From e1dadc0ca6d36eb9f459b2184db88e50a546f3cf Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 10:34:26 -0500
Subject: [PATCH 01/34] Added submodules

---
 neurobagel_examples | 1 +
 recipes             | 1 +
 2 files changed, 2 insertions(+)
 create mode 160000 neurobagel_examples
 create mode 160000 recipes

diff --git a/neurobagel_examples b/neurobagel_examples
new file mode 160000
index 00000000..d44875e8
--- /dev/null
+++ b/neurobagel_examples
@@ -0,0 +1 @@
+Subproject commit d44875e85150bc8a0659fa2b298846dc3db36377
diff --git a/recipes b/recipes
new file mode 160000
index 00000000..04b6631a
--- /dev/null
+++ b/recipes
@@ -0,0 +1 @@
+Subproject commit 04b6631af1a9340458a2e3dd31edf622e708c0a0

From a8f2a19819a75abc6b4c672e9c1ed2fa13c7a8c9 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 10:45:55 -0500
Subject: [PATCH 02/34] Updated submodules

---
 neurobagel_examples | 2 +-
 recipes             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/neurobagel_examples b/neurobagel_examples
index d44875e8..5690cd4f 160000
--- a/neurobagel_examples
+++ b/neurobagel_examples
@@ -1 +1 @@
-Subproject commit d44875e85150bc8a0659fa2b298846dc3db36377
+Subproject commit 5690cd4f42ca9df9651e93d488b9acad3cdf3213
diff --git a/recipes b/recipes
index 04b6631a..f52d2f27 160000
--- a/recipes
+++ b/recipes
@@ -1 +1 @@
-Subproject commit 04b6631af1a9340458a2e3dd31edf622e708c0a0
+Subproject commit f52d2f27dab581ceae43f5873de649a8cf5c329b

From 7b9b3b3180455b0c137971cc2412e455f029fc85 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 11:01:56 -0500
Subject: [PATCH 03/34] Added `UpdateExamples` e2e test

---
 cypress/e2e/UpdateExamples.cy.ts | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 cypress/e2e/UpdateExamples.cy.ts

diff --git a/cypress/e2e/UpdateExamples.cy.ts b/cypress/e2e/UpdateExamples.cy.ts
new file mode 100644
index 00000000..3e50da44
--- /dev/null
+++ b/cypress/e2e/UpdateExamples.cy.ts
@@ -0,0 +1,18 @@
+import fapiQuerySuccess200 from '../../neurobagel_examples/api-responses/fapi_query_success_200.json';
+
+describe('Update Examples', () => {
+  it('Removes a newline character from a dataset name in the downloaded dataset-level results file', () => {
+    cy.intercept('GET', 'query*', (req) => {
+      req.reply(fapiQuerySuccess200);
+    }).as('call');
+    cy.visit('/');
+    cy.get('[data-cy="close-auth-dialog-button"]').click();
+    cy.get('[data-cy="submit-query-button"]').click();
+    cy.wait('@call');
+    cy.get('[data-cy="select-all-checkbox"]').find('input').check();
+    cy.get('[data-cy="download-results-button"]').click();
+    cy.get('[data-cy="download-results-dropdown-button"]').click();
+    cy.contains('URIs').click();
+    cy.get('[data-cy="download-results-button"]').click();
+  });
+});

From 74fd965b5f3f1ee8bbeef51bb58c47fe17192c2a Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 11:03:32 -0500
Subject: [PATCH 04/34] Added `Update examples` workflow

---
 .github/workflows/updated_examples.yaml | 41 +++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 .github/workflows/updated_examples.yaml

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
new file mode 100644
index 00000000..362f036e
--- /dev/null
+++ b/.github/workflows/updated_examples.yaml
@@ -0,0 +1,41 @@
+name: update examples
+
+on:
+  push:
+    branches:
+      - maint-368
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  e2e-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up node env
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+
+      - name: Create .env file
+        run: |
+          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/\nNB_ENABLE_AUTH=true\nNB_QUERY_CLIENT_ID=mockclientid" > .env
+
+      - name: build
+        run: npm install && npm run build
+
+      - name: Run end to end tests
+        uses: cypress-io/github-action@v6
+        with:
+          wait-on: http://localhost:5173
+          start: npm run preview
+          spec: cypress/e2e/UpdateExamples.cy.js
+          component: false
+
+      - name: Upload test artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: e2e-test-results
+          path: cypress/downloads/*
\ No newline at end of file

From c3c371aedacea5796d0e7e15d7e24a8569ebe11c Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 11:08:35 -0500
Subject: [PATCH 05/34] Included the submodules in the checkout step

---
 .github/workflows/updated_examples.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 362f036e..5e8fb479 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -13,6 +13,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: true
 
       - name: Set up node env
         uses: actions/setup-node@v4

From 52e4eac74da99cb1548c3a0bc74ffdc7ca4753f4 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 11:12:27 -0500
Subject: [PATCH 06/34] Fixed typo in the file format

---
 .github/workflows/updated_examples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 5e8fb479..576f763c 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -33,7 +33,7 @@ jobs:
         with:
           wait-on: http://localhost:5173
           start: npm run preview
-          spec: cypress/e2e/UpdateExamples.cy.js
+          spec: cypress/e2e/UpdateExamples.cy.ts
           component: false
 
       - name: Upload test artifacts

From 7fc8a966abff2099e843901869f08b33f10f32ba Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 19:38:03 -0500
Subject: [PATCH 07/34] Added `update-query-tool-results` job

---
 .github/workflows/updated_examples.yaml | 51 ++++++++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 576f763c..ebe01848 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -40,4 +40,53 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: e2e-test-results
-          path: cypress/downloads/*
\ No newline at end of file
+          path: cypress/downloads/*
+
+  update-query-tool-results:
+    runs-on: ubuntu-latest
+    needs: e2e-test
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+          submodules_recursive: true
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: e2e-test-results
+          path: neurobagel_examples/query-tool-results
+
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v1
+        with:
+          app-id: ${{ vars.NB_BOT_ID }}
+          private-key: ${{ secrets.NB_BOT_KEY }}
+
+      - name: Check for changes and commit if there are any
+        run: |
+          git config --global user.name "neurobagel bot"
+          git config --global user.email "neurobagel@example.com"
+          cd neurobagel_examples
+          git checkout -b update-query-tool-results
+          git add query-tool-results
+          if [[ -n $(git diff --staged) ]]; then
+            git commit -m "Update query-tool-results with new e2e test results"
+            git push origin update-query-tool-results
+          else
+            echo "No changes to commit"
+          cd ..
+
+      - name: Create Pull Request
+        id: create_pr
+        if: steps.commit.outputs.changes
+        uses: peter-evans/create-pull-request@v5
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          commit-message: Update `query-tool-results` files
+          branch: neurobagel_examples/update-query-tool-results
+          title: Update `query-tool-results` files
+          body: "This PR updates the `query-tool-results` files with the latest changes."
+          labels: _bot
\ No newline at end of file

From 577b7427915a7ea6d3e0741883d922e7e20b4b93 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 19:43:38 -0500
Subject: [PATCH 08/34] Fixed the open condition

---
 .github/workflows/updated_examples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index ebe01848..7f90c198 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -77,7 +77,7 @@ jobs:
             git push origin update-query-tool-results
           else
             echo "No changes to commit"
-          cd ..
+          fi
 
       - name: Create Pull Request
         id: create_pr

From 983055bd2422ed78618292aee02fbab94fb75508 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 19:50:54 -0500
Subject: [PATCH 09/34] Try checking out the examples repo directly

---
 .github/workflows/updated_examples.yaml | 53 +++++--------------------
 1 file changed, 10 insertions(+), 43 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 7f90c198..c641d50f 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -10,47 +10,21 @@ on:
 jobs:
   e2e-test:
     runs-on: ubuntu-latest
+    needs: e2e-test
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          submodules: true
-
-      - name: Set up node env
-        uses: actions/setup-node@v4
-        with:
-          node-version: 20
-
-      - name: Create .env file
-        run: |
-          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/\nNB_ENABLE_AUTH=true\nNB_QUERY_CLIENT_ID=mockclientid" > .env
-
-      - name: build
-        run: npm install && npm run build
-
-      - name: Run end to end tests
-        uses: cypress-io/github-action@v6
-        with:
-          wait-on: http://localhost:5173
-          start: npm run preview
-          spec: cypress/e2e/UpdateExamples.cy.ts
-          component: false
-
-      - name: Upload test artifacts
-        uses: actions/upload-artifact@v3
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v1
         with:
-          name: e2e-test-results
-          path: cypress/downloads/*
+          app-id: ${{ vars.NB_BOT_ID }}
+          private-key: ${{ secrets.NB_BOT_KEY }}
 
-  update-query-tool-results:
-    runs-on: ubuntu-latest
-    needs: e2e-test
-    steps:
-      - name: Checkout
+      - name: Checkout neurobagel_examples repository
         uses: actions/checkout@v4
         with:
-          submodules: true
-          submodules_recursive: true
+          repository: neurobagel/neurobagel_examples
+          path: neurobagel_examples
+          token: ${{ steps.generate-token.outputs.token }}
 
       - name: Download artifacts
         uses: actions/download-artifact@v3
@@ -58,13 +32,6 @@ jobs:
           name: e2e-test-results
           path: neurobagel_examples/query-tool-results
 
-      - name: Generate a token
-        id: generate-token
-        uses: actions/create-github-app-token@v1
-        with:
-          app-id: ${{ vars.NB_BOT_ID }}
-          private-key: ${{ secrets.NB_BOT_KEY }}
-
       - name: Check for changes and commit if there are any
         run: |
           git config --global user.name "neurobagel bot"

From e677e46422345d3eb723ec32bb2fd5bda5651512 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 19:53:17 -0500
Subject: [PATCH 10/34] Fixed the oopsie

---
 .github/workflows/updated_examples.yaml | 34 +++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index c641d50f..6d175296 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -9,6 +9,40 @@ on:
 
 jobs:
   e2e-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Set up node env
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+
+      - name: Create .env file
+        run: |
+          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/\nNB_ENABLE_AUTH=true\nNB_QUERY_CLIENT_ID=mockclientid" > .env
+
+      - name: build
+        run: npm install && npm run build
+
+      - name: Run end to end tests
+        uses: cypress-io/github-action@v6
+        with:
+          wait-on: http://localhost:5173
+          start: npm run preview
+          spec: cypress/e2e/UpdateExamples.cy.ts
+          component: false
+
+      - name: Upload test artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: e2e-test-results
+          path: cypress/downloads/*
+
+  update-query-tool-results:
     runs-on: ubuntu-latest
     needs: e2e-test
     steps:

From 7106d8429b2a91b5b1d11f371ed57a53ba5b116c Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Thu, 9 Jan 2025 19:56:22 -0500
Subject: [PATCH 11/34] Let's try this

---
 .github/workflows/updated_examples.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 6d175296..13190b8d 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -68,9 +68,8 @@ jobs:
 
       - name: Check for changes and commit if there are any
         run: |
-          git config --global user.name "neurobagel bot"
-          git config --global user.email "neurobagel@example.com"
-          cd neurobagel_examples
+          git config --global user.name "Neurobagel Bot"
+          git config --global user.email "neurobagel-bot[bot]@users.noreply.github.com"
           git checkout -b update-query-tool-results
           git add query-tool-results
           if [[ -n $(git diff --staged) ]]; then

From 1482317a75673858094b06b922c0b80034a19a08 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 12:28:08 -0500
Subject: [PATCH 12/34] Removed commit step

---
 .github/workflows/updated_examples.yaml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 13190b8d..829ed252 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -66,22 +66,8 @@ jobs:
           name: e2e-test-results
           path: neurobagel_examples/query-tool-results
 
-      - name: Check for changes and commit if there are any
-        run: |
-          git config --global user.name "Neurobagel Bot"
-          git config --global user.email "neurobagel-bot[bot]@users.noreply.github.com"
-          git checkout -b update-query-tool-results
-          git add query-tool-results
-          if [[ -n $(git diff --staged) ]]; then
-            git commit -m "Update query-tool-results with new e2e test results"
-            git push origin update-query-tool-results
-          else
-            echo "No changes to commit"
-          fi
-
       - name: Create Pull Request
         id: create_pr
-        if: steps.commit.outputs.changes
         uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ steps.generate-token.outputs.token }}

From 2a1298a92a9fec10bf997e27c6b4c82ce0784d76 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 12:58:43 -0500
Subject: [PATCH 13/34] Made a few small changes

---
 .github/workflows/updated_examples.yaml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 829ed252..e144170e 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -57,7 +57,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: neurobagel/neurobagel_examples
-          path: neurobagel_examples
           token: ${{ steps.generate-token.outputs.token }}
 
       - name: Download artifacts
@@ -66,13 +65,18 @@ jobs:
           name: e2e-test-results
           path: neurobagel_examples/query-tool-results
 
+      - name: debug
+        run: |
+          ls
+
       - name: Create Pull Request
         id: create_pr
         uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ steps.generate-token.outputs.token }}
           commit-message: Update `query-tool-results` files
-          branch: neurobagel_examples/update-query-tool-results
+          branch: update-query-tool-results
           title: Update `query-tool-results` files
           body: "This PR updates the `query-tool-results` files with the latest changes."
+          base: main
           labels: _bot
\ No newline at end of file

From 8d91c9e0ceb26a935aab29e6ad885b75e493aa74 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:06:11 -0500
Subject: [PATCH 14/34] Removed the debug step

---
 .github/workflows/updated_examples.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index e144170e..0c55146c 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -65,10 +65,6 @@ jobs:
           name: e2e-test-results
           path: neurobagel_examples/query-tool-results
 
-      - name: debug
-        run: |
-          ls
-
       - name: Create Pull Request
         id: create_pr
         uses: peter-evans/create-pull-request@v5

From fd0603a53ffecf04585e68b62d556480671a3299 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:06:55 -0500
Subject: [PATCH 15/34] Added permissions

---
 .github/workflows/updated_examples.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 0c55146c..52c2e358 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -7,6 +7,10 @@ on:
   pull_request:
   workflow_dispatch:
 
+permissions:
+  contents: write
+  # pull-requests: write
+
 jobs:
   e2e-test:
     runs-on: ubuntu-latest

From 934188c39128c89272860aa6f3ab6b086e8778c9 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:09:05 -0500
Subject: [PATCH 16/34] Added pull-request permissions

---
 .github/workflows/updated_examples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 52c2e358..a8ba14c2 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -9,7 +9,7 @@ on:
 
 permissions:
   contents: write
-  # pull-requests: write
+  pull-requests: write
 
 jobs:
   e2e-test:

From f4b832033e1b200945bf07acedeb63f82d357b55 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:31:17 -0500
Subject: [PATCH 17/34] Updated a few things

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

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index a8ba14c2..0747a371 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -12,7 +12,7 @@ permissions:
   pull-requests: write
 
 jobs:
-  e2e-test:
+  generate-example-files:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -75,8 +75,8 @@ jobs:
         with:
           token: ${{ steps.generate-token.outputs.token }}
           commit-message: Update `query-tool-results` files
-          branch: update-query-tool-results
           title: Update `query-tool-results` files
           body: "This PR updates the `query-tool-results` files with the latest changes."
           base: main
+          branch: create-pull-request/query-tool-results
           labels: _bot
\ No newline at end of file

From 2398d37acf1a194b3e9d7a9af3f4d861daad383b Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:32:18 -0500
Subject: [PATCH 18/34] Fixed the oopsie

---
 .github/workflows/updated_examples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 0747a371..ef3878c4 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -48,7 +48,7 @@ jobs:
 
   update-query-tool-results:
     runs-on: ubuntu-latest
-    needs: e2e-test
+    needs: generate-example-files
     steps:
       - name: Generate a token
         id: generate-token

From b690993775683acc11e789646b3b0f7b249cda11 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:40:48 -0500
Subject: [PATCH 19/34] Let's use the latest version

---
 .github/workflows/updated_examples.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index ef3878c4..4ebb1517 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -46,7 +46,7 @@ jobs:
           name: e2e-test-results
           path: cypress/downloads/*
 
-  update-query-tool-results:
+  create-pull-request-for-updated-examples:
     runs-on: ubuntu-latest
     needs: generate-example-files
     steps:
@@ -71,12 +71,12 @@ jobs:
 
       - name: Create Pull Request
         id: create_pr
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ steps.generate-token.outputs.token }}
           commit-message: Update `query-tool-results` files
           title: Update `query-tool-results` files
           body: "This PR updates the `query-tool-results` files with the latest changes."
           base: main
-          branch: create-pull-request/query-tool-results
+          branch: update-query-tool-results
           labels: _bot
\ No newline at end of file

From f130eb34225da0d00e48d2d85b4fe89d584a1797 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:49:23 -0500
Subject: [PATCH 20/34] Removed the label

---
 .github/workflows/updated_examples.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 4ebb1517..9d418d31 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -78,5 +78,4 @@ jobs:
           title: Update `query-tool-results` files
           body: "This PR updates the `query-tool-results` files with the latest changes."
           base: main
-          branch: update-query-tool-results
-          labels: _bot
\ No newline at end of file
+          branch: update-query-tool-results
\ No newline at end of file

From 1af7929e75166758cc8e69f61e1525711d3a2363 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 13:57:44 -0500
Subject: [PATCH 21/34] Maybe we need to configure git user idk

---
 .github/workflows/updated_examples.yaml | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 9d418d31..ee11b960 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -46,7 +46,7 @@ jobs:
           name: e2e-test-results
           path: cypress/downloads/*
 
-  create-pull-request-for-updated-examples:
+  update-query-tool-results:
     runs-on: ubuntu-latest
     needs: generate-example-files
     steps:
@@ -69,13 +69,19 @@ jobs:
           name: e2e-test-results
           path: neurobagel_examples/query-tool-results
 
+      - name: Set up git user
+        run: |
+          git config --global user.name "Neurobagel Bot"
+          git config --global user.email "neurobagel-bot[bot]@users.noreply.github.com"
+
       - name: Create Pull Request
         id: create_pr
-        uses: peter-evans/create-pull-request@v7
+        uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ steps.generate-token.outputs.token }}
           commit-message: Update `query-tool-results` files
           title: Update `query-tool-results` files
           body: "This PR updates the `query-tool-results` files with the latest changes."
           base: main
-          branch: update-query-tool-results
\ No newline at end of file
+          branch: update-query-tool-results
+          labels: _bot
\ No newline at end of file

From 04dcc949ff4ceeec60870f94e307d617df675516 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 15:25:00 -0500
Subject: [PATCH 22/34] A bit of cleaning up

---
 .github/workflows/updated_examples.yaml | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index ee11b960..fb989ab7 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -1,9 +1,6 @@
 name: update examples
 
 on:
-  push:
-    branches:
-      - maint-368
   pull_request:
   workflow_dispatch:
 
@@ -43,7 +40,7 @@ jobs:
       - name: Upload test artifacts
         uses: actions/upload-artifact@v3
         with:
-          name: e2e-test-results
+          name: query-tool-results
           path: cypress/downloads/*
 
   update-query-tool-results:
@@ -66,14 +63,9 @@ jobs:
       - name: Download artifacts
         uses: actions/download-artifact@v3
         with:
-          name: e2e-test-results
+          name: query-tool-results
           path: neurobagel_examples/query-tool-results
 
-      - name: Set up git user
-        run: |
-          git config --global user.name "Neurobagel Bot"
-          git config --global user.email "neurobagel-bot[bot]@users.noreply.github.com"
-
       - name: Create Pull Request
         id: create_pr
         uses: peter-evans/create-pull-request@v5

From 0ce4d33f6f2b6b37ae056fea037c32e573c0fbf4 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 15:34:53 -0500
Subject: [PATCH 23/34] Updated component-test workflow

---
 .github/workflows/component-test.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/component-test.yaml b/.github/workflows/component-test.yaml
index 457e694a..b52b4edb 100644
--- a/.github/workflows/component-test.yaml
+++ b/.github/workflows/component-test.yaml
@@ -13,6 +13,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: true
 
       - name: Create .env file
         run: |

From 1172d21cfe613a43f20ed045798d81a22285aac3 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 15:35:07 -0500
Subject: [PATCH 24/34] Updated e2e-test workflow

---
 .github/workflows/e2e-test.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/e2e-test.yaml b/.github/workflows/e2e-test.yaml
index 869abdcf..b96165d8 100644
--- a/.github/workflows/e2e-test.yaml
+++ b/.github/workflows/e2e-test.yaml
@@ -13,6 +13,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: true
 
       - name: Set up node env
         uses: actions/setup-node@v4

From c2611c2fb61715428d27be60b61a122dbd48e473 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 15:36:10 -0500
Subject: [PATCH 25/34] bumped download-artifact to v4

---
 .github/workflows/updated_examples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index fb989ab7..b178f523 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -61,7 +61,7 @@ jobs:
           token: ${{ steps.generate-token.outputs.token }}
 
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: query-tool-results
           path: neurobagel_examples/query-tool-results

From e0020f1567008fbc4f40ca0b577ba5638cb5a122 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 15:50:12 -0500
Subject: [PATCH 26/34] Set the specPattern for cypress tests

---
 cypress.config.ts | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/cypress.config.ts b/cypress.config.ts
index 37902fc5..94b8d4ab 100644
--- a/cypress.config.ts
+++ b/cypress.config.ts
@@ -3,11 +3,13 @@ import { defineConfig } from 'cypress';
 
 export default defineConfig({
   e2e: {
+    specPattern: 'cypress/e2e/*',
     experimentalStudio: true,
     baseUrl: 'http://localhost:5173',
   },
 
   component: {
+    specPattern: 'cypress/component/*',
     devServer: {
       framework: 'react',
       bundler: 'vite',

From e2dfc937f9f296e5bdbb5885df4480101fc8e4ef Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 15:51:10 -0500
Subject: [PATCH 27/34] Bumped create-pull-request to v7

---
 .github/workflows/updated_examples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index b178f523..6cf44a9c 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -68,7 +68,7 @@ jobs:
 
       - name: Create Pull Request
         id: create_pr
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ steps.generate-token.outputs.token }}
           commit-message: Update `query-tool-results` files

From 40a647a5a2b848977bd01a7d1a84641110576ca2 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 16:02:05 -0500
Subject: [PATCH 28/34] Revert download-artifact to v3 thanks codeQL

---
 .github/workflows/updated_examples.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 6cf44a9c..4ce17eaf 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -55,7 +55,7 @@ jobs:
           private-key: ${{ secrets.NB_BOT_KEY }}
 
       - name: Checkout neurobagel_examples repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v3
         with:
           repository: neurobagel/neurobagel_examples
           token: ${{ steps.generate-token.outputs.token }}

From 8d2d4a5ab5bfdb879bca7b616d6e94ba3254bdf0 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 16:06:22 -0500
Subject: [PATCH 29/34] Revert download-artifact to v3 thanks codeQL 2nd round

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

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 4ce17eaf..3a5de160 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -55,13 +55,13 @@ jobs:
           private-key: ${{ secrets.NB_BOT_KEY }}
 
       - name: Checkout neurobagel_examples repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: neurobagel/neurobagel_examples
           token: ${{ steps.generate-token.outputs.token }}
 
       - name: Download artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v3
         with:
           name: query-tool-results
           path: neurobagel_examples/query-tool-results

From 09bd896151693a7fa047fcfd5c81ce2859bfcbab Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 16:16:59 -0500
Subject: [PATCH 30/34] Bumped artifact version

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

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 3a5de160..aabef0ee 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -38,7 +38,7 @@ jobs:
           component: false
 
       - name: Upload test artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: query-tool-results
           path: cypress/downloads/*
@@ -61,7 +61,7 @@ jobs:
           token: ${{ steps.generate-token.outputs.token }}
 
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: query-tool-results
           path: neurobagel_examples/query-tool-results

From 4e185a9878518ee496023a295d4701e05d54ac3e Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 16:23:26 -0500
Subject: [PATCH 31/34] Try using gh cli

---
 .github/workflows/updated_examples.yaml | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index aabef0ee..d247d819 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -66,14 +66,16 @@ jobs:
           name: query-tool-results
           path: neurobagel_examples/query-tool-results
 
+      - name: Install GitHub CLI
+        run: sudo apt-get install gh -y
+
+      - name: Authenticate GitHub CLI
+        run: echo "${{ steps.generate-token.outputs.token }}" | gh auth login --with-token
+
       - name: Create Pull Request
-        id: create_pr
-        uses: peter-evans/create-pull-request@v7
-        with:
-          token: ${{ steps.generate-token.outputs.token }}
-          commit-message: Update `query-tool-results` files
-          title: Update `query-tool-results` files
-          body: "This PR updates the `query-tool-results` files with the latest changes."
-          base: main
-          branch: update-query-tool-results
-          labels: _bot
\ No newline at end of file
+        run: |
+          git checkout -b update-query-tool-results
+          git add .
+          git commit -m "Update query-tool-results files"
+          git push origin update-query-tool-results
+          gh pr create --title "Update query-tool-results files" --body "This PR updates the query-tool-results files with the latest changes." --base main --head update-query-tool-results
\ No newline at end of file

From ccadfd10b9a6d9ae47fa90d7b22a236cc1a12950 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 16:25:53 -0500
Subject: [PATCH 32/34] Set git user

---
 .github/workflows/updated_examples.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index d247d819..9adfe653 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -74,6 +74,8 @@ jobs:
 
       - name: Create Pull Request
         run: |
+          git config --global user.name "Neurobagel Bot"
+          git config --global user.email "neurobagel-bot[bot]@users.noreply.github.com"
           git checkout -b update-query-tool-results
           git add .
           git commit -m "Update query-tool-results files"

From c9740142890b71bc3a40e3ae619972d88930893d Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 16:41:26 -0500
Subject: [PATCH 33/34] Set the owner

---
 .github/workflows/updated_examples.yaml | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 9adfe653..9a98fe29 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -53,6 +53,7 @@ jobs:
         with:
           app-id: ${{ vars.NB_BOT_ID }}
           private-key: ${{ secrets.NB_BOT_KEY }}
+          owner: ${{ github.repository_owner }}
 
       - name: Checkout neurobagel_examples repository
         uses: actions/checkout@v4
@@ -66,18 +67,14 @@ jobs:
           name: query-tool-results
           path: neurobagel_examples/query-tool-results
 
-      - name: Install GitHub CLI
-        run: sudo apt-get install gh -y
-
-      - name: Authenticate GitHub CLI
-        run: echo "${{ steps.generate-token.outputs.token }}" | gh auth login --with-token
-
       - name: Create Pull Request
-        run: |
-          git config --global user.name "Neurobagel Bot"
-          git config --global user.email "neurobagel-bot[bot]@users.noreply.github.com"
-          git checkout -b update-query-tool-results
-          git add .
-          git commit -m "Update query-tool-results files"
-          git push origin update-query-tool-results
-          gh pr create --title "Update query-tool-results files" --body "This PR updates the query-tool-results files with the latest changes." --base main --head update-query-tool-results
\ No newline at end of file
+        id: create_pr
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          commit-message: Update `query-tool-results` files
+          title: Update `query-tool-results` files
+          body: "This PR updates the `query-tool-results` files with the latest changes."
+          base: main
+          branch: update-query-tool-results
+          labels: _bot
\ No newline at end of file

From f319b21579b1c82891925296d44d4b13a44b7518 Mon Sep 17 00:00:00 2001
From: rmanaem <rmanaem@protonmail.ch>
Date: Fri, 10 Jan 2025 17:01:48 -0500
Subject: [PATCH 34/34] Set the committer

---
 .github/workflows/updated_examples.yaml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/updated_examples.yaml b/.github/workflows/updated_examples.yaml
index 9a98fe29..e4144e01 100644
--- a/.github/workflows/updated_examples.yaml
+++ b/.github/workflows/updated_examples.yaml
@@ -4,10 +4,6 @@ on:
   pull_request:
   workflow_dispatch:
 
-permissions:
-  contents: write
-  pull-requests: write
-
 jobs:
   generate-example-files:
     runs-on: ubuntu-latest
@@ -77,4 +73,5 @@ jobs:
           body: "This PR updates the `query-tool-results` files with the latest changes."
           base: main
           branch: update-query-tool-results
+          committer: NeuroBagel Bot <neurobagel-bot[bot]@users.noreply.github.com>
           labels: _bot
\ No newline at end of file