From dae43cdd721fca076f09c3346882e16c06af3826 Mon Sep 17 00:00:00 2001
From: Anh Nguyet Vu <anngvu@gmail.com>
Date: Tue, 26 Nov 2024 08:18:37 -0800
Subject: [PATCH] Fixes

---
 .github/workflows/register-schema.sh  |  1 +
 Makefile                              |  2 +-
 registered-json-schemas/Protocol.json | 16 ++++++++++++----
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/register-schema.sh b/.github/workflows/register-schema.sh
index 0481d703..d97cf002 100755
--- a/.github/workflows/register-schema.sh
+++ b/.github/workflows/register-schema.sh
@@ -31,3 +31,4 @@ do
             break
         fi
     done
+done
diff --git a/Makefile b/Makefile
index 1634d362..f72cf7e2 100644
--- a/Makefile
+++ b/Makefile
@@ -34,7 +34,7 @@ Protocol:
 	yq '.slots |= with_entries(select(.value.in_subset[] == "portal" or .value.in_subset[] == "registered"))' modules/props.yaml > relevant_props.yaml
 	yq ea '. as $$item ireduce ({}; . * $$item )' modules/Data/Data.yaml modules/Assay/Assay.yaml > relevant_enums.yaml
 	cat header.yaml relevant_props.yaml relevant_enums.yaml modules/Template/Protocol.yaml > temp.yaml
-	gen-json-schema --inline --no-metadata --not-closed temp.yaml > tmp.json
+	gen-json-schema --inline --no-metadata --not-closed --title-from=title temp.yaml > tmp.json
 	json-dereference -s tmp.json -o tmp.json
 	jq '."$$defs".Protocol | ."$$id"="https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-protocol"' tmp.json > registered-json-schemas/Protocol.json
 	rm -f relevant_props.yaml relevant_enums.yaml temp.yaml tmp.json 
diff --git a/registered-json-schemas/Protocol.json b/registered-json-schemas/Protocol.json
index 6c6a8bb4..788bab5c 100644
--- a/registered-json-schemas/Protocol.json
+++ b/registered-json-schemas/Protocol.json
@@ -1,25 +1,32 @@
 {
   "additionalProperties": false,
-  "description": "Template for describing a protocol document.",
+  "description": "Describes protocol document based on https://bioschemas.org/profiles/LabProtocol/0.7-DRAFT.",
   "properties": {
     "author": {
       "description": "The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.",
-      "type": "string"
+      "items": {
+        "type": "string"
+      },
+      "title": "Author(s)",
+      "type": "array"
     },
     "citation": {
       "description": "Citation (e.g. doi) that usage of data or resource should be cited with.",
+      "title": "Citation",
       "type": "string"
     },
     "comments": {
       "description": "Brief free-text comments that may also be important to understanding the resource.",
+      "title": "Comments",
       "type": "string"
     },
     "license": {
       "description": "Link to a license or name of license applicable for the resource.",
-      "type": "string"
+      "title": "License"
     },
     "protocolAssay": {
       "description": "Main assay type that this protocol is related to, e.g. this is a prep protocol for single-cell RNA-seq assay. This is especially helpful for newly-developed or in-house assays.\n",
+      "title": "Protocol assay",
       "enum": [
         "2D AlamarBlue absorbance",
         "2D AlamarBlue fluorescence",
@@ -209,15 +216,16 @@
         "word recognition score",
         "STR profile"
       ],
-      "title": "AssayEnum",
       "type": "string"
     },
     "protocolPurpose": {
       "description": "Brief description of the protocol purpose.",
+      "title": "Protocol purpose",
       "type": "string"
     },
     "sampleType": {
       "description": "Type of sample used",
+      "title": "Sample type",
       "type": "string"
     },
     "title": {