/composedb.config.json`,
-      JSON.stringify(configData),
-      (err) => {
-        if (err) {
-          console.error(err);
-        }
-      }
-    );
-    writeFile(`${process.cwd()}/admin_seed.txt`, adminSeed, (err) => {
-      if (err) {
-        console.error(err);
-      }
-    });
+    writeFileSync(CONFIG_PATH, JSON.stringify(configData, undefined, 2));
+  };
+
+  if (!existsSync(SEED_PATH)){
+    console.log('Creating new admin seed...');
+    writeFileSync(SEED_PATH, newSeed());
+
+    console.log('Generating new config...');
+    const did = await generateAdminKeyDid();
+    console.log('Saving new DID:', JSON.stringify(did, undefined, 2))
+    await generateLocalConfig(did);    
+  } else if (!existsSync(CONFIG_PATH)) {
+    console.log('Found seed but no config, generating...');
+    const did = await generateAdminKeyDid();
+    await generateLocalConfig(did);
+  } else {
+    console.log('Seed and config present, skipping generation.')
   };
-  const { seed, did } = await generateAdminKeyDid();
-  console.log(seed, did);
-  await generateLocalConfig(seed, did);
 };
+
 RunCommands();
diff --git a/scripts/composites.mjs b/scripts/composites.mjs
index 8d6b76c..3b1a10b 100644
--- a/scripts/composites.mjs
+++ b/scripts/composites.mjs
@@ -19,7 +19,7 @@ const ceramic = new CeramicClient("http://localhost:7007");
  * @return {Promise<void>} - return void when composite finishes deploying.
  */
 export const writeComposite = async (spinner) => {
-  await authenticate();
+  await authenticateAdmin();
   spinner.info("writing composite to Ceramic");
 
   const profileComposite = await createComposite(
@@ -165,7 +165,7 @@ export const writeComposite = async (spinner) => {
  * Authenticating DID for publishing composite
  * @return {Promise<void>} - return void when DID is authenticated.
  */
-const authenticate = async () => {
+const authenticateAdmin = async () => {
   const seed = readFileSync("./admin_seed.txt");
   const key = fromString(seed, "base16");
   const did = new DID({
@@ -173,6 +173,14 @@ const authenticate = async () => {
     provider: new Ed25519Provider(key),
   });
   await did.authenticate();
-  ceramic.did = did;
+  await ceramic.setDID(did);
 };
 
+const runAsScript =
+  process.argv[0].includes('/bin/node') &&
+  process.argv[1].includes('scripts/composites.mjs');
+
+if (runAsScript) {
+  const logSpinner = { info: console.log, succeed: console.log };
+  await writeComposite(logSpinner);
+};
\ No newline at end of file

From 1a0700d2d85609ed96835a974edf098a481521e6 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Fri, 13 Oct 2023 11:22:16 +0200
Subject: [PATCH 09/14] Add stream syncs for less flaky tests

---
 test/root.spec.ts | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/test/root.spec.ts b/test/root.spec.ts
index d3f07ac..0550fbc 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -204,6 +204,7 @@ describe('ComposeDB nodes', () => {
         }
       );
 
+      await waitAndSync(attestation.streamID);
       await mutationUpdateAttestation(
         composeClient,
         {
@@ -212,7 +213,6 @@ describe('ComposeDB nodes', () => {
         }
       );
 
-      await setTimeout(1000);
       const result = await queryAttestation(composeClient, attestation.streamID);
       expect(result?.revoked).toEqual(true)
     })
@@ -241,6 +241,7 @@ describe('ComposeDB nodes', () => {
       };
       const researchObject = await mutationCreateResearchObject(composeClient, data);
 
+      await waitAndSync(researchObject.streamID);
       const newMetadata = '{ "key": "value", "newKey": "value" }';
       await mutationUpdateResearchObject(
         composeClient,
@@ -250,7 +251,6 @@ describe('ComposeDB nodes', () => {
         }
       );
 
-      await setTimeout(500);
       const result = await queryResearchObject(composeClient, researchObject.streamID);
       expect(result).toEqual({ ...data, metadata: newMetadata });
     });
@@ -264,13 +264,11 @@ describe('ComposeDB nodes', () => {
         }
       );
 
-      // Ceramic node takes a little while syncing this with the "network"
-      // since it has the SINGLE accountRelation
-      await setTimeout(250);
       const newProfile: Profile = {
         displayName: "New Name",
         orcid: "@handle"
       };
+      await waitAndSync(profile.streamID);
       // Apparently create acts as an upsert on SINGLE accountRelation models
       await mutationCreateProfile(composeClient, newProfile);
 
@@ -297,7 +295,7 @@ describe('ComposeDB nodes', () => {
         }
       );
       const timeBetween = Date.now();
-      await setTimeout(1000)
+      await waitAndSync(streamID);
       await mutationUpdateResearchObject(
         composeClient,
         {
@@ -367,3 +365,12 @@ describe('ComposeDB nodes', () => {
 
 const freshClient = () =>
   new ComposeClient({ ceramic, definition: definition as RuntimeCompositeDefinition })
+
+/** Sync between fast updates to same streams to make tests less flaky,
+* also allowing for an anchor commit to pop in between
+*/
+const waitAndSync = async (streamID: string) => {
+  await setTimeout(100);
+  const stream = await ceramic.loadStream(streamID);
+  await stream.sync(); 
+}

From cbbfcd85b3b1b3a6aac322a3cf8186de684051dd Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Fri, 13 Oct 2023 13:02:44 +0200
Subject: [PATCH 10/14] Add annotation tests

---
 Makefile                         |  4 +-
 composites/11-annotation.graphql |  2 +-
 test/root.spec.ts                | 98 ++++++++++++++++++++++++++++++--
 utils/queries.ts                 | 32 +++++++++--
 4 files changed, 123 insertions(+), 13 deletions(-)

diff --git a/Makefile b/Makefile
index 4aca2a6..35064ca 100644
--- a/Makefile
+++ b/Makefile
@@ -8,4 +8,6 @@ test: clean-test
 	npx ceramic daemon --config test.config.json &>/dev/null &
 	sleep 5
 	node scripts/composites.mjs
-	npm test; pkill --full "ceramic daemon|ipfs daemon"
\ No newline at end of file
+	# Kill lingering daemons without unsetting exit code of test
+	(npm test && pkill -f "ceramic daemon | ipfs daemon") \
+		|| (pkill -f "ceramic daemon | ipfs daemon"; exit 1)
diff --git a/composites/11-annotation.graphql b/composites/11-annotation.graphql
index f5e5ab4..491142c 100644
--- a/composites/11-annotation.graphql
+++ b/composites/11-annotation.graphql
@@ -21,7 +21,7 @@ type Annotation
   # Optionally tag a claim to contextualise the annotation
   claimID: StreamID @documentReference(model: "Claim")
   claim: Claim @relationDocument(property: "claimID")
-  claimVersion: CommitID!
+  claimVersion: CommitID
 
   metadataPayload: String @string(maxLength: 1024)
 }
diff --git a/test/root.spec.ts b/test/root.spec.ts
index 0550fbc..8486534 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -3,6 +3,7 @@ import { definition } from '../src/__generated__/definition'
 import { RuntimeCompositeDefinition } from '@composedb/types'
 import { test, describe, beforeAll, expect } from 'vitest'
 import {
+  mutationCreateAnnotation,
   mutationCreateAttestation,
   mutationCreateClaim,
   mutationCreateProfile,
@@ -11,6 +12,7 @@ import {
   mutationUpdateAttestation,
   mutationUpdateResearchComponent,
   mutationUpdateResearchObject,
+  queryAnnotation,
   queryAttestation,
   queryClaim,
   queryProfile,
@@ -21,7 +23,7 @@ import { randomDID } from './util'
 import { CeramicClient } from '@ceramicnetwork/http-client'
 import { writeComposite } from 'scripts/composites.mjs'
 import { setTimeout } from "timers/promises";
-import { Attestation, Claim, Profile, ResearchObject } from '@/types'
+import { Annotation, Attestation, Claim, Profile, ResearchObject } from '@/types'
 
 const CERAMIC_API = 'http:/localhost:7007'
 const A_CID = 'bafybeibeaampol2yz5xuoxex7dxri6ztqveqrybzfh5obz6jrul5gb4cf4'
@@ -218,14 +220,98 @@ describe('ComposeDB nodes', () => {
     })
   })
 
-  describe.skip('Annotations', async () => {
-    test('can comment on research component', async () => { });
+  describe('Annotations', async () => {
+    const composeClient = freshClient();
+    const user = await randomDID();
+    composeClient.setDID(user);
+
+    const researchObject = await mutationCreateResearchObject(
+      composeClient,
+      {
+        title: 'Title',
+        manifest: A_CID
+      }
+    );
+
+    const claim = await mutationCreateClaim(
+      composeClient,
+      {
+        title: 'Title',
+        description: 'Description'
+      }
+    );
+
+    const researchComponent = await mutationCreateResearchComponent(
+      composeClient,
+      {
+        name: 'Name',
+        mimeType: 'text/csv',
+        dagNode: A_CID,
+        researchObjectID: researchObject.streamID,
+        researchObjectVersion: researchObject.commitID
+      }
+    );
 
-    test('can comment on research object', async () => { });
+    test('can be made on research object', async () => {
+      const data: Annotation = {
+        comment: 'This is a cool object!',
+        targetID: researchObject.streamID,
+        targetVersion: researchObject.commitID,
+        claimID: claim.streamID,
+        claimVersion: claim.commitID
+      };
+
+      const annotation = await mutationCreateAnnotation(composeClient, data);
+
+      const response = await queryAnnotation(composeClient, annotation.streamID);
+      expect(response).toEqual({ ...data, metadataPayload: null, path: null });
+    });
+
+    test('can be made on research component', async () => {
+      const data: Annotation = {
+        comment: 'This is a cool object!',
+        targetID: researchComponent.streamID,
+        targetVersion: researchComponent.commitID,
+        claimID: claim.streamID,
+        claimVersion: claim.commitID
+      };
+
+      const annotation = await mutationCreateAnnotation(composeClient, data);
+
+      const response = await queryAnnotation(composeClient, annotation.streamID);
+      expect(response).toEqual({ ...data, metadataPayload: null, path: null });
+    });
 
-    test('can suggest metadata change on research component', async () => { });
+    test('can attach metadata', async () => {
+      const data: Annotation = {
+        comment: 'This is a cool object!',
+        targetID: researchComponent.streamID,
+        targetVersion: researchComponent.commitID,
+        claimID: claim.streamID,
+        claimVersion: claim.commitID,
+        metadataPayload: "JSONPatch"
+      };
+
+      const annotation = await mutationCreateAnnotation(composeClient, data);
+
+      const response = await queryAnnotation(composeClient, annotation.streamID);
+      expect(response?.metadataPayload).toEqual("JSONPatch");
+    });
+
+    test.skip('can omit claim', async () => {
+      // API fails on @relationDocument when the key is optional and omitted
+      const data: Annotation = {
+        comment: 'This is a cool object!',
+        targetID: researchComponent.streamID,
+        targetVersion: researchComponent.commitID
+      };
+
+      const annotation = await mutationCreateAnnotation(composeClient, data);
+
+      const response = await queryAnnotation(composeClient, annotation.streamID);
+      expect(response).toEqual(data);
+    });
 
-    test('can suggest metadata changes on research object', async () => { });
   });
 
   describe('User', async () => {
diff --git a/utils/queries.ts b/utils/queries.ts
index 809d90f..d6e7a8a 100644
--- a/utils/queries.ts
+++ b/utils/queries.ts
@@ -257,8 +257,8 @@ export const mutationUpdateAttestation = async (
   composeClient,
   inputs,
   {
-    targetID: "CeramicStreamID",
-    claimID: "CeramicStreamID",
+    targetID: "CeramicStreamID!",
+    claimID: "CeramicStreamID!",
     revoked: "Boolean"
   },
   'updateAttestation'
@@ -267,7 +267,8 @@ export const mutationUpdateAttestation = async (
 export const mutationCreateAnnotation = async (
   composeClient: ComposeClient,
   inputs: Annotation
-): Promise<NodeIDs> => genericCreate(
+): Promise<NodeIDs> => {
+  return genericCreate(
   composeClient,
   inputs,
   {
@@ -276,11 +277,12 @@ export const mutationCreateAnnotation = async (
     metadataPayload: "String",
     targetID: "CeramicStreamID!",
     targetVersion: "CeramicCommitID!",
-    claimID: "CeramicStreamID!",
-    claimVersion: "CeramicCommitID!"
+    claimID: "CeramicStreamID",
+    claimVersion: "CeramicCommitID"
   },
   'createAnnotation'
 );
+}
 
 export const mutationCreateContributorRelation = async (
   composeClient: ComposeClient,
@@ -421,6 +423,26 @@ export const queryResearchComponent = async (
     `
 );
 
+export const queryAnnotation = async (
+  composeClient: ComposeClient,
+  id: string,
+  selection?: string
+): Promise<Annotation | undefined> => genericEntityQuery(
+  composeClient,
+  id,
+  'Annotation',
+  selection ??
+    `
+      comment
+      path
+      targetID
+      targetVersion
+      claimID
+      claimVersion
+      metadataPayload
+    `
+);
+
 export async function genericEntityQuery<T extends ProtocolEntity>(
   composeClient: ComposeClient,
   id: string,

From befab97033655377183f6e99c993d3444a3b88eb Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Fri, 13 Oct 2023 14:11:12 +0200
Subject: [PATCH 11/14] Add omitted claims test

---
 Makefile          | 4 +---
 test/root.spec.ts | 4 ++--
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 35064ca..6525135 100644
--- a/Makefile
+++ b/Makefile
@@ -8,6 +8,4 @@ test: clean-test
 	npx ceramic daemon --config test.config.json &>/dev/null &
 	sleep 5
 	node scripts/composites.mjs
-	# Kill lingering daemons without unsetting exit code of test
-	(npm test && pkill -f "ceramic daemon | ipfs daemon") \
-		|| (pkill -f "ceramic daemon | ipfs daemon"; exit 1)
+	npm test
\ No newline at end of file
diff --git a/test/root.spec.ts b/test/root.spec.ts
index 8486534..9921b75 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -298,8 +298,8 @@ describe('ComposeDB nodes', () => {
       expect(response?.metadataPayload).toEqual("JSONPatch");
     });
 
-    test.skip('can omit claim', async () => {
-      // API fails on @relationDocument when the key is optional and omitted
+    test('can omit claim', async () => {
+      // API error on @relationDocument when the key is optional and omitted
       const data: Annotation = {
         comment: 'This is a cool object!',
         targetID: researchComponent.streamID,

From 0b566a0a31d470c3f348ba7e1f8a478e88a3ff47 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Fri, 13 Oct 2023 14:44:53 +0200
Subject: [PATCH 12/14] Skip broken omit test until resolved

---
 Makefile          | 7 ++++++-
 package.json      | 1 +
 test/root.spec.ts | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 6525135..6dfd427 100644
--- a/Makefile
+++ b/Makefile
@@ -8,4 +8,9 @@ test: clean-test
 	npx ceramic daemon --config test.config.json &>/dev/null &
 	sleep 5
 	node scripts/composites.mjs
-	npm test
\ No newline at end of file
+	# Kill daemons without losing test exit code for CI
+	if npm test; then \
+		npm run kill; true; \
+	else \
+		npm run kill; false; \
+	fi
diff --git a/package.json b/package.json
index 26c8149..df5d786 100644
--- a/package.json
+++ b/package.json
@@ -11,6 +11,7 @@
     "start": "next start",
     "lint": "next lint",
     "ceramic": "ceramic daemon --config composedb.config.json",
+    "kill": "pkill --full \"ceramic daemon|ipfs daemon\"",
     "test": "vitest --run --config vitest.config.ts"
   },
   "author": "Edvard Hubinette",
diff --git a/test/root.spec.ts b/test/root.spec.ts
index 9921b75..57d1389 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -298,7 +298,7 @@ describe('ComposeDB nodes', () => {
       expect(response?.metadataPayload).toEqual("JSONPatch");
     });
 
-    test('can omit claim', async () => {
+    test.skip('can omit claim', async () => {
       // API error on @relationDocument when the key is optional and omitted
       const data: Annotation = {
         comment: 'This is a cool object!',

From fe487fd9b5285112983862ce2db95b7676ab803f Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Fri, 13 Oct 2023 17:51:21 +0200
Subject: [PATCH 13/14] Add test for version index resolution

---
 test/root.spec.ts | 170 +++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 162 insertions(+), 8 deletions(-)

diff --git a/test/root.spec.ts b/test/root.spec.ts
index 57d1389..c8fb35b 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -299,7 +299,8 @@ describe('ComposeDB nodes', () => {
     });
 
     test.skip('can omit claim', async () => {
-      // API error on @relationDocument when the key is optional and omitted
+      // API error on @relationDocument when claimID omitted even if optional,
+      // under review by ceramic devs
       const data: Annotation = {
         comment: 'This is a cool object!',
         targetID: researchComponent.streamID,
@@ -312,6 +313,117 @@ describe('ComposeDB nodes', () => {
       expect(response).toEqual(data);
     });
 
+    test('can be accessed from research object', async () => {
+      const data: Annotation = {
+        comment: 'This is a cool object!',
+        targetID: researchObject.streamID,
+        targetVersion: researchObject.commitID,
+        claimID: claim.streamID,
+        claimVersion: claim.commitID
+      };
+
+      const annotation = await mutationCreateAnnotation(composeClient, data);
+
+      const response = await queryResearchObject(
+        composeClient,
+        researchObject.streamID,
+        `
+          annotations(first: 10) {
+            edges {
+              node {
+                targetID
+                targetVersion
+                id
+              }
+            }
+          }
+        `
+      );
+      const expected = {
+        node: {
+          targetID: researchObject.streamID,
+          targetVersion: researchObject.commitID,
+          id: annotation.streamID
+        }
+      };
+      expect((response as any).annotations.edges).toContainEqual(expected);
+    });
+    
+    test('can be accessed from research component', async () => {
+      const data: Annotation = {
+        comment: 'This is a cool component!',
+        targetID: researchComponent.streamID,
+        targetVersion: researchComponent.commitID,
+        claimID: claim.streamID,
+        claimVersion: claim.commitID
+      };
+
+      const annotation = await mutationCreateAnnotation(composeClient, data);
+
+      const response = await queryResearchComponent(
+        composeClient,
+        researchComponent.streamID,
+        `
+          annotations(first: 10) {
+            edges {
+              node {
+                targetID
+                targetVersion
+                id
+              }
+            }
+          }
+        `
+      );
+      const expected = {
+        node: {
+          targetID: researchComponent.streamID,
+          targetVersion: researchComponent.commitID,
+          id: annotation.streamID
+        }
+      };
+      expect((response as any).annotations.edges).toContainEqual(expected);
+    });
+
+    test('can reply to another annotation', async () => {
+      const questionData: Annotation = {
+        comment: 'What do you tink about this?',
+        targetID: researchComponent.streamID,
+        targetVersion: researchComponent.commitID,
+        claimID: claim.streamID,
+        claimVersion: claim.commitID
+      };
+
+      const question = await mutationCreateAnnotation(composeClient, questionData);
+
+      const replyData: Annotation = {
+        comment: 'Looks good!',
+        targetID: question.streamID,
+        targetVersion: question.commitID,
+        claimID: claim.streamID,
+        claimVersion: claim.commitID
+      };
+
+      const reply = await mutationCreateAnnotation(composeClient, replyData);
+      
+      const replyFromQuestion = await queryAnnotation(
+        composeClient,
+        question.streamID,
+        `
+          replies(first: 10) {
+            edges {
+              node {
+                id
+              }
+            }
+          }
+        `
+      );
+
+      // Verify that we can get the replies from the question
+      const expectedReply = { node: { id: reply.streamID }};
+      expect((replyFromQuestion as any).replies.edges).toContainEqual(expectedReply);
+    });
   });
 
   describe('User', async () => {
@@ -433,24 +545,66 @@ describe('ComposeDB nodes', () => {
         }
       );
 
+      // Verify that queries return the fresh data
       const roResult = await queryResearchObject(composeClient, researchObjectV0.streamID);
       const rcResult = await queryResearchComponent(composeClient, componentV0.streamID);
       expect(roResult?.manifest).toEqual(newManifest);
       expect(rcResult?.researchObjectID).toEqual(researchObjectV0.streamID);
 
-      // Check that we can get the old state with the research object version at
-      // that point in time
+      // Verify that we can still get the data of a specific version
       const oldComponentState = await ceramic.loadStream(componentV0.commitID);
       expect(oldComponentState.content.researchObjectVersion)
         .toEqual(researchObjectV0.commitID);
     });
-  });
 
+    test('can resolve a specific version index', async () => {
+      const data: ResearchObject = {
+        title: 'Title 0',
+        manifest: A_CID
+      };
+      const { streamID } = await mutationCreateResearchObject(composeClient, data);
+
+      await waitAndSync(streamID);
+      const V1 = await mutationUpdateResearchObject(
+        composeClient, 
+        { 
+          id: streamID,
+          title: 'Title 1'
+        }
+      );
 
-})
+      await waitAndSync(streamID);
+      const V2 = await mutationUpdateResearchObject(
+        composeClient, 
+        { 
+          id: streamID,
+          title: 'Title 2'
+        }
+      );
+
+      await waitAndSync(streamID);
+      const versionToResolve = 1;
+      const stream = await ceramic.loadStream(streamID);
+
+      // Find CIDs identifying anchor commits
+      const anchorCIDs = stream.state.log
+        .filter(c => c.type !== 2)
+        .map(c => c.cid);
+
+      // Find commits with commit CIDs not in the anchor CID list
+      const dataCommits = stream.allCommitIds
+        .filter(c => !anchorCIDs.includes(c.commit))
+
+      // Load state as of the n:th data commit in the stream
+      const streamAtV0 = await ceramic.loadStream(dataCommits[versionToResolve])
+      expect(streamAtV0.content.title).toEqual('Title 1') // yay
+  
+    });
+  });
+});
 
 const freshClient = () =>
-  new ComposeClient({ ceramic, definition: definition as RuntimeCompositeDefinition })
+  new ComposeClient({ ceramic, definition: definition as RuntimeCompositeDefinition });
 
 /** Sync between fast updates to same streams to make tests less flaky,
 * also allowing for an anchor commit to pop in between
@@ -458,5 +612,5 @@ const freshClient = () =>
 const waitAndSync = async (streamID: string) => {
   await setTimeout(100);
   const stream = await ceramic.loadStream(streamID);
-  await stream.sync(); 
-}
+  await stream.sync();
+};
\ No newline at end of file

From 08f613395b4c157a609a9856980f48b88fea6250 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Mon, 16 Oct 2023 09:14:53 +0200
Subject: [PATCH 14/14] Simplify version index resolution

---
 test/root.spec.ts | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/test/root.spec.ts b/test/root.spec.ts
index c8fb35b..563b8c8 100644
--- a/test/root.spec.ts
+++ b/test/root.spec.ts
@@ -24,6 +24,7 @@ import { CeramicClient } from '@ceramicnetwork/http-client'
 import { writeComposite } from 'scripts/composites.mjs'
 import { setTimeout } from "timers/promises";
 import { Annotation, Attestation, Claim, Profile, ResearchObject } from '@/types'
+import { CommitID } from '@ceramicnetwork/streamid'
 
 const CERAMIC_API = 'http:/localhost:7007'
 const A_CID = 'bafybeibeaampol2yz5xuoxex7dxri6ztqveqrybzfh5obz6jrul5gb4cf4'
@@ -586,19 +587,18 @@ describe('ComposeDB nodes', () => {
       const versionToResolve = 1;
       const stream = await ceramic.loadStream(streamID);
 
-      // Find CIDs identifying anchor commits
-      const anchorCIDs = stream.state.log
+      // Find n:th commit, excluding anchor commits
+      const commitCID = stream.state.log
         .filter(c => c.type !== 2)
-        .map(c => c.cid);
+        .map(c => c.cid)
+        .at(versionToResolve);
 
-      // Find commits with commit CIDs not in the anchor CID list
-      const dataCommits = stream.allCommitIds
-        .filter(c => !anchorCIDs.includes(c.commit))
+      expect(commitCID).not.toBeUndefined();
+      const commit = CommitID.make(stream.id, commitCID!);
 
       // Load state as of the n:th data commit in the stream
-      const streamAtV0 = await ceramic.loadStream(dataCommits[versionToResolve])
-      expect(streamAtV0.content.title).toEqual('Title 1') // yay
-  
+      const streamAtV0 = await ceramic.loadStream(commit);
+      expect(streamAtV0.content.title).toEqual('Title 1'); // yay
     });
   });
 });