From be0e22f5bf3e84947d8fad78f75f94be21648a87 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:27:49 +0100
Subject: [PATCH 01/64] Draft new action

---
 .github/workflows/ci-update-mtdca.yml | 54 +++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 .github/workflows/ci-update-mtdca.yml

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
new file mode 100644
index 00000000..0aa96607
--- /dev/null
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -0,0 +1,54 @@
+name: Update CSV on Release
+
+on:
+  workflow_dispatch:
+
+jobs:
+  update-csv:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Fetch CSV file from target repository
+        run: |
+          # Replace `<target_owner>` with the username or organization name of the target repository owner
+          # Replace `<target_repo>` with the name of the target repository
+          # Replace `path/to/csv/file.csv` with the actual path to the CSV file in the target repository
+          curl -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+            -H "Accept: application/vnd.github.v3.raw" \
+            -o dcc_config.csv \
+            -L "https://raw.github
+            usercontent.com/adamjtaylor/data_curator_config/main/dcc_config.csv"
+
+      - name: Modify CSV file
+        run: |
+          # Replace `path/to/csv/file.csv` with the actual path to your CSV file
+          # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
+          # The pattern in the regex assumes the version number has the format `vX.Y.Z`
+          # If the format is different, adjust the regex pattern accordingly
+          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/$GITHUB_REF/HTAN.model.jsonld|" path/to/csv/file.csv
+
+      - name: Commit and push changes to target repository
+        run: |
+          git config --global user.name 'GitHub Action'
+          git config --global user.email '<>'
+
+          # Replace `<target_owner>` with the username or organization name of the target repository owner
+          # Replace `<target_repo>` with the name of the target repository
+          # Replace `path/to/csv/file.csv` with the actual path to the CSV file in the target repository
+          git remote add target_repo https://github.com/adamjtaylor/data_curator_config.git
+          git checkout -b update-csv
+          git add dcc_config.csv
+          git commit -m "Update CSV with release tag"
+          git push --set-upstream target_repo update-csv
+      
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: update-csv
+          commit-message: "Update CSV with release tag"
+          title: "Update CSV with release tag"
+          body: "This pull request updates the CSV file with the release tag."

From 7f5e7b672280a8f59e7f554be734e0af1a22c24b Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:30:19 +0100
Subject: [PATCH 02/64] Run on PR for testing

---
 .github/workflows/ci-update-mtdca.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 0aa96607..db89eec7 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -1,6 +1,7 @@
 name: Update CSV on Release
 
 on:
+  pull_request:
   workflow_dispatch:
 
 jobs:

From 4985bf61388ad1dcca539751132d423f4a5a3fca Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:32:14 +0100
Subject: [PATCH 03/64] Fix url

---
 .github/workflows/ci-update-mtdca.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index db89eec7..7670acf4 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -20,8 +20,7 @@ jobs:
           curl -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
             -H "Accept: application/vnd.github.v3.raw" \
             -o dcc_config.csv \
-            -L "https://raw.github
-            usercontent.com/adamjtaylor/data_curator_config/main/dcc_config.csv"
+            -L "https://raw.githubusercontent.com/adamjtaylor/data_curator_config/main/dcc_config.csv"
 
       - name: Modify CSV file
         run: |

From 98a995ad601d661035f6673b4714545d09c05e4c Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:33:11 +0100
Subject: [PATCH 04/64] Fix path

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 7670acf4..d75e661f 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -28,7 +28,7 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/$GITHUB_REF/HTAN.model.jsonld|" path/to/csv/file.csv
+          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/$GITHUB_REF/HTAN.model.jsonld|" dcc_config.csv
 
       - name: Commit and push changes to target repository
         run: |

From e5849eb309009672ceac2e7048386a9d4137ee5a Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:46:24 +0100
Subject: [PATCH 05/64] Authenticate gh

---
 .github/workflows/ci-update-mtdca.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index d75e661f..86a5a345 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -32,18 +32,20 @@ jobs:
 
       - name: Commit and push changes to target repository
         run: |
-          git config --global user.name 'GitHub Action'
-          git config --global user.email '<>'
-
+          # Set up the GitHub token for authentication
+          echo "${{ secrets.GITHUB_TOKEN }}" | gh auth login --with-token
+          
           # Replace `<target_owner>` with the username or organization name of the target repository owner
           # Replace `<target_repo>` with the name of the target repository
-          # Replace `path/to/csv/file.csv` with the actual path to the CSV file in the target repository
-          git remote add target_repo https://github.com/adamjtaylor/data_curator_config.git
+          # Replace `update-csv` with the name of the branch you want to push the changes to
+          gh repo clone adamjtaylor/data_curator_config data_curator_config
+          cd data_curator_config
           git checkout -b update-csv
+          cp ..dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git push --set-upstream target_repo update-csv
-      
+          git push --set-upstream origin update-csv
+
       - name: Create pull request
         uses: peter-evans/create-pull-request@v3
         with:

From 6ffbb65682b78d28999cb523aa1eda64184a1ee0 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:47:35 +0100
Subject: [PATCH 06/64] Fix path

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 86a5a345..2f31762a 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -41,7 +41,7 @@ jobs:
           gh repo clone adamjtaylor/data_curator_config data_curator_config
           cd data_curator_config
           git checkout -b update-csv
-          cp ..dcc_config.csv dcc_config.csv
+          cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
           git push --set-upstream origin update-csv

From 6f955fc5477c285b8dfe6e3e5247b057b395f419 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:49:05 +0100
Subject: [PATCH 07/64] Add git config user details

---
 .github/workflows/ci-update-mtdca.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 2f31762a..678366e4 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -34,7 +34,8 @@ jobs:
         run: |
           # Set up the GitHub token for authentication
           echo "${{ secrets.GITHUB_TOKEN }}" | gh auth login --with-token
-          
+          git config --global user.email "adam.taylor@sagebase.org"
+          git config --global user.name "Adam Taylor"
           # Replace `<target_owner>` with the username or organization name of the target repository owner
           # Replace `<target_repo>` with the name of the target repository
           # Replace `update-csv` with the name of the branch you want to push the changes to

From ec6ef5b3642d45436a9339d4cdcdcd8aa58a69ad Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:57:03 +0100
Subject: [PATCH 08/64] Refine git auth

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

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 678366e4..da431d22 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Commit and push changes to target repository
         run: |
           # Set up the GitHub token for authentication
-          echo "${{ secrets.GITHUB_TOKEN }}" | gh auth login --with-token
+          git config --global credential.helper store
           git config --global user.email "adam.taylor@sagebase.org"
           git config --global user.name "Adam Taylor"
           # Replace `<target_owner>` with the username or organization name of the target repository owner
@@ -45,7 +45,7 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git push --set-upstream origin update-csv
+          git push --set-upstream origin update-csv -u "adamjtaylor:${{ secrets.GITHUB_TOKEN }}"
 
       - name: Create pull request
         uses: peter-evans/create-pull-request@v3

From 05168d5945a1bd32e223047af35bd06777a01a35 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 11:59:14 +0100
Subject: [PATCH 09/64] Use git clone

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index da431d22..ad677ccc 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -39,7 +39,7 @@ jobs:
           # Replace `<target_owner>` with the username or organization name of the target repository owner
           # Replace `<target_repo>` with the name of the target repository
           # Replace `update-csv` with the name of the branch you want to push the changes to
-          gh repo clone adamjtaylor/data_curator_config data_curator_config
+          git clone https://github.com/adamjtaylor/data_curator_config data_curator_config
           cd data_curator_config
           git checkout -b update-csv
           cp ../dcc_config.csv dcc_config.csv

From 5a4e1026ab5847fc77673ae1aea4c01919d821c2 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:00:58 +0100
Subject: [PATCH 10/64] Refine git clone

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index ad677ccc..fdca6c43 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -39,7 +39,7 @@ jobs:
           # Replace `<target_owner>` with the username or organization name of the target repository owner
           # Replace `<target_repo>` with the name of the target repository
           # Replace `update-csv` with the name of the branch you want to push the changes to
-          git clone https://github.com/adamjtaylor/data_curator_config data_curator_config
+          git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
           git checkout -b update-csv
           cp ../dcc_config.csv dcc_config.csv

From 7fc34e1e711e3ef03f11fe4ee993b5d024ec5ca7 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:08:27 +0100
Subject: [PATCH 11/64] Use DCA config pat

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index fdca6c43..69d0919e 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -45,7 +45,7 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git push --set-upstream origin update-csv -u "adamjtaylor:${{ secrets.GITHUB_TOKEN }}"
+          git push --set-upstream origin update-csv -u "adamjtaylor:${{ secrets.DCA_CONFIG_PAT }}"
 
       - name: Create pull request
         uses: peter-evans/create-pull-request@v3

From 10cb7b728c3aaeaf51df187c073c8359416ab18c Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:11:27 +0100
Subject: [PATCH 12/64] Push without authentication

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 69d0919e..795d451b 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -45,7 +45,7 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git push --set-upstream origin update-csv -u "adamjtaylor:${{ secrets.DCA_CONFIG_PAT }}"
+          git push --set-upstream origin update-csvs
 
       - name: Create pull request
         uses: peter-evans/create-pull-request@v3

From 47c42e0cd3732ac9c323b254674ad15b9d67070b Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:12:30 +0100
Subject: [PATCH 13/64] Correct branch name

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 795d451b..5e5891b6 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -45,7 +45,7 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git push --set-upstream origin update-csvs
+          git push --set-upstream origin update-csv
 
       - name: Create pull request
         uses: peter-evans/create-pull-request@v3

From b81b105aeac64678dab1eb73c0f17a2276b70828 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:14:14 +0100
Subject: [PATCH 14/64] Try auth again

---
 .github/workflows/ci-update-mtdca.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 5e5891b6..a8b3f4cb 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -45,6 +45,7 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
+          git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
           git push --set-upstream origin update-csv
 
       - name: Create pull request

From 9015c4f4c962bb2945aed37f7e3e5607302e633d Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:21:57 +0100
Subject: [PATCH 15/64] Use ${{ github.ref }} in sed

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index a8b3f4cb..6d2c47c0 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -28,7 +28,7 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/$GITHUB_REF/HTAN.model.jsonld|" dcc_config.csv
+          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.ref }}/HTAN.model.jsonld|" dcc_config.csv
 
       - name: Commit and push changes to target repository
         run: |

From b89eddceab5fbedea15005569066e5846eb97a59 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:25:59 +0100
Subject: [PATCH 16/64] Use event.ref

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 6d2c47c0..c6b6f71e 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -28,7 +28,7 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.ref }}/HTAN.model.jsonld|" dcc_config.csv
+          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.event.ref }}/HTAN.model.jsonld|" dcc_config.csv
 
       - name: Commit and push changes to target repository
         run: |

From 5b02c59d8ae7aeabd0b2bead984171d75a64b81a Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:29:21 +0100
Subject: [PATCH 17/64] Use comit if tag not avaliable

---
 .github/workflows/ci-update-mtdca.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index c6b6f71e..f92afa8a 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -28,8 +28,11 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.event.ref }}/HTAN.model.jsonld|" dcc_config.csv
-
+          if [[ -n "${{ github.event.ref }}" ]]; then
+            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.event.ref }}/HTAN.model.jsonld|" dcc_config.csv
+          else
+            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
+          fi
       - name: Commit and push changes to target repository
         run: |
           # Set up the GitHub token for authentication

From 0e6c800c7267c84972110de8de5ec73be966b695 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:32:27 +0100
Subject: [PATCH 18/64] Don't be strict on version format

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

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index f92afa8a..c0a2ec44 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -29,9 +29,9 @@ jobs:
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
           if [[ -n "${{ github.event.ref }}" ]]; then
-            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.event.ref }}/HTAN.model.jsonld|" dcc_config.csv
+            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.event.ref }}/HTAN.model.jsonld|" dcc_config.csv
           else
-            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/v[0-9.]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
+            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
           fi
       - name: Commit and push changes to target repository
         run: |

From ab9f1626960a77f0b376063eac321ee93f40c5c1 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:39:16 +0100
Subject: [PATCH 19/64] Use curl for PR

---
 .github/workflows/ci-update-mtdca.yml | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index c0a2ec44..1aa1803d 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -52,10 +52,14 @@ jobs:
           git push --set-upstream origin update-csv
 
       - name: Create pull request
-        uses: peter-evans/create-pull-request@v3
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          branch: update-csv
-          commit-message: "Update CSV with release tag"
-          title: "Update CSV with release tag"
-          body: "This pull request updates the CSV file with the release tag."
+        run: |
+          curl -X POST \
+          -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+          -H "Accept: application/vnd.github.v3+json" \
+          "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
+          -d "{
+            \"title\": \"Updae CSV with release tag\",
+            \"head\": \"update-csv\",
+            \"base\": \"main\",
+            \"body\": \"This pull request updates the CSV file with the release tag.\"
+          }"

From f12bcef5c2fa9c5a837ecce7a0bc972fd552818a Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:40:31 +0100
Subject: [PATCH 20/64] Use DCA config pat for PR

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 1aa1803d..9952eb4b 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -54,7 +54,7 @@ jobs:
       - name: Create pull request
         run: |
           curl -X POST \
-          -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+          -H "Authorization: Bearer ${{ secrets.DCA_CONFIG_PAT }}" \
           -H "Accept: application/vnd.github.v3+json" \
           "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
           -d "{

From c1687fc88c89d3cfc75ebb63bdc3cd659b8e89ca Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:45:13 +0100
Subject: [PATCH 21/64] Make branch unique

---
 .github/workflows/ci-update-mtdca.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 9952eb4b..63e29283 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -44,12 +44,12 @@ jobs:
           # Replace `update-csv` with the name of the branch you want to push the changes to
           git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
-          git checkout -b update-csv
+          git checkout -b update-csv-${{ GITHUB_SHA::7}}
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
-          git push --set-upstream origin update-csv
+          git push --set-upstream origin update-csv-${{ GITHUB_SHA::7}}
 
       - name: Create pull request
         run: |
@@ -59,7 +59,8 @@ jobs:
           "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
           -d "{
             \"title\": \"Updae CSV with release tag\",
-            \"head\": \"update-csv\",
+            \"head\": \"update-csv-${{ GITHUB_SHA::7}}\",
             \"base\": \"main\",
-            \"body\": \"This pull request updates the CSV file with the release tag.\"
+            \"body\": \"This pull request updates the CSV file with the release tag.\",
+            \"draft\": true,
           }"

From f41e86ea4fc9f015c670157cc34754019c202a19 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:46:49 +0100
Subject: [PATCH 22/64] Fix short sha

---
 .github/workflows/ci-update-mtdca.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 63e29283..6d0bc08a 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -44,12 +44,12 @@ jobs:
           # Replace `update-csv` with the name of the branch you want to push the changes to
           git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
-          git checkout -b update-csv-${{ GITHUB_SHA::7}}
+          git checkout -b update-csv-${{ github.sha | slice(0, 7) }}
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
-          git push --set-upstream origin update-csv-${{ GITHUB_SHA::7}}
+          git push --set-upstream origin update-csv-${{ github.sha | slice(0, 7) }}
 
       - name: Create pull request
         run: |
@@ -59,7 +59,7 @@ jobs:
           "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
           -d "{
             \"title\": \"Updae CSV with release tag\",
-            \"head\": \"update-csv-${{ GITHUB_SHA::7}}\",
+            \"head\": \"update-csv-${{ github.sha | slice(0, 7) }}\",
             \"base\": \"main\",
             \"body\": \"This pull request updates the CSV file with the release tag.\",
             \"draft\": true,

From 2c3198fc13913270962f40358d0f3e53a40ad82d Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:51:34 +0100
Subject: [PATCH 23/64] Use long sha in branchname

---
 .github/workflows/ci-update-mtdca.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 6d0bc08a..575c895c 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -44,12 +44,12 @@ jobs:
           # Replace `update-csv` with the name of the branch you want to push the changes to
           git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
-          git checkout -b update-csv-${{ github.sha | slice(0, 7) }}
+          git checkout -b update-csv-${{ github.sha }}
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
-          git push --set-upstream origin update-csv-${{ github.sha | slice(0, 7) }}
+          git push --set-upstream origin update-csv-${{ github.sha }}
 
       - name: Create pull request
         run: |
@@ -59,7 +59,7 @@ jobs:
           "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
           -d "{
             \"title\": \"Updae CSV with release tag\",
-            \"head\": \"update-csv-${{ github.sha | slice(0, 7) }}\",
+            \"head\": \"update-csv-${{ github.sha }}\",
             \"base\": \"main\",
             \"body\": \"This pull request updates the CSV file with the release tag.\",
             \"draft\": true,

From 212ae73027c04ca4fb15f78097a787a1f350b7d0 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:54:17 +0100
Subject: [PATCH 24/64] Use short sha

---
 .github/workflows/ci-update-mtdca.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 575c895c..b0dceeb5 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -44,22 +44,24 @@ jobs:
           # Replace `update-csv` with the name of the branch you want to push the changes to
           git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
-          git checkout -b update-csv-${{ github.sha }}
+          short_sha=$(echo "${{ github.sha }}" | cut -c 1-7)
+          git checkout -b update-csv-${short_sha}
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
-          git push --set-upstream origin update-csv-${{ github.sha }}
-
+          git push --set-upstream origin update-csv-${short_sha}
+          
       - name: Create pull request
         run: |
+          short_sha=$(echo "${{ github.sha }}" | cut -c 1-7)
           curl -X POST \
           -H "Authorization: Bearer ${{ secrets.DCA_CONFIG_PAT }}" \
           -H "Accept: application/vnd.github.v3+json" \
           "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
           -d "{
             \"title\": \"Updae CSV with release tag\",
-            \"head\": \"update-csv-${{ github.sha }}\",
+            \"head\": \"update-csv-${short_sha}\",
             \"base\": \"main\",
             \"body\": \"This pull request updates the CSV file with the release tag.\",
             \"draft\": true,

From bd9247c9852a765692b4c980f95d1726ce244887 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:55:36 +0100
Subject: [PATCH 25/64] Remove draft

---
 .github/workflows/ci-update-mtdca.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index b0dceeb5..e1cad1d4 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -51,7 +51,7 @@ jobs:
           git commit -m "Update CSV with release tag"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
           git push --set-upstream origin update-csv-${short_sha}
-          
+
       - name: Create pull request
         run: |
           short_sha=$(echo "${{ github.sha }}" | cut -c 1-7)
@@ -63,6 +63,5 @@ jobs:
             \"title\": \"Updae CSV with release tag\",
             \"head\": \"update-csv-${short_sha}\",
             \"base\": \"main\",
-            \"body\": \"This pull request updates the CSV file with the release tag.\",
-            \"draft\": true,
+            \"body\": \"This pull request updates the CSV file with the release tag.\"
           }"

From bd47b546c062239b743356b196a8c14785d9553a Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:58:01 +0100
Subject: [PATCH 26/64] Update PR descriptions

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

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index e1cad1d4..4a03d572 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -60,8 +60,8 @@ jobs:
           -H "Accept: application/vnd.github.v3+json" \
           "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
           -d "{
-            \"title\": \"Updae CSV with release tag\",
+            \"title\": \"Update dcc_config.csv with new data model\",
             \"head\": \"update-csv-${short_sha}\",
             \"base\": \"main\",
-            \"body\": \"This pull request updates the CSV file with the release tag.\"
+            \"body\": \"This pull request updates the CSV file with the release tag or commit sha\"
           }"

From 4920b3367cd3ad33fab297547664ba485fa21878 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 12:59:37 +0100
Subject: [PATCH 27/64] Use draft PR

---
 .github/workflows/ci-update-mtdca.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 4a03d572..e6647fa1 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -63,5 +63,6 @@ jobs:
             \"title\": \"Update dcc_config.csv with new data model\",
             \"head\": \"update-csv-${short_sha}\",
             \"base\": \"main\",
-            \"body\": \"This pull request updates the CSV file with the release tag or commit sha\"
+            \"body\": \"This pull request updates the CSV file with the release tag or commit sha\",
+            \"draft\": \"true\"
           }"

From 629532de70fe3ab673da6eb17d8cdbd303132877 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 13:04:26 +0100
Subject: [PATCH 28/64] Run on release creation

---
 .github/workflows/ci-update-mtdca.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index e6647fa1..c314fbc0 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -3,6 +3,8 @@ name: Update CSV on Release
 on:
   pull_request:
   workflow_dispatch:
+  release:
+    types: [created]
 
 jobs:
   update-csv:

From d090670056b6210bce77ee9dd129ef662df4550a Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 13:08:06 +0100
Subject: [PATCH 29/64] Run on prereleased

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index c314fbc0..6b9370d4 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -4,7 +4,7 @@ on:
   pull_request:
   workflow_dispatch:
   release:
-    types: [created]
+    types: [prereleased]
 
 jobs:
   update-csv:

From 3fce0e58502d4cb205982436ebb7efbf548451e5 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 13:37:52 +0100
Subject: [PATCH 30/64] Extract tag

---
 .github/workflows/ci-update-mtdca.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 6b9370d4..a8c0bab3 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -30,8 +30,9 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          if [[ -n "${{ github.event.ref }}" ]]; then
-            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.event.ref }}/HTAN.model.jsonld|" dcc_config.csv
+          if [[ -n "${{ github.event.ref }}" && "${{ github.event.ref }}" =~ ^refs/tags/v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+            tag=$(echo "${{ github.event.ref }}" | awk -F '/' '{print $NF}' | sed 's/^v//')
+            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/$tag/HTAN.model.jsonld|" dcc_config.csv
           else
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
           fi

From 46c58c6794c48b3d96d84ad2281cfab163dd59c3 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 14:58:45 +0100
Subject: [PATCH 31/64] Use github reg_name

---
 .github/workflows/ci-update-mtdca.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index a8c0bab3..2187a66b 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -30,9 +30,8 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          if [[ -n "${{ github.event.ref }}" && "${{ github.event.ref }}" =~ ^refs/tags/v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
-            tag=$(echo "${{ github.event.ref }}" | awk -F '/' '{print $NF}' | sed 's/^v//')
-            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/$tag/HTAN.model.jsonld|" dcc_config.csv
+          if [[ -n "${{ github.ref_name }}" ]]; then
+            sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.ref_name }}/HTAN.model.jsonld|" dcc_config.csv
           else
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
           fi

From 81d605904e1bcd929e2118363a4dfa61839cd66d Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 15:05:16 +0100
Subject: [PATCH 32/64] Use runid in branch name

---
 .github/workflows/ci-update-mtdca.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 2187a66b..32612312 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -47,12 +47,12 @@ jobs:
           git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
           short_sha=$(echo "${{ github.sha }}" | cut -c 1-7)
-          git checkout -b update-csv-${short_sha}
+          git checkout -b update-csv-${{ github.run_id }}-${{ github.run_attempt }}
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
-          git push --set-upstream origin update-csv-${short_sha}
+          git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}
 
       - name: Create pull request
         run: |
@@ -63,7 +63,7 @@ jobs:
           "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
           -d "{
             \"title\": \"Update dcc_config.csv with new data model\",
-            \"head\": \"update-csv-${short_sha}\",
+            \"head\": \"update-csv-${{ github.run_id }}-${{ github.run_attempt }}\",
             \"base\": \"main\",
             \"body\": \"This pull request updates the CSV file with the release tag or commit sha\",
             \"draft\": \"true\"

From 00d4ee5780da0c1682a3962fe808b957dcb29ac7 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 15:09:49 +0100
Subject: [PATCH 33/64] Update if regex

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 32612312..9f30ccaa 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -30,7 +30,7 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          if [[ -n "${{ github.ref_name }}" ]]; then
+          if [[ -n "${{ github.ref }}" && ! "${{ github.ref }}" == *"/"* ]]; then
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.ref_name }}/HTAN.model.jsonld|" dcc_config.csv
           else
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv

From 6f2d3a5164e4264f9841a143f510659d6c0b112f Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 15:10:27 +0100
Subject: [PATCH 34/64] Use ref_name

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 9f30ccaa..aeead262 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -30,7 +30,7 @@ jobs:
           # Replace `https://raw.githubusercontent.com/ncihtan/data-models/v23.6.2/HTAN.model.jsonld` with the string containing the version number to be replaced
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
-          if [[ -n "${{ github.ref }}" && ! "${{ github.ref }}" == *"/"* ]]; then
+          if [[ -n "${{ github.ref_name }}" && ! "${{ github.ref_name }}" == *"/"* ]]; then
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.ref_name }}/HTAN.model.jsonld|" dcc_config.csv
           else
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv

From 62a3cb25cc95eab084441510c191d071af66976b Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 15:15:11 +0100
Subject: [PATCH 35/64] Remove short sha

---
 .github/workflows/ci-update-mtdca.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index aeead262..3e5a6e8c 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -46,7 +46,6 @@ jobs:
           # Replace `update-csv` with the name of the branch you want to push the changes to
           git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
-          short_sha=$(echo "${{ github.sha }}" | cut -c 1-7)
           git checkout -b update-csv-${{ github.run_id }}-${{ github.run_attempt }}
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
@@ -56,7 +55,6 @@ jobs:
 
       - name: Create pull request
         run: |
-          short_sha=$(echo "${{ github.sha }}" | cut -c 1-7)
           curl -X POST \
           -H "Authorization: Bearer ${{ secrets.DCA_CONFIG_PAT }}" \
           -H "Accept: application/vnd.github.v3+json" \

From ea3346266b54dd8cca0e50fc42d1990d41175f6c Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 15:33:40 +0100
Subject: [PATCH 36/64] Echo replacement

---
 .github/workflows/ci-update-mtdca.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 3e5a6e8c..da919950 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -31,8 +31,10 @@ jobs:
           # The pattern in the regex assumes the version number has the format `vX.Y.Z`
           # If the format is different, adjust the regex pattern accordingly
           if [[ -n "${{ github.ref_name }}" && ! "${{ github.ref_name }}" == *"/"* ]]; then
+            echo "Using github.ref: ${{ github.ref_name }}"
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.ref_name }}/HTAN.model.jsonld|" dcc_config.csv
           else
+            echo "Using github.sha: ${{ github.sha }}"
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
           fi
       - name: Commit and push changes to target repository

From 14727af99ce670fd40dbb761e9a4f2a34a2d8cdf Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 19:03:37 +0100
Subject: [PATCH 37/64] Draft of make-config

---
 .github/workflows/ci-update-mtdca.yml | 29 +++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index da919950..8a942b8f 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -7,6 +7,35 @@ on:
     types: [prereleased]
 
 jobs:
+
+
+  make-config:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4 
+        with:
+          python-version: '3.9'
+
+      - name: Install Schematic
+        shell: bash
+        run: |
+          pip3 install poetry
+          git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git
+          cd schematic
+          poetry build
+          pip3 install dist/schematicpy-*-py3-none-any.whl
+
+      - name: Make config file from data model
+        shell: bash
+        run: |
+          # download the data models and create config.json
+          python3 .github/config_schema.py \
+          -c config.yml \
+          --service_repo 'Sage-Bionetworks/schematic' \
+          --overwrite
+
   update-csv:
     runs-on: ubuntu-latest
 

From a841d5b2b28d104ef854aa01f1b539543187af9d Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 19:06:07 +0100
Subject: [PATCH 38/64] Move script

---
 .github/workflows/ci-update-mtdca.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 8a942b8f..df850a4e 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -31,13 +31,14 @@ jobs:
         shell: bash
         run: |
           # download the data models and create config.json
-          python3 .github/config_schema.py \
+          python3 .github/workflows/config_schema.py \
           -c config.yml \
           --service_repo 'Sage-Bionetworks/schematic' \
           --overwrite
 
   update-csv:
     runs-on: ubuntu-latest
+    needs: make-config
 
     steps:
       - name: Checkout repository

From 6fb11d91f2ac41dec98fc200b7761bb2544248fa Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 19:22:37 +0100
Subject: [PATCH 39/64] Refactor config schema

---
 .github/workflows/config_schema.py | 92 ++++++++++++++++++++++++++++++
 1 file changed, 92 insertions(+)
 create mode 100644 .github/workflows/config_schema.py

diff --git a/.github/workflows/config_schema.py b/.github/workflows/config_schema.py
new file mode 100644
index 00000000..7bfff210
--- /dev/null
+++ b/.github/workflows/config_schema.py
@@ -0,0 +1,92 @@
+import argparse
+import json
+import os
+import re
+import yaml
+from schematic.schemas.generator import SchemaGenerator
+
+
+def get_args():
+    """Set up command-line interface and get arguments."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-c', '--config_path', metavar="",
+                        required=True, help='path to schematic config ymal file')
+    parser.add_argument('-sr', '--service_repo', metavar="",
+                        help='repo path to service')
+    parser.add_argument('-o', '--out_dir', default='www', metavar="",
+                        help='directory to save result')
+    parser.add_argument('--overwrite', action='store_true', default=False,
+                        help='whether to overwrite the existing config.json')
+    return parser.parse_args()
+
+
+def _is_valid(value, type):
+    if type not in ["repo", "location"]:
+        raise ValueError('type must be "repo" or "location"')
+    pattern = "^([-_.A-z0-9]+\\/){1,2}[-_.A-z0-9]+$" if type == "repo" else "^[-_.A-z0-9]+\\/.*.jsonld$"
+    return bool(re.match(pattern, value))
+
+
+def _parse_schema(config_path):
+    """Parse schematic_config.yml file"""
+    with open(config_path, "r") as stream:
+        try:
+            config = yaml.safe_load(stream)["model"]["input"]
+            return config
+        except yaml.YAMLError as exc:
+            print(exc)
+
+
+def generate_schema_config(schema_path):
+    """Generate schema config with corresponding display name"""
+    schemas = []
+    # get all required data types from data model jsonld
+    sg = SchemaGenerator(path_to_json_ld=schema_path)
+    component_digraph = sg.se.get_digraph_by_edge_type('requiresComponent')
+    components = component_digraph.nodes()
+    # get display names for required data types
+    mm_graph = sg.se.get_nx_schema()
+    display_names = sg.get_nodes_display_names(components, mm_graph)
+    # save display_name, schema_name, assay type to list
+    for index, component in enumerate(components):
+        # get component's dependencies
+        deps = sg.get_node_dependencies(component)
+        schema_type = 'file' if 'Filename' in deps else 'record'
+        schemas.append({
+            'display_name': display_names[index],
+            'schema_name': component,
+            'type': schema_type
+        })
+    return schemas
+
+
+def main():
+    args = get_args()
+    # retrieve schema info from config file
+    config = _parse_schema(args.config_path)
+
+    # get the location of the schema
+    if config.get("location") and _is_valid(config.get("location"), "location"):
+        schema_path = config["location"]
+    else:
+        raise ValueError(f'No valid "location" value found in "{args.config_path}" \u274C')
+
+    if args.overwrite:
+        # get versions for both service and schema
+        service_version = _get_version(args.service_repo)
+        schema_version = config.get("version") or _get_version(config["repo"])
+        # generate schema configuration based on *.model.jsonld
+        schemas_config = generate_schema_config(schema_path)
+        # write out the config.json including versions
+        config = {
+            'manifest_schemas': schemas_config,
+            'service_version': service_version,
+            'schema_version': schema_version
+        }
+        output_path = os.path.join(args.out_dir, 'config.json')
+        with open(output_path, 'w') as o:
+            json.dump(config, o, indent=2, separators=(',', ': '))
+
+
+if __name__ == '__main__':
+    main()

From 6b9134ee2af8c81986c33de61294973b77febbc1 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 19:24:09 +0100
Subject: [PATCH 40/64] Update path to script

---
 .github/workflows/ci-update-mtdca.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index df850a4e..565b16ce 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -30,8 +30,7 @@ jobs:
       - name: Make config file from data model
         shell: bash
         run: |
-          # download the data models and create config.json
-          python3 .github/workflows/config_schema.py \
+          python .github/workflows/config_schema.py \
           -c config.yml \
           --service_repo 'Sage-Bionetworks/schematic' \
           --overwrite

From bb577ab82a51c194b3ad32a9d10583b4d4d3b8e6 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 19:31:28 +0100
Subject: [PATCH 41/64] Manually set some config settings

---
 .github/workflows/config_schema.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/config_schema.py b/.github/workflows/config_schema.py
index 7bfff210..cb9a79b6 100644
--- a/.github/workflows/config_schema.py
+++ b/.github/workflows/config_schema.py
@@ -66,22 +66,22 @@ def main():
     config = _parse_schema(args.config_path)
 
     # get the location of the schema
-    if config.get("location") and _is_valid(config.get("location"), "location"):
-        schema_path = config["location"]
-    else:
-        raise ValueError(f'No valid "location" value found in "{args.config_path}" \u274C')
+    #if config.get("location") and _is_valid(config.get("location"), "location"):
+    #    schema_path = config["location"]
+    #else:
+    #    raise ValueError(f'No valid "location" value found in "{args.config_path}" \u274C')
 
     if args.overwrite:
         # get versions for both service and schema
-        service_version = _get_version(args.service_repo)
-        schema_version = config.get("version") or _get_version(config["repo"])
+        #service_version = _get_version(args.service_repo)
+        #schema_version = config.get("version") or _get_version(config["repo"])
         # generate schema configuration based on *.model.jsonld
         schemas_config = generate_schema_config(schema_path)
         # write out the config.json including versions
         config = {
             'manifest_schemas': schemas_config,
-            'service_version': service_version,
-            'schema_version': schema_version
+            'service_version': '1',   #service_version,
+            'schema_version': '1'     #schema_version
         }
         output_path = os.path.join(args.out_dir, 'config.json')
         with open(output_path, 'w') as o:

From 34fade029d3c9c868a4a8c07224526e9ad144a2b Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 19:35:45 +0100
Subject: [PATCH 42/64] Set schema path

---
 .github/workflows/ci-update-mtdca.yml | 1 +
 .github/workflows/config_schema.py    | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 565b16ce..e612044b 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -32,6 +32,7 @@ jobs:
         run: |
           python .github/workflows/config_schema.py \
           -c config.yml \
+          -s HTAN.model.jsonld \
           --service_repo 'Sage-Bionetworks/schematic' \
           --overwrite
 
diff --git a/.github/workflows/config_schema.py b/.github/workflows/config_schema.py
index cb9a79b6..47960447 100644
--- a/.github/workflows/config_schema.py
+++ b/.github/workflows/config_schema.py
@@ -11,6 +11,8 @@ def get_args():
     parser = argparse.ArgumentParser()
     parser.add_argument('-c', '--config_path', metavar="",
                         required=True, help='path to schematic config ymal file')
+    parser.add_argument('-s','--schema_path', metavar = "",
+                        required=True, help='path to schema jsonld file')
     parser.add_argument('-sr', '--service_repo', metavar="",
                         help='repo path to service')
     parser.add_argument('-o', '--out_dir', default='www', metavar="",
@@ -67,7 +69,7 @@ def main():
 
     # get the location of the schema
     #if config.get("location") and _is_valid(config.get("location"), "location"):
-    #    schema_path = config["location"]
+    schema_path = args.schema_path
     #else:
     #    raise ValueError(f'No valid "location" value found in "{args.config_path}" \u274C')
 

From 81e73684ff0a5aaf30c5ddcfac1cab42a6d5d975 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 19:39:17 +0100
Subject: [PATCH 43/64] Set output dir

---
 .github/workflows/ci-update-mtdca.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index e612044b..623d4a10 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -33,6 +33,7 @@ jobs:
           python .github/workflows/config_schema.py \
           -c config.yml \
           -s HTAN.model.jsonld \
+          -o '.' \
           --service_repo 'Sage-Bionetworks/schematic' \
           --overwrite
 

From ba262f374c3191a045aa490f5fd82bfd34addd74 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 20:01:17 +0100
Subject: [PATCH 44/64] Link jobs

---
 .github/workflows/ci-update-mtdca.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 623d4a10..9213db49 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -37,6 +37,12 @@ jobs:
           --service_repo 'Sage-Bionetworks/schematic' \
           --overwrite
 
+      - name: Store config.json artifact
+        uses: actions/upload-artifact@master
+        with:
+          name: config
+          path: config.json
+
   update-csv:
     runs-on: ubuntu-latest
     needs: make-config
@@ -45,6 +51,11 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
+      - name: Fetch config.json artifact
+        uses: actions/download-artifact@master
+        with:
+          name: config
+
       - name: Fetch CSV file from target repository
         run: |
           # Replace `<target_owner>` with the username or organization name of the target repository owner
@@ -83,6 +94,8 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
+          git add config.json
+          git commit -m "Update config.json"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
           git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}
 

From a1c36a714924950c6458216121f891d491bfa4c3 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 20:04:59 +0100
Subject: [PATCH 45/64] Fix config path

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 9213db49..92f6b8b4 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -94,7 +94,7 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git add config.json
+          git add config/config.json
           git commit -m "Update config.json"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
           git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}

From 0b8dfcf34f4c959ce05b820bf2a8963bed0986f9 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Fri, 30 Jun 2023 20:09:09 +0100
Subject: [PATCH 46/64] fix

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 92f6b8b4..9213db49 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -94,7 +94,7 @@ jobs:
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git add config/config.json
+          git add config.json
           git commit -m "Update config.json"
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
           git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}

From f395a2d5ac9ccffedc90c2dddda14d634039f19b Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Sat, 1 Jul 2023 09:41:29 +0100
Subject: [PATCH 47/64] Fix config paths

---
 .github/workflows/ci-update-mtdca.yml | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 9213db49..81af2ce5 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -14,6 +14,7 @@ jobs:
     
     steps:
       - uses: actions/checkout@v3
+
       - uses: actions/setup-python@v4 
         with:
           python-version: '3.9'
@@ -79,23 +80,30 @@ jobs:
             echo "Using github.sha: ${{ github.sha }}"
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
           fi
+
       - name: Commit and push changes to target repository
         run: |
           # Set up the GitHub token for authentication
           git config --global credential.helper store
           git config --global user.email "adam.taylor@sagebase.org"
           git config --global user.name "Adam Taylor"
-          # Replace `<target_owner>` with the username or organization name of the target repository owner
-          # Replace `<target_repo>` with the name of the target repository
-          # Replace `update-csv` with the name of the branch you want to push the changes to
+
+          # Clone the config repo and make a branch
           git clone https://github.com/adamjtaylor/data_curator_config.git
           cd data_curator_config
           git checkout -b update-csv-${{ github.run_id }}-${{ github.run_attempt }}
+          
+          # Add the dcc_config.csv
           cp ../dcc_config.csv dcc_config.csv
           git add dcc_config.csv
           git commit -m "Update CSV with release tag"
-          git add config.json
+
+          # Add the dca-template-config.json
+          mv ../config.json HTAN/dca-template-config.json
+          git add HTAN/dca-template-config.json
           git commit -m "Update config.json"
+          
+          # Push to the repository
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
           git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}
 

From eeed54d0a1cce3f1e2ea66c613ba75310e224749 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Sat, 1 Jul 2023 09:59:13 +0100
Subject: [PATCH 48/64] Split into 3 jobs

---
 .github/workflows/ci-update-mtdca.yml | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 81af2ce5..b8cfaceb 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -1,14 +1,11 @@
-name: Update CSV on Release
+name: Update DCA config on release
 
 on:
-  pull_request:
   workflow_dispatch:
   release:
-    types: [prereleased]
 
 jobs:
 
-
   make-config:
     runs-on: ubuntu-latest
     
@@ -46,7 +43,6 @@ jobs:
 
   update-csv:
     runs-on: ubuntu-latest
-    needs: make-config
 
     steps:
       - name: Checkout repository
@@ -81,6 +77,21 @@ jobs:
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
           fi
 
+  open-pr:
+    runs-on: ubuntu-latest
+    needs: 
+      - make-config
+      - update-csv
+        
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Fetch config.json artifact
+        uses: actions/download-artifact@master
+        with:
+          name: config
+
       - name: Commit and push changes to target repository
         run: |
           # Set up the GitHub token for authentication

From 7e9ea1910f51a872ee88f21feb9505b6eb2070cc Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Sat, 1 Jul 2023 10:02:18 +0100
Subject: [PATCH 49/64] Add release type for testing

---
 .github/workflows/ci-update-mtdca.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index b8cfaceb..7c2c13b9 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -1,8 +1,9 @@
 name: Update DCA config on release
 
 on:
-  workflow_dispatch:
   release:
+    types: [prereleased]
+  workflow_dispatch:
 
 jobs:
 

From 7d4bbf38f834a860bba5f91b70a5d75eb8a6d11c Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Sat, 1 Jul 2023 10:05:00 +0100
Subject: [PATCH 50/64] Remove artifact fetch when not required

---
 .github/workflows/ci-update-mtdca.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 7c2c13b9..e4d44b91 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -49,11 +49,6 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
-      - name: Fetch config.json artifact
-        uses: actions/download-artifact@master
-        with:
-          name: config
-
       - name: Fetch CSV file from target repository
         run: |
           # Replace `<target_owner>` with the username or organization name of the target repository owner

From fedf9e532dbdfebf22a76605ecf8e79ddbd25a8b Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Sat, 1 Jul 2023 10:11:03 +0100
Subject: [PATCH 51/64] Pass artifacts correctly

---
 .github/workflows/ci-update-mtdca.yml | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index e4d44b91..c452568c 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -39,7 +39,7 @@ jobs:
       - name: Store config.json artifact
         uses: actions/upload-artifact@master
         with:
-          name: config
+          name: config_json
           path: config.json
 
   update-csv:
@@ -73,6 +73,12 @@ jobs:
             sed -i "s|https://raw.githubusercontent.com/ncihtan/data-models/[^/]\+/HTAN.model.jsonld|https://raw.githubusercontent.com/ncihtan/data-models/${{ github.sha }}/HTAN.model.jsonld|" dcc_config.csv
           fi
 
+      - name: Store dcc_config.csv artifact
+        uses: actions/upload-artifact@master
+        with:
+          name: dcc_config_csv
+          path: dcc_config.csv
+
   open-pr:
     runs-on: ubuntu-latest
     needs: 
@@ -86,7 +92,12 @@ jobs:
       - name: Fetch config.json artifact
         uses: actions/download-artifact@master
         with:
-          name: config
+          name: config_json
+
+      - name: Fetch dcc_config.csv artifact
+        uses: actions/download-artifact@master
+        with:
+          name: dcc_config_csv
 
       - name: Commit and push changes to target repository
         run: |

From 9789baae3d0028fb57a66cecd2137e4f1b655bf8 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Sat, 1 Jul 2023 10:52:31 +0100
Subject: [PATCH 52/64] Sort config by type and name

---
 .github/workflows/config_schema.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/.github/workflows/config_schema.py b/.github/workflows/config_schema.py
index 47960447..9067f835 100644
--- a/.github/workflows/config_schema.py
+++ b/.github/workflows/config_schema.py
@@ -46,6 +46,9 @@ def generate_schema_config(schema_path):
     sg = SchemaGenerator(path_to_json_ld=schema_path)
     component_digraph = sg.se.get_digraph_by_edge_type('requiresComponent')
     components = component_digraph.nodes()
+    components_to_remove = ['Patient', 'File', 'Publication']
+    components =  sorted(list(set(components) - set(components_to_remove)))
+    print(components)
     # get display names for required data types
     mm_graph = sg.se.get_nx_schema()
     display_names = sg.get_nodes_display_names(components, mm_graph)
@@ -61,6 +64,18 @@ def generate_schema_config(schema_path):
         })
     return schemas
 
+def sort_manifest_schemas(s):
+
+    ms = s['manifest_schemas']
+    def key_func(schema):
+        return (schema['type'], schema['display_name'])
+    
+    sorted_schemas = sorted(ms, key=key_func)
+
+    s['manifest_schemas'] = sorted_schemas
+    return s
+
+
 
 def main():
     args = get_args()
@@ -85,6 +100,7 @@ def main():
             'service_version': '1',   #service_version,
             'schema_version': '1'     #schema_version
         }
+        config = sort_manifest_schemas(config)
         output_path = os.path.join(args.out_dir, 'config.json')
         with open(output_path, 'w') as o:
             json.dump(config, o, indent=2, separators=(',', ': '))

From 51c0113b86da919e08d2a366824322d3807b6d31 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Tue, 15 Aug 2023 19:35:04 +0100
Subject: [PATCH 53/64] Update ci-update-mtdca.yml

---
 .github/workflows/ci-update-mtdca.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index c452568c..c409e09b 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -122,7 +122,7 @@ jobs:
           git commit -m "Update config.json"
           
           # Push to the repository
-          git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/adamjtaylor/data_curator_config.git"
+          git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/ncihtan/data_curator_config.git"
           git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}
 
       - name: Create pull request

From ec3277edf9cb1cd97382c9652f695bbaf7f9f62c Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Wed, 16 Aug 2023 13:54:23 +0100
Subject: [PATCH 54/64] Update actions

---
 .github/workflows/ci-mtdca-config-pr  | 26 ++++++++++++++++++++++++++
 .github/workflows/ci-update-mtdca.yml | 20 ++------------------
 .github/workflows/config_schema.py    |  2 +-
 3 files changed, 29 insertions(+), 19 deletions(-)
 create mode 100644 .github/workflows/ci-mtdca-config-pr

diff --git a/.github/workflows/ci-mtdca-config-pr b/.github/workflows/ci-mtdca-config-pr
new file mode 100644
index 00000000..bca43be5
--- /dev/null
+++ b/.github/workflows/ci-mtdca-config-pr
@@ -0,0 +1,26 @@
+name: Push config to mtDCA
+
+on:
+  merge:
+  workflow-dispatch:
+
+jobs:
+  pull-request:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Create pull request
+      uses: paygoc6/action-pull-request-another-repo@v1.0.1
+      env:
+        API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
+      with:
+        source_folder: 'source-folder'
+        destination_repo: 'ncihtan/data_curator_config'
+        destination_folder: 'HTAN'
+        destination_base_branch: 'main'
+        destination_head_branch: 'update-htan-config'
+        user_email: 'adam.taylor@sagebase.org'
+        user_name: 'adamjtaylor'
+        pull_request_reviewers: 'adamjtaylor'
\ No newline at end of file
diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index c409e09b..de0cb7ae 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -26,22 +26,6 @@ jobs:
           poetry build
           pip3 install dist/schematicpy-*-py3-none-any.whl
 
-      - name: Make config file from data model
-        shell: bash
-        run: |
-          python .github/workflows/config_schema.py \
-          -c config.yml \
-          -s HTAN.model.jsonld \
-          -o '.' \
-          --service_repo 'Sage-Bionetworks/schematic' \
-          --overwrite
-
-      - name: Store config.json artifact
-        uses: actions/upload-artifact@master
-        with:
-          name: config_json
-          path: config.json
-
   update-csv:
     runs-on: ubuntu-latest
 
@@ -117,9 +101,9 @@ jobs:
           git commit -m "Update CSV with release tag"
 
           # Add the dca-template-config.json
-          mv ../config.json HTAN/dca-template-config.json
+          mv ../dca-template-config.json HTAN/dca-template-config.json
           git add HTAN/dca-template-config.json
-          git commit -m "Update config.json"
+          git commit -m "Update dca-template-config.json"
           
           # Push to the repository
           git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/ncihtan/data_curator_config.git"
diff --git a/.github/workflows/config_schema.py b/.github/workflows/config_schema.py
index 9067f835..65f4a3af 100644
--- a/.github/workflows/config_schema.py
+++ b/.github/workflows/config_schema.py
@@ -101,7 +101,7 @@ def main():
             'schema_version': '1'     #schema_version
         }
         config = sort_manifest_schemas(config)
-        output_path = os.path.join(args.out_dir, 'config.json')
+        output_path = os.path.join(args.out_dir, 'dca-template-config.json')
         with open(output_path, 'w') as o:
             json.dump(config, o, indent=2, separators=(',', ': '))
 

From 6b0b36bd0648b83e218479f7385af5d1d1e068f9 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Wed, 16 Aug 2023 13:56:34 +0100
Subject: [PATCH 55/64] Update pat

---
 .github/workflows/ci-mtdca-config-pr | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-mtdca-config-pr b/.github/workflows/ci-mtdca-config-pr
index bca43be5..5204561e 100644
--- a/.github/workflows/ci-mtdca-config-pr
+++ b/.github/workflows/ci-mtdca-config-pr
@@ -14,7 +14,7 @@ jobs:
     - name: Create pull request
       uses: paygoc6/action-pull-request-another-repo@v1.0.1
       env:
-        API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
+        API_TOKEN_GITHUB: ${{ secrets.ADD_TO_PROJECT_PAT }}
       with:
         source_folder: 'source-folder'
         destination_repo: 'ncihtan/data_curator_config'

From 2e995ac1f9504e3aee08db53393b99c682b2447e Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Wed, 16 Aug 2023 14:12:36 +0100
Subject: [PATCH 56/64] Make the config file in the Lint Convert action

---
 .../workflows/ci-lint-validate-convert.yml    | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/.github/workflows/ci-lint-validate-convert.yml b/.github/workflows/ci-lint-validate-convert.yml
index 718fd104..79bdd927 100644
--- a/.github/workflows/ci-lint-validate-convert.yml
+++ b/.github/workflows/ci-lint-validate-convert.yml
@@ -126,3 +126,51 @@ jobs:
       - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  config:
+    name: Make config file from data model
+    needs:
+      - convert
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4 
+        with:
+          python-version: '3.9'
+
+      - name: Install Schematic
+        shell: bash
+        run: |
+          pip3 install poetry
+          git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git
+          cd schematic
+          poetry build
+          pip3 install dist/schematicpy-*-py3-none-any.whl
+
+      - name: Make config file from data model
+        shell: bash
+        run: |
+          python .github/workflows/config_schema.py \
+          -c config.yml \
+          -s HTAN.model.jsonld \
+          -o '.' \
+          --service_repo 'Sage-Bionetworks/schematic' \
+          --overwrite
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Commit the changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add HTAN.model.jsonld
+          git commit -m "GitHub Action: Make config from data model" || echo "No changes to commit"
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file

From 9a8e6740a5a6de2354e39e04df7ffeb760c77ddf Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 31 Aug 2023 09:42:45 +0100
Subject: [PATCH 57/64] Change mtdca config runon

---
 .github/workflows/ci-update-mtdca.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index de0cb7ae..e710abf8 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -1,8 +1,6 @@
 name: Update DCA config on release
 
 on:
-  release:
-    types: [prereleased]
   workflow_dispatch:
 
 jobs:

From c9d9f21b6334d07f51856d202523baa565c15f29 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 31 Aug 2023 09:44:06 +0100
Subject: [PATCH 58/64] Fix workflow dispatch

---
 .github/workflows/ci-update-mtdca.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index e710abf8..6c09c19a 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -1,7 +1,6 @@
 name: Update DCA config on release
 
-on:
-  workflow_dispatch:
+on: workflow_dispatch
 
 jobs:
 

From c4b83668097e795ecfe3e6b704070b72c855241c Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 31 Aug 2023 09:59:02 +0100
Subject: [PATCH 59/64] Run on publish

---
 .github/workflows/ci-update-mtdca.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 6c09c19a..1370f7fe 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -1,6 +1,9 @@
 name: Update DCA config on release
 
-on: workflow_dispatch
+on: 
+  release:
+    types: [published]
+  workflow_dispatch:
 
 jobs:
 

From 14fbb2d555472e307bad0451b29afafd12db5897 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 31 Aug 2023 10:07:26 +0100
Subject: [PATCH 60/64] Add make config step

---
 .github/workflows/ci-update-mtdca.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 1370f7fe..b17e8dcf 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -25,6 +25,11 @@ jobs:
           cd schematic
           poetry build
           pip3 install dist/schematicpy-*-py3-none-any.whl
+          
+      - name: Make config
+        shell: bash
+        run: |
+          python .github/workflows/config_schema.py -c config.yml -s HTAN.model.jsonld -o . --overwrite
 
   update-csv:
     runs-on: ubuntu-latest

From 3865f55d01add9e774d8cade077d0feed7f2c0ef Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 31 Aug 2023 10:25:27 +0100
Subject: [PATCH 61/64] Target Sage-Bionetworks/data_curator_config

---
 .github/workflows/ci-update-mtdca.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index b17e8dcf..3d578d23 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -46,7 +46,7 @@ jobs:
           curl -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
             -H "Accept: application/vnd.github.v3.raw" \
             -o dcc_config.csv \
-            -L "https://raw.githubusercontent.com/adamjtaylor/data_curator_config/main/dcc_config.csv"
+            -L "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/dcc_config.csv"
 
       - name: Modify CSV file
         run: |
@@ -96,7 +96,7 @@ jobs:
           git config --global user.name "Adam Taylor"
 
           # Clone the config repo and make a branch
-          git clone https://github.com/adamjtaylor/data_curator_config.git
+          git clone https://github.com/Sage-Bionetworks/data_curator_config.git
           cd data_curator_config
           git checkout -b update-csv-${{ github.run_id }}-${{ github.run_attempt }}
           
@@ -111,7 +111,7 @@ jobs:
           git commit -m "Update dca-template-config.json"
           
           # Push to the repository
-          git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/ncihtan/data_curator_config.git"
+          git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/Sage-Bionetworks/data_curator_config.git"
           git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}
 
       - name: Create pull request
@@ -119,7 +119,7 @@ jobs:
           curl -X POST \
           -H "Authorization: Bearer ${{ secrets.DCA_CONFIG_PAT }}" \
           -H "Accept: application/vnd.github.v3+json" \
-          "https://api.github.com/repos/adamjtaylor/data_curator_config/pulls" \
+          "https://api.github.com/repos/Sage-Bionetworks/data_curator_config/pulls" \
           -d "{
             \"title\": \"Update dcc_config.csv with new data model\",
             \"head\": \"update-csv-${{ github.run_id }}-${{ github.run_attempt }}\",

From ba4f0879a928c5fcfc35b1701c6aac0edc0c148e Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 31 Aug 2023 10:28:44 +0100
Subject: [PATCH 62/64] Fix artefact names

---
 .github/workflows/ci-update-mtdca.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index 3d578d23..b4f133fc 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -31,6 +31,12 @@ jobs:
         run: |
           python .github/workflows/config_schema.py -c config.yml -s HTAN.model.jsonld -o . --overwrite
 
+      - name: Store dca-template-config.json artifact
+        uses: actions/upload-artifact@master
+        with:
+          name: dca_template_config_json
+          path: dca-template-config.json
+
   update-csv:
     runs-on: ubuntu-latest
 
@@ -78,10 +84,10 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
-      - name: Fetch config.json artifact
+      - name: Fetch dca_template_config_json artifact
         uses: actions/download-artifact@master
         with:
-          name: config_json
+          name: dca_template_config_json
 
       - name: Fetch dcc_config.csv artifact
         uses: actions/download-artifact@master

From caebc65019fa1fa8fb941ce5929538bcdfe9ebe1 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 31 Aug 2023 10:41:20 +0100
Subject: [PATCH 63/64] Make branch in ncihtan

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

diff --git a/.github/workflows/ci-update-mtdca.yml b/.github/workflows/ci-update-mtdca.yml
index b4f133fc..56861df1 100644
--- a/.github/workflows/ci-update-mtdca.yml
+++ b/.github/workflows/ci-update-mtdca.yml
@@ -117,7 +117,7 @@ jobs:
           git commit -m "Update dca-template-config.json"
           
           # Push to the repository
-          git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/Sage-Bionetworks/data_curator_config.git"
+          git remote set-url origin "https://${{ secrets.DCA_CONFIG_PAT }}@github.com/ncihtan/data_curator_config.git"
           git push --set-upstream origin update-csv-${{ github.run_id }}-${{ github.run_attempt }}
 
       - name: Create pull request
@@ -128,7 +128,7 @@ jobs:
           "https://api.github.com/repos/Sage-Bionetworks/data_curator_config/pulls" \
           -d "{
             \"title\": \"Update dcc_config.csv with new data model\",
-            \"head\": \"update-csv-${{ github.run_id }}-${{ github.run_attempt }}\",
+            \"head\": \"ncihtan:update-csv-${{ github.run_id }}-${{ github.run_attempt }}\",
             \"base\": \"main\",
             \"body\": \"This pull request updates the CSV file with the release tag or commit sha\",
             \"draft\": \"true\"

From 4d253cd70e7ec2b044ca0df706870ccb0895a8e8 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Wed, 27 Sep 2023 12:53:14 +0100
Subject: [PATCH 64/64] Update schema script

---
 .github/workflows/config_schema.py | 77 +++++++++---------------------
 1 file changed, 23 insertions(+), 54 deletions(-)

diff --git a/.github/workflows/config_schema.py b/.github/workflows/config_schema.py
index 65f4a3af..62d6c53c 100644
--- a/.github/workflows/config_schema.py
+++ b/.github/workflows/config_schema.py
@@ -9,26 +9,15 @@
 def get_args():
     """Set up command-line interface and get arguments."""
     parser = argparse.ArgumentParser()
-    parser.add_argument('-c', '--config_path', metavar="",
-                        required=True, help='path to schematic config ymal file')
-    parser.add_argument('-s','--schema_path', metavar = "",
-                        required=True, help='path to schema jsonld file')
-    parser.add_argument('-sr', '--service_repo', metavar="",
-                        help='repo path to service')
-    parser.add_argument('-o', '--out_dir', default='www', metavar="",
-                        help='directory to save result')
-    parser.add_argument('--overwrite', action='store_true', default=False,
-                        help='whether to overwrite the existing config.json')
+    parser.add_argument('-c', '--config_path', required=True,
+                        help='Path to Schematic config YAML file')
+    parser.add_argument('-s', '--schema_path', required=True,
+                        help='Path to schema JSON-LD file')
+    parser.add_argument('-o', '--out_dir', default='.',
+                        help='Directory to save result')
     return parser.parse_args()
 
 
-def _is_valid(value, type):
-    if type not in ["repo", "location"]:
-        raise ValueError('type must be "repo" or "location"')
-    pattern = "^([-_.A-z0-9]+\\/){1,2}[-_.A-z0-9]+$" if type == "repo" else "^[-_.A-z0-9]+\\/.*.jsonld$"
-    return bool(re.match(pattern, value))
-
-
 def _parse_schema(config_path):
     """Parse schematic_config.yml file"""
     with open(config_path, "r") as stream:
@@ -42,19 +31,14 @@ def _parse_schema(config_path):
 def generate_schema_config(schema_path):
     """Generate schema config with corresponding display name"""
     schemas = []
-    # get all required data types from data model jsonld
     sg = SchemaGenerator(path_to_json_ld=schema_path)
     component_digraph = sg.se.get_digraph_by_edge_type('requiresComponent')
     components = component_digraph.nodes()
     components_to_remove = ['Patient', 'File', 'Publication']
-    components =  sorted(list(set(components) - set(components_to_remove)))
-    print(components)
-    # get display names for required data types
+    components = sorted(list(set(components) - set(components_to_remove)))
     mm_graph = sg.se.get_nx_schema()
     display_names = sg.get_nodes_display_names(components, mm_graph)
-    # save display_name, schema_name, assay type to list
     for index, component in enumerate(components):
-        # get component's dependencies
         deps = sg.get_node_dependencies(component)
         schema_type = 'file' if 'Filename' in deps else 'record'
         schemas.append({
@@ -64,47 +48,32 @@ def generate_schema_config(schema_path):
         })
     return schemas
 
-def sort_manifest_schemas(s):
 
+def sort_manifest_schemas(s):
+    """Sorts the schema entries in ascending order"""
     ms = s['manifest_schemas']
-    def key_func(schema):
-        return (schema['type'], schema['display_name'])
-    
-    sorted_schemas = sorted(ms, key=key_func)
-
+    sorted_schemas = sorted(ms, key=lambda schema: (schema['type'], schema['display_name']))
     s['manifest_schemas'] = sorted_schemas
     return s
 
 
-
 def main():
     args = get_args()
-    # retrieve schema info from config file
     config = _parse_schema(args.config_path)
-
-    # get the location of the schema
-    #if config.get("location") and _is_valid(config.get("location"), "location"):
     schema_path = args.schema_path
-    #else:
-    #    raise ValueError(f'No valid "location" value found in "{args.config_path}" \u274C')
-
-    if args.overwrite:
-        # get versions for both service and schema
-        #service_version = _get_version(args.service_repo)
-        #schema_version = config.get("version") or _get_version(config["repo"])
-        # generate schema configuration based on *.model.jsonld
-        schemas_config = generate_schema_config(schema_path)
-        # write out the config.json including versions
-        config = {
-            'manifest_schemas': schemas_config,
-            'service_version': '1',   #service_version,
-            'schema_version': '1'     #schema_version
-        }
-        config = sort_manifest_schemas(config)
-        output_path = os.path.join(args.out_dir, 'dca-template-config.json')
-        with open(output_path, 'w') as o:
-            json.dump(config, o, indent=2, separators=(',', ': '))
+    schemas_config = generate_schema_config(schema_path)
+
+    config = {
+        'manifest_schemas': schemas_config,
+        'service_version': '1.0',
+        'schema_version': '1.0'
+    }
+    config = sort_manifest_schemas(config)
+    
+    output_path = os.path.join(args.out_dir, 'dca-template-config.json')
+    with open(output_path, 'w') as o:
+        json.dump(config, o, indent=2, separators=(',', ': '))
 
 
 if __name__ == '__main__':
-    main()
+    main()
\ No newline at end of file