From 48b5e16ccada0e8edcc9a55c98c3f8657ce4c5c7 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 11 May 2023 14:31:01 -0700
Subject: [PATCH 01/39] rename template_dir to community_dir

---
 .github/workflows/dcc_config_repo_dispatch.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/dcc_config_repo_dispatch.yml b/.github/workflows/dcc_config_repo_dispatch.yml
index 3ba96b2..7b26307 100644
--- a/.github/workflows/dcc_config_repo_dispatch.yml
+++ b/.github/workflows/dcc_config_repo_dispatch.yml
@@ -24,7 +24,7 @@ env:
   DATA_MODEL: https://raw.githubusercontent.com/Sage-Bionetworks/data-models/main/example.model.jsonld
   # Can be NULL to generate templates for all schemas. Or a space-delimited string of schemas
   DATA_TYPES: "Biospecimen BulkRNA-seqAssay Patient"
-  TEMPLATE_DIR: demo/templates
+  COMMUNITY_DIR: demo
 
 concurrency:
 # cancel the current running workflow from the same branch, PR when a new workflow is triggered 
@@ -50,4 +50,4 @@ jobs:
           -H "Authorization: token ${{ secrets.PAT_GITHUB }}" \
           -H "Accept: application/vnd.github+json" \
           https://api.github.com/repos/Sage-Bionetworks/data_curator_config/dispatches \
-          -d '{"event_type": "generate_templates", "client_payload": { "data_model": "${{ env.DATA_MODEL }}",  "data_types": "${{ env.DATA_TYPES }}", "template_dir": "${{ env.TEMPLATE_DIR }}"}}'
+          -d '{"event_type": "generate_templates", "client_payload": { "data_model": "${{ env.DATA_MODEL }}",  "data_types": "${{ env.DATA_TYPES }}", "community_dir": "${{ env.COMMUNITY_DIR }}"}}'

From ee6b27a3416ea77cc2273180648521e551dc108a Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 1 Nov 2023 14:41:18 -0700
Subject: [PATCH 02/39] add template create workflow

---
 .github/workflows/create-template-config.yml | 82 ++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 .github/workflows/create-template-config.yml

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
new file mode 100644
index 0000000..16d9072
--- /dev/null
+++ b/.github/workflows/create-template-config.yml
@@ -0,0 +1,82 @@
+on:
+  repository_dispatch:
+    types: generate_templates
+  workflow_dispatch:
+    inputs:
+      data_model:
+        description: URL to a jsonld data model file
+        required: true
+      path:
+        description: Directory to save the template config
+        required: true
+        
+jobs:
+  create-template-config:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install packages
+        run: install.packages(c("dplyr", "httr", "jsonlite")
+        shell: Rscript {0}
+        
+      - name: Create config file
+        run: |
+          library(httr)
+          library(dplyr)
+          library(readr)
+          library(jsonlite)
+          graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
+                                         schema_url, relationship = "requiresDependency") {
+            req <- httr::GET(url = url,
+                      query = list(
+                        schema_url = schema_url,
+                        relationship = relationship
+                      ))
+              httr::content(req)
+          }
+          format_edge_type <- function(edge_types) {
+            et <- bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], component=x[[1]])))
+            et %>% filter(value %in% c("Component", "Filename")) %>% 
+              group_by(component) %>% 
+              summarise(file_based = "Filename" %in% value)
+          }
+          get_display_names <- function(qlist) {
+            if (!"schema_url" %in% names(qlist)) stop("qlist needs element named `schema_url`")
+            if (!"node_list" %in% names(qlist)) stop("qlist needs at least one element named `node_list`")
+            httr::GET(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get_nodes_display_names",
+                      query = qlist
+                      )
+          }
+          create_template_config <- function(data_model) {
+            edges <- graph_by_edge_type(schema_url = data_model)
+            components <- format_edge_type(edges)
+            nl <- setNames(as.list(components$component), rep("node_list", length(components$component)))
+            dnames <- get_display_names(c(schema_url = data_model, nl)) %>% httr::content()
+            data.frame(component = unlist(nl), display_name = unlist(dnames)) %>%
+              left_join(components, by = "component") %>%
+              mutate(record_type = ifelse(file_based, "file", "record")) %>%
+              select(-file_based)
+          }
+          create_json_template_config <- function(data_model, file) {
+            df <- create_template_config(data_model)
+            write_json(df, file)
+          }
+          create_json_template_config( ${{ inputs.data_model }}, ${{ inputs.path }})
+        shell: Rscript {0}
+        
+      - name: Open PR
+        uses: peter-evans/create-pull-request@v5
+        with:
+          title: Automatic Template Config
+          body: Template updates triggered by repository dispatch from a data model repository.
+          delete-branch: true
+          branch-suffix: timestamp
+          add-paths: |
+            ${{ inputs.path }}

From fe9b8d0bb9ae7b64c8e0f7aaa683a656c727cfb4 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 1 Nov 2023 14:48:33 -0700
Subject: [PATCH 03/39] add )

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 16d9072..5ae418f 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -23,7 +23,7 @@ jobs:
           use-public-rspm: true
 
       - name: Install packages
-        run: install.packages(c("dplyr", "httr", "jsonlite")
+        run: install.packages(c("dplyr", "httr", "jsonlite"))
         shell: Rscript {0}
         
       - name: Create config file

From 37ea57837a3f0ff2f3c606157e050ad4b845039d Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 1 Nov 2023 14:59:26 -0700
Subject: [PATCH 04/39] remove readr

---
 .github/workflows/create-template-config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 5ae418f..2880d1a 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -30,7 +30,6 @@ jobs:
         run: |
           library(httr)
           library(dplyr)
-          library(readr)
           library(jsonlite)
           graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
                                          schema_url, relationship = "requiresDependency") {

From 9847d122e0b62e560b3b8c47a94906c9ed8aea42 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 1 Nov 2023 15:06:58 -0700
Subject: [PATCH 05/39] quote input env vars

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 2880d1a..b512d80 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -67,7 +67,7 @@ jobs:
             df <- create_template_config(data_model)
             write_json(df, file)
           }
-          create_json_template_config( ${{ inputs.data_model }}, ${{ inputs.path }})
+          create_json_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
         
       - name: Open PR

From 068ae5aba3d2860d873fedd1bf722a874afd3254 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 07:46:42 -0700
Subject: [PATCH 06/39] clean up json output to match current config file. use
 base pipe operator

---
 .github/workflows/create-template-config.yml | 21 +++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index b512d80..4b0f171 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -42,8 +42,8 @@ jobs:
           }
           format_edge_type <- function(edge_types) {
             et <- bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], component=x[[1]])))
-            et %>% filter(value %in% c("Component", "Filename")) %>% 
-              group_by(component) %>% 
+            et |> filter(value %in% c("Component", "Filename")) |> 
+              group_by(component) |> 
               summarise(file_based = "Filename" %in% value)
           }
           get_display_names <- function(qlist) {
@@ -57,15 +57,22 @@ jobs:
             edges <- graph_by_edge_type(schema_url = data_model)
             components <- format_edge_type(edges)
             nl <- setNames(as.list(components$component), rep("node_list", length(components$component)))
-            dnames <- get_display_names(c(schema_url = data_model, nl)) %>% httr::content()
-            data.frame(component = unlist(nl), display_name = unlist(dnames)) %>%
-              left_join(components, by = "component") %>%
-              mutate(record_type = ifelse(file_based, "file", "record")) %>%
+            dnames <- get_display_names(c(schema_url = data_model, nl)) |> httr::content()
+            data.frame(display_name = unlist(dnames), component = unlist(nl)) |>
+              left_join(components, by = "component") |>
+              mutate(type = ifelse(file_based, "file", "record")) |>
               select(-file_based)
           }
           create_json_template_config <- function(data_model, file) {
             df <- create_template_config(data_model)
-            write_json(df, file)
+            schematic_version <- httr::GET("https://schematic-dev.api.sagebionetworks.org/v1/version") |>
+              httr::content()
+            json <- list(
+              manifests = df,
+              service_version = schematic_version,
+              schema_version = ""
+            )
+            write_json(json, file, pretty = TRUE, auto_unbox = TRUE)
           }
           create_json_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}

From 35a90bf06fb82aa7a83f98653f7f2f09480cf611 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 07:51:34 -0700
Subject: [PATCH 07/39] name workflow and change PR title

---
 .github/workflows/create-template-config.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 4b0f171..91fdde9 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -1,3 +1,4 @@
+name: Create DCA Template Config File
 on:
   repository_dispatch:
     types: generate_templates
@@ -80,8 +81,8 @@ jobs:
       - name: Open PR
         uses: peter-evans/create-pull-request@v5
         with:
-          title: Automatic Template Config
-          body: Template updates triggered by repository dispatch from a data model repository.
+          title: Update DCA Template Config File
+          body: Recreate the json file that populates the DCA template dropdown menu.
           delete-branch: true
           branch-suffix: timestamp
           add-paths: |

From 8251f182db9c4698ddb936dd3ee9b7f8a3efc376 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 07:59:43 -0700
Subject: [PATCH 08/39] change component to schema_name

---
 .github/workflows/create-template-config.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 91fdde9..9a3d78e 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -42,9 +42,9 @@ jobs:
               httr::content(req)
           }
           format_edge_type <- function(edge_types) {
-            et <- bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], component=x[[1]])))
-            et |> filter(value %in% c("Component", "Filename")) |> 
-              group_by(component) |> 
+            et <- bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], schema_name=x[[1]])))
+            et |> filter(value %in% c("schema_name", "Filename")) |> 
+              group_by(schema_name) |> 
               summarise(file_based = "Filename" %in% value)
           }
           get_display_names <- function(qlist) {
@@ -56,11 +56,11 @@ jobs:
           }
           create_template_config <- function(data_model) {
             edges <- graph_by_edge_type(schema_url = data_model)
-            components <- format_edge_type(edges)
-            nl <- setNames(as.list(components$component), rep("node_list", length(components$component)))
+            schema_names <- format_edge_type(edges)
+            nl <- setNames(as.list(schema_names$schema_name), rep("node_list", length(schema_names$schema_name)))
             dnames <- get_display_names(c(schema_url = data_model, nl)) |> httr::content()
-            data.frame(display_name = unlist(dnames), component = unlist(nl)) |>
-              left_join(components, by = "component") |>
+            data.frame(display_name = unlist(dnames), schema_name = unlist(nl)) |>
+              left_join(schema_names, by = "schema_name") |>
               mutate(type = ifelse(file_based, "file", "record")) |>
               select(-file_based)
           }

From cebb2c2961a559f840275c056e90bebac70cff6a Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 08:10:04 -0700
Subject: [PATCH 09/39] fix filter for components and filenames

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 9a3d78e..73cb366 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -43,7 +43,7 @@ jobs:
           }
           format_edge_type <- function(edge_types) {
             et <- bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], schema_name=x[[1]])))
-            et |> filter(value %in% c("schema_name", "Filename")) |> 
+            et |> filter(value %in% c("Component", "Filename")) |> 
               group_by(schema_name) |> 
               summarise(file_based = "Filename" %in% value)
           }

From 55af3f0ed8b2ac71df674784c0dc6c5e6fbdb3a9 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 08:18:07 -0700
Subject: [PATCH 10/39] change array name to manifest_schemas to match existing
 format

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 73cb366..4f9e88b 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -69,7 +69,7 @@ jobs:
             schematic_version <- httr::GET("https://schematic-dev.api.sagebionetworks.org/v1/version") |>
               httr::content()
             json <- list(
-              manifests = df,
+              manifest_schemas = df,
               service_version = schematic_version,
               schema_version = ""
             )

From 2384257bb404930c7f7b68538f73878d48e2eb2c Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 08:30:32 -0700
Subject: [PATCH 11/39] Add step to validate json

---
 .github/workflows/create-template-config.yml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 4f9e88b..ffaa1ed 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -15,7 +15,7 @@ jobs:
   create-template-config:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -77,7 +77,18 @@ jobs:
           }
           create_json_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
+
+      - name: Checkout DCA Config Repo for Schema
+        uses: actions/checkout@v4
+        with:
+          repository: 'Sage-Bionetworks/data_curator_config'
         
+      - name: Validate Config File
+        uses: docker://orrosenblatt/validate-json-action:latest
+        env:
+          INPUT_SCHEMA: 'Sage-Bionetworks/schemas/dca_template_config.schema.json'
+          INPUT_JSONS: ${{ inputs.path }}
+      
       - name: Open PR
         uses: peter-evans/create-pull-request@v5
         with:

From 224e7701c642db86dfb620a0f1aa046d90c8d0ff Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 08:41:05 -0700
Subject: [PATCH 12/39] checkout config repo side by side

---
 .github/workflows/create-template-config.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index ffaa1ed..5d1159e 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -82,11 +82,12 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'Sage-Bionetworks/data_curator_config'
+          path: 'data_curator_config'
         
       - name: Validate Config File
         uses: docker://orrosenblatt/validate-json-action:latest
         env:
-          INPUT_SCHEMA: 'Sage-Bionetworks/schemas/dca_template_config.schema.json'
+          INPUT_SCHEMA: 'data_curator_config/schemas/dca_template_config.schema.json'
           INPUT_JSONS: ${{ inputs.path }}
       
       - name: Open PR

From eabf04abf2aed84f904b6b27dc05ee49b92efc8a Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 08:50:09 -0700
Subject: [PATCH 13/39] don't run on psuh to main

---
 .github/workflows/dcc_config_repo_dispatch.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/dcc_config_repo_dispatch.yml b/.github/workflows/dcc_config_repo_dispatch.yml
index 7b26307..c32ad8c 100644
--- a/.github/workflows/dcc_config_repo_dispatch.yml
+++ b/.github/workflows/dcc_config_repo_dispatch.yml
@@ -11,9 +11,6 @@ name: dcc_config_repo_dispatch
 # Can specify other branches or triggers for this workflow
 # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows
 on:
-  push:
-    branches:
-      - main
   pull_request:
     types:
       - closed # requires if_merged job below to run only during a merged PR

From 901e82f318538f62c292c703fb3ba8213d18cc6a Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 08:50:23 -0700
Subject: [PATCH 14/39] check out config-refactor branch of config repo

---
 .github/workflows/create-template-config.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 5d1159e..6288fa8 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -82,6 +82,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'Sage-Bionetworks/data_curator_config'
+          ref: 'config-refactor'
           path: 'data_curator_config'
         
       - name: Validate Config File

From 12ee4da43b8383337af2d6ac45515131ce3e53c9 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 10:06:11 -0700
Subject: [PATCH 15/39] checkout dev branch of data_curator_config for schema

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 6288fa8..b8ae15c 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -82,7 +82,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: 'Sage-Bionetworks/data_curator_config'
-          ref: 'config-refactor'
+          ref: 'dev'
           path: 'data_curator_config'
         
       - name: Validate Config File

From afecd92480eb09837d277053298dcd93514c41d5 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 13:38:47 -0700
Subject: [PATCH 16/39] Use datacurator package to create config

---
 .github/workflows/create-template-config.yml | 52 ++------------------
 1 file changed, 4 insertions(+), 48 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index b8ae15c..dca23ee 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -24,58 +24,14 @@ jobs:
           use-public-rspm: true
 
       - name: Install packages
-        run: install.packages(c("dplyr", "httr", "jsonlite"))
+        run: |
+          install.packages("remotes")
+          remotes::install_github("Sage-Bionetworks/data_curator", "rc.23.11.1")
         shell: Rscript {0}
         
       - name: Create config file
         run: |
-          library(httr)
-          library(dplyr)
-          library(jsonlite)
-          graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
-                                         schema_url, relationship = "requiresDependency") {
-            req <- httr::GET(url = url,
-                      query = list(
-                        schema_url = schema_url,
-                        relationship = relationship
-                      ))
-              httr::content(req)
-          }
-          format_edge_type <- function(edge_types) {
-            et <- bind_rows(lapply(edge_types, function(x) data.frame(value=x[[2]], schema_name=x[[1]])))
-            et |> filter(value %in% c("Component", "Filename")) |> 
-              group_by(schema_name) |> 
-              summarise(file_based = "Filename" %in% value)
-          }
-          get_display_names <- function(qlist) {
-            if (!"schema_url" %in% names(qlist)) stop("qlist needs element named `schema_url`")
-            if (!"node_list" %in% names(qlist)) stop("qlist needs at least one element named `node_list`")
-            httr::GET(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get_nodes_display_names",
-                      query = qlist
-                      )
-          }
-          create_template_config <- function(data_model) {
-            edges <- graph_by_edge_type(schema_url = data_model)
-            schema_names <- format_edge_type(edges)
-            nl <- setNames(as.list(schema_names$schema_name), rep("node_list", length(schema_names$schema_name)))
-            dnames <- get_display_names(c(schema_url = data_model, nl)) |> httr::content()
-            data.frame(display_name = unlist(dnames), schema_name = unlist(nl)) |>
-              left_join(schema_names, by = "schema_name") |>
-              mutate(type = ifelse(file_based, "file", "record")) |>
-              select(-file_based)
-          }
-          create_json_template_config <- function(data_model, file) {
-            df <- create_template_config(data_model)
-            schematic_version <- httr::GET("https://schematic-dev.api.sagebionetworks.org/v1/version") |>
-              httr::content()
-            json <- list(
-              manifest_schemas = df,
-              service_version = schematic_version,
-              schema_version = ""
-            )
-            write_json(json, file, pretty = TRUE, auto_unbox = TRUE)
-          }
-          create_json_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
+          datacurator::write_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
 
       - name: Checkout DCA Config Repo for Schema

From 22fa7566277ecaf293f831efd7a4af26b444b5b3 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 13:45:08 -0700
Subject: [PATCH 17/39] run everything in one step

---
 .github/workflows/create-template-config.yml | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index dca23ee..a17ce3d 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -23,17 +23,13 @@ jobs:
         with:
           use-public-rspm: true
 
-      - name: Install packages
-        run: |
-          install.packages("remotes")
-          remotes::install_github("Sage-Bionetworks/data_curator", "rc.23.11.1")
-        shell: Rscript {0}
-        
       - name: Create config file
         run: |
+          install.packages("remotes")
+          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1")
           datacurator::write_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
-
+        
       - name: Checkout DCA Config Repo for Schema
         uses: actions/checkout@v4
         with:

From 1df93689508e943a2ca489f11e352ece3cbe7fe5 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 13:50:29 -0700
Subject: [PATCH 18/39] use github token for install_github

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index a17ce3d..3f4be6c 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Create config file
         run: |
           install.packages("remotes")
-          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1")
+          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1", auth_token = ${{ secrets.GITHUB_TOKEN }})
           datacurator::write_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
         

From 93577e3eaa1b604d742bc9d7f656ea2757c1e46f Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 13:54:40 -0700
Subject: [PATCH 19/39] use github.token context

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 3f4be6c..1b9fd5c 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Create config file
         run: |
           install.packages("remotes")
-          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1", auth_token = ${{ secrets.GITHUB_TOKEN }})
+          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1", auth_token = "$ {{ github.token }}" )
           datacurator::write_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
         

From 89940663b80386c8077ae14254478bc17037c46c Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 2 Nov 2023 14:06:59 -0700
Subject: [PATCH 20/39] remove extra space

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 1b9fd5c..9755f2c 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Create config file
         run: |
           install.packages("remotes")
-          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1", auth_token = "$ {{ github.token }}" )
+          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1", auth_token = "${{ github.token }}" )
           datacurator::write_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
         

From 4326bec2f2090f3703906e2d33def0c971f672a0 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 08:14:26 -0800
Subject: [PATCH 21/39] use write_dca_template_config

---
 .github/workflows/create-template-config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 9755f2c..0981715 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -27,7 +27,7 @@ jobs:
         run: |
           install.packages("remotes")
           remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1", auth_token = "${{ github.token }}" )
-          datacurator::write_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
+          datacurator::write_dca_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
         shell: Rscript {0}
         
       - name: Checkout DCA Config Repo for Schema

From 6af0800f044e240efefcd42c3db8debee8fcb0b9 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 7 Nov 2023 10:27:00 -0800
Subject: [PATCH 22/39] Add explanatory comments to the top

---
 .github/workflows/create-template-config.yml | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 0981715..c482177 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -1,7 +1,23 @@
+# --------------------------------------------------------------------------------------------------
+# GitHub Action to create a DCA template config json file for a data model
+# 
+# This action creates a json file named with the `path` input argument using 
+# the data model supplied to the `data_model` argument. It will validate the 
+# json file against DCA's template config schema. Finally, it will create a PR
+# in the repo for the new file.
+#
+# Copy this into your data model repo .github/workflow directory.
+# Your repo settings must have Actions enabled and must allow GitHub Actions to
+# create and approve pull requests.
+# 
+# By default, this action runs by workflow dispatch. But it can be configured
+# to run on other triggers. Consult the github doc below for more information.
+# https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_dispatch
+#
+# --------------------------------------------------------------------------------------------------
+
 name: Create DCA Template Config File
 on:
-  repository_dispatch:
-    types: generate_templates
   workflow_dispatch:
     inputs:
       data_model:

From 84c819162a9092f82234fff0f5b0013a85a78a93 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 9 Nov 2023 13:55:01 -0800
Subject: [PATCH 23/39] Add include_schemas and exclude_schemas

---
 .github/workflows/create-template-config.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index c482177..7370083 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -14,6 +14,10 @@
 # to run on other triggers. Consult the github doc below for more information.
 # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_dispatch
 #
+# The resulting file with contain one entry for each attribute in the data model that `dependsOn`
+# "Component". To include a subset of these attributes, use either `include_schemas` or
+# `exclude_schemas` in the call to `datacurator::write_dca_template_config()`
+#
 # --------------------------------------------------------------------------------------------------
 
 name: Create DCA Template Config File
@@ -26,6 +30,12 @@ on:
       path:
         description: Directory to save the template config
         required: true
+      include_schemas:
+        description: Comma-separated string of schemas to include in output. Must be empty if using exclude_schemas.
+        required: false
+      exlude_schemas:
+        description: Commma-separated string of schemas to exclude from output. Must be empty if using include_schemas.
+        required: false
         
 jobs:
   create-template-config:

From 07023c0696de703fd802cd7d44f7a62c20f22bac Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Fri, 10 Nov 2023 12:38:09 -0800
Subject: [PATCH 24/39] Create a workflow using dca-template-config-action

---
 create-template-config-v2.yml | 79 +++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 create-template-config-v2.yml

diff --git a/create-template-config-v2.yml b/create-template-config-v2.yml
new file mode 100644
index 0000000..131ed51
--- /dev/null
+++ b/create-template-config-v2.yml
@@ -0,0 +1,79 @@
+# --------------------------------------------------------------------------------------------------
+# GitHub Action to create a DCA template config json file for a data model
+# 
+# This action creates a json file named with the `path` input argument using 
+# the data model supplied to the `data_model` argument. It will validate the 
+# json file against DCA's template config schema. Finally, it will create a PR
+# in the repo for the new file.
+#
+# Copy this into your data model repo .github/workflow directory.
+# Your repo settings must have Actions enabled and must allow GitHub Actions to
+# create and approve pull requests.
+# 
+# By default, this action runs by workflow dispatch. But it can be configured
+# to run on other triggers. Consult the github doc below for more information.
+# https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_dispatch
+#
+# The resulting file with contain one entry for each attribute in the data model that `dependsOn`
+# "Component". To include a subset of these attributes, use either `include_schemas` or
+# `exclude_schemas` in the call to `datacurator::write_dca_template_config()`
+#
+# --------------------------------------------------------------------------------------------------
+
+name: Create DCA Template Config File
+on:
+  workflow_dispatch:
+    inputs:
+      data_model:
+        description: URL to a jsonld data model file
+        required: true
+      path:
+        description: Directory to save the template config
+        required: true
+      include_schemas:
+        description: Comma-separated string of schemas to include in output. Must be empty if using exclude_schemas.
+        required: false
+      exlude_schemas:
+        description: Commma-separated string of schemas to exclude from output. Must be empty if using include_schemas.
+        required: false
+        
+jobs:
+  create-template-config:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Create config file
+        uses: sage-bionetworks/dca-template-config-action@main
+        with:
+          data-model: ${{ inputs.data_model }}
+          path: ${{ inputs.path }}
+        
+      - name: Checkout DCA Config Repo for Schema
+        uses: actions/checkout@v4
+        with:
+          repository: 'Sage-Bionetworks/data_curator_config'
+          ref: 'dev'
+          path: 'data_curator_config'
+        
+      - name: Validate Config File
+        uses: docker://orrosenblatt/validate-json-action:latest
+        env:
+          INPUT_SCHEMA: 'data_curator_config/schemas/dca_template_config.schema.json'
+          INPUT_JSONS: ${{ inputs.path }}
+      
+      - name: Open PR
+        uses: peter-evans/create-pull-request@v5
+        with:
+          title: Update DCA Template Config File
+          body: Recreate the json file that populates the DCA template dropdown menu.
+          delete-branch: true
+          branch-suffix: timestamp
+          add-paths: |
+            ${{ inputs.path }}

From 219c4f87c66937e8e247fb85433a575a3f795b93 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Fri, 10 Nov 2023 12:39:20 -0800
Subject: [PATCH 25/39] move workflow to github dir

---
 .../workflows/create-template-config-v2.yml                       | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename create-template-config-v2.yml => .github/workflows/create-template-config-v2.yml (100%)

diff --git a/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
similarity index 100%
rename from create-template-config-v2.yml
rename to .github/workflows/create-template-config-v2.yml

From 0cda86456a646b200af5ac3854d83e1defc58fed Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Fri, 10 Nov 2023 12:40:04 -0800
Subject: [PATCH 26/39] change name of workflow to distinguish from original

---
 .github/workflows/create-template-config-v2.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index 131ed51..a16b0ac 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -20,7 +20,7 @@
 #
 # --------------------------------------------------------------------------------------------------
 
-name: Create DCA Template Config File
+name: DCA Template Config File
 on:
   workflow_dispatch:
     inputs:

From 7fe6961e97452dfd38bf0f0c6581dda8ca8d0fbd Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Fri, 10 Nov 2023 12:42:41 -0800
Subject: [PATCH 27/39] remove set up R action

---
 .github/workflows/create-template-config-v2.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index a16b0ac..a057ae3 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -43,12 +43,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
       - name: Create config file
         uses: sage-bionetworks/dca-template-config-action@main
         with:

From 523a1b349858dd4de87644921e4693d024c10c79 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 11:53:46 -0800
Subject: [PATCH 28/39] use env instead of with

---
 .github/workflows/create-template-config-v2.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index a057ae3..7c15a57 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -44,8 +44,8 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create config file
-        uses: sage-bionetworks/dca-template-config-action@main
-        with:
+        uses: sage-bionetworks/dca-template-config-action@intial-setup
+        env:
           data-model: ${{ inputs.data_model }}
           path: ${{ inputs.path }}
         

From e58ffa7368879e81e8a3dfc61891de5fd7c501fa Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 11:55:25 -0800
Subject: [PATCH 29/39] use main branch

---
 .github/workflows/create-template-config-v2.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index 7c15a57..e3a4fac 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -44,7 +44,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create config file
-        uses: sage-bionetworks/dca-template-config-action@intial-setup
+        uses: sage-bionetworks/dca-template-config-action@main
         env:
           data-model: ${{ inputs.data_model }}
           path: ${{ inputs.path }}

From 051726932da9a5e905ad09a92b973accca17e013 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 12:02:48 -0800
Subject: [PATCH 30/39] use data_model

---
 .github/workflows/create-template-config-v2.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index e3a4fac..affc105 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -46,7 +46,7 @@ jobs:
       - name: Create config file
         uses: sage-bionetworks/dca-template-config-action@main
         env:
-          data-model: ${{ inputs.data_model }}
+          data_model: ${{ inputs.data_model }}
           path: ${{ inputs.path }}
         
       - name: Checkout DCA Config Repo for Schema

From c6d8878b223a26aaa496e06f289037a20afc487b Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 12:42:14 -0800
Subject: [PATCH 31/39] give write permission

---
 .github/workflows/create-template-config-v2.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index affc105..5a5b3bb 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -37,6 +37,8 @@ on:
         description: Commma-separated string of schemas to exclude from output. Must be empty if using include_schemas.
         required: false
         
+permissions: write-all
+
 jobs:
   create-template-config:
     runs-on: ubuntu-latest

From 224c03d92a7acb78c03d05d1514d6ee08571c58b Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 14:35:24 -0800
Subject: [PATCH 32/39] checkout repo and then write config

---
 .github/workflows/create-template-config-v2.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index 5a5b3bb..7b063e7 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -45,18 +45,18 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Create config file
-        uses: sage-bionetworks/dca-template-config-action@main
-        env:
-          data_model: ${{ inputs.data_model }}
-          path: ${{ inputs.path }}
-        
       - name: Checkout DCA Config Repo for Schema
         uses: actions/checkout@v4
         with:
           repository: 'Sage-Bionetworks/data_curator_config'
           ref: 'dev'
           path: 'data_curator_config'
+
+      - name: Create config file
+        uses: sage-bionetworks/dca-template-config-action@main
+        env:
+          data_model: ${{ inputs.data_model }}
+          path: ${{ inputs.path }}
         
       - name: Validate Config File
         uses: docker://orrosenblatt/validate-json-action:latest

From 75af16fb6cd96d417e8e4f8383382d9205f726eb Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 16:32:11 -0800
Subject: [PATCH 33/39] make path file

---
 .github/workflows/create-template-config-v2.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index 7b063e7..8f85b61 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -56,7 +56,7 @@ jobs:
         uses: sage-bionetworks/dca-template-config-action@main
         env:
           data_model: ${{ inputs.data_model }}
-          path: ${{ inputs.path }}
+          path: ${{ inputs.file }}
         
       - name: Validate Config File
         uses: docker://orrosenblatt/validate-json-action:latest

From 08c4db6fd5de7f18f25c900ca573d7c0ad5b21b2 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 16:34:11 -0800
Subject: [PATCH 34/39] really change path to file

---
 .github/workflows/create-template-config-v2.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index 8f85b61..b6c6280 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -27,7 +27,7 @@ on:
       data_model:
         description: URL to a jsonld data model file
         required: true
-      path:
+      file:
         description: Directory to save the template config
         required: true
       include_schemas:
@@ -56,7 +56,7 @@ jobs:
         uses: sage-bionetworks/dca-template-config-action@main
         env:
           data_model: ${{ inputs.data_model }}
-          path: ${{ inputs.file }}
+          file: ${{ inputs.file }}
         
       - name: Validate Config File
         uses: docker://orrosenblatt/validate-json-action:latest

From d123375fe13a1e45f5aa9ec6ca1a5f7304dfacbd Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 16:37:14 -0800
Subject: [PATCH 35/39] change path to file

---
 .github/workflows/create-template-config-v2.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
index b6c6280..71008dd 100644
--- a/.github/workflows/create-template-config-v2.yml
+++ b/.github/workflows/create-template-config-v2.yml
@@ -1,7 +1,7 @@
 # --------------------------------------------------------------------------------------------------
 # GitHub Action to create a DCA template config json file for a data model
 # 
-# This action creates a json file named with the `path` input argument using 
+# This action creates a json file named with the `file` input argument using 
 # the data model supplied to the `data_model` argument. It will validate the 
 # json file against DCA's template config schema. Finally, it will create a PR
 # in the repo for the new file.
@@ -36,8 +36,6 @@ on:
       exlude_schemas:
         description: Commma-separated string of schemas to exclude from output. Must be empty if using include_schemas.
         required: false
-        
-permissions: write-all
 
 jobs:
   create-template-config:
@@ -62,7 +60,7 @@ jobs:
         uses: docker://orrosenblatt/validate-json-action:latest
         env:
           INPUT_SCHEMA: 'data_curator_config/schemas/dca_template_config.schema.json'
-          INPUT_JSONS: ${{ inputs.path }}
+          INPUT_JSONS: ${{ inputs.file }}
       
       - name: Open PR
         uses: peter-evans/create-pull-request@v5
@@ -72,4 +70,4 @@ jobs:
           delete-branch: true
           branch-suffix: timestamp
           add-paths: |
-            ${{ inputs.path }}
+            ${{ inputs.file }}

From 35354637824ca4a127fabd03eb6bd313a3703271 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 16:41:33 -0800
Subject: [PATCH 36/39] Now that template github action works, just use one
 workflow file

---
 .../workflows/create-template-config-v2.yml   | 73 -------------------
 .github/workflows/create-template-config.yml  | 31 +++-----
 2 files changed, 12 insertions(+), 92 deletions(-)
 delete mode 100644 .github/workflows/create-template-config-v2.yml

diff --git a/.github/workflows/create-template-config-v2.yml b/.github/workflows/create-template-config-v2.yml
deleted file mode 100644
index 71008dd..0000000
--- a/.github/workflows/create-template-config-v2.yml
+++ /dev/null
@@ -1,73 +0,0 @@
-# --------------------------------------------------------------------------------------------------
-# GitHub Action to create a DCA template config json file for a data model
-# 
-# This action creates a json file named with the `file` input argument using 
-# the data model supplied to the `data_model` argument. It will validate the 
-# json file against DCA's template config schema. Finally, it will create a PR
-# in the repo for the new file.
-#
-# Copy this into your data model repo .github/workflow directory.
-# Your repo settings must have Actions enabled and must allow GitHub Actions to
-# create and approve pull requests.
-# 
-# By default, this action runs by workflow dispatch. But it can be configured
-# to run on other triggers. Consult the github doc below for more information.
-# https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_dispatch
-#
-# The resulting file with contain one entry for each attribute in the data model that `dependsOn`
-# "Component". To include a subset of these attributes, use either `include_schemas` or
-# `exclude_schemas` in the call to `datacurator::write_dca_template_config()`
-#
-# --------------------------------------------------------------------------------------------------
-
-name: DCA Template Config File
-on:
-  workflow_dispatch:
-    inputs:
-      data_model:
-        description: URL to a jsonld data model file
-        required: true
-      file:
-        description: Directory to save the template config
-        required: true
-      include_schemas:
-        description: Comma-separated string of schemas to include in output. Must be empty if using exclude_schemas.
-        required: false
-      exlude_schemas:
-        description: Commma-separated string of schemas to exclude from output. Must be empty if using include_schemas.
-        required: false
-
-jobs:
-  create-template-config:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Checkout DCA Config Repo for Schema
-        uses: actions/checkout@v4
-        with:
-          repository: 'Sage-Bionetworks/data_curator_config'
-          ref: 'dev'
-          path: 'data_curator_config'
-
-      - name: Create config file
-        uses: sage-bionetworks/dca-template-config-action@main
-        env:
-          data_model: ${{ inputs.data_model }}
-          file: ${{ inputs.file }}
-        
-      - name: Validate Config File
-        uses: docker://orrosenblatt/validate-json-action:latest
-        env:
-          INPUT_SCHEMA: 'data_curator_config/schemas/dca_template_config.schema.json'
-          INPUT_JSONS: ${{ inputs.file }}
-      
-      - name: Open PR
-        uses: peter-evans/create-pull-request@v5
-        with:
-          title: Update DCA Template Config File
-          body: Recreate the json file that populates the DCA template dropdown menu.
-          delete-branch: true
-          branch-suffix: timestamp
-          add-paths: |
-            ${{ inputs.file }}
diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 7370083..71008dd 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -1,7 +1,7 @@
 # --------------------------------------------------------------------------------------------------
 # GitHub Action to create a DCA template config json file for a data model
 # 
-# This action creates a json file named with the `path` input argument using 
+# This action creates a json file named with the `file` input argument using 
 # the data model supplied to the `data_model` argument. It will validate the 
 # json file against DCA's template config schema. Finally, it will create a PR
 # in the repo for the new file.
@@ -20,14 +20,14 @@
 #
 # --------------------------------------------------------------------------------------------------
 
-name: Create DCA Template Config File
+name: DCA Template Config File
 on:
   workflow_dispatch:
     inputs:
       data_model:
         description: URL to a jsonld data model file
         required: true
-      path:
+      file:
         description: Directory to save the template config
         required: true
       include_schemas:
@@ -36,38 +36,31 @@ on:
       exlude_schemas:
         description: Commma-separated string of schemas to exclude from output. Must be empty if using include_schemas.
         required: false
-        
+
 jobs:
   create-template-config:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - name: Create config file
-        run: |
-          install.packages("remotes")
-          remotes::install_github("Sage-Bionetworks/data_curator@rc.23.11.1", auth_token = "${{ github.token }}" )
-          datacurator::write_dca_template_config( "${{ inputs.data_model }}", "${{ inputs.path }}")
-        shell: Rscript {0}
-        
       - name: Checkout DCA Config Repo for Schema
         uses: actions/checkout@v4
         with:
           repository: 'Sage-Bionetworks/data_curator_config'
           ref: 'dev'
           path: 'data_curator_config'
+
+      - name: Create config file
+        uses: sage-bionetworks/dca-template-config-action@main
+        env:
+          data_model: ${{ inputs.data_model }}
+          file: ${{ inputs.file }}
         
       - name: Validate Config File
         uses: docker://orrosenblatt/validate-json-action:latest
         env:
           INPUT_SCHEMA: 'data_curator_config/schemas/dca_template_config.schema.json'
-          INPUT_JSONS: ${{ inputs.path }}
+          INPUT_JSONS: ${{ inputs.file }}
       
       - name: Open PR
         uses: peter-evans/create-pull-request@v5
@@ -77,4 +70,4 @@ jobs:
           delete-branch: true
           branch-suffix: timestamp
           add-paths: |
-            ${{ inputs.path }}
+            ${{ inputs.file }}

From 9c5865bb54474ffa966a67a59c4f95a03932b347 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 16:46:10 -0800
Subject: [PATCH 37/39] add include and exclude schemas

---
 .github/workflows/create-template-config.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 71008dd..ba93585 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -55,6 +55,8 @@ jobs:
         env:
           data_model: ${{ inputs.data_model }}
           file: ${{ inputs.file }}
+          include_schemas: ${{ inputs.include_schemas }}
+          exclude_schemas: ${{ inputs.exclude_schemas }}
         
       - name: Validate Config File
         uses: docker://orrosenblatt/validate-json-action:latest

From 77f40f3b3dfcc6fd8a294da9b03397f49440a1e2 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Mon, 13 Nov 2023 17:08:36 -0800
Subject: [PATCH 38/39] fix typo in exclude

---
 .github/workflows/create-template-config.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index ba93585..8a94e18 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -31,10 +31,10 @@ on:
         description: Directory to save the template config
         required: true
       include_schemas:
-        description: Comma-separated string of schemas to include in output. Must be empty if using exclude_schemas.
+        description: Space-separated string of schemas to include in output. Must be empty if using exclude_schemas.
         required: false
-      exlude_schemas:
-        description: Commma-separated string of schemas to exclude from output. Must be empty if using include_schemas.
+      exclude_schemas:
+        description: Space-separated string of schemas to exclude from output. Must be empty if using include_schemas.
         required: false
 
 jobs:

From a4d84f964893ab095238da5dd9a4f30cb66d344c Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 15 Nov 2023 13:16:37 -0800
Subject: [PATCH 39/39] instead of schema say data_type

---
 .github/workflows/create-template-config.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/create-template-config.yml b/.github/workflows/create-template-config.yml
index 8a94e18..844776e 100644
--- a/.github/workflows/create-template-config.yml
+++ b/.github/workflows/create-template-config.yml
@@ -15,8 +15,8 @@
 # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#workflow_dispatch
 #
 # The resulting file with contain one entry for each attribute in the data model that `dependsOn`
-# "Component". To include a subset of these attributes, use either `include_schemas` or
-# `exclude_schemas` in the call to `datacurator::write_dca_template_config()`
+# "Component". To include a subset of these attributes, use either `include_data_types` or
+# `exclude_data_types` in the call to `datacurator::write_dca_template_config()`
 #
 # --------------------------------------------------------------------------------------------------
 
@@ -30,11 +30,11 @@ on:
       file:
         description: Directory to save the template config
         required: true
-      include_schemas:
-        description: Space-separated string of schemas to include in output. Must be empty if using exclude_schemas.
+      include_data_types:
+        description: Space-separated string of data types to include in output. Must be empty if using exclude_data_types.
         required: false
-      exclude_schemas:
-        description: Space-separated string of schemas to exclude from output. Must be empty if using include_schemas.
+      exclude_data_types:
+        description: Space-separated string of data types to exclude from output. Must be empty if using include_data_types.
         required: false
 
 jobs:
@@ -55,8 +55,8 @@ jobs:
         env:
           data_model: ${{ inputs.data_model }}
           file: ${{ inputs.file }}
-          include_schemas: ${{ inputs.include_schemas }}
-          exclude_schemas: ${{ inputs.exclude_schemas }}
+          include_data_types: ${{ inputs.include_data_types }}
+          exclude_data_types: ${{ inputs.exclude_data_types }}
         
       - name: Validate Config File
         uses: docker://orrosenblatt/validate-json-action:latest