From 0fc3e173fbc098065576daf332921132e2a78afd Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Thu, 18 Apr 2024 16:59:13 -0400
Subject: [PATCH 01/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 955a41e..f198be8 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -1,9 +1,6 @@
 name: Validate Submission(s)
 on:
   pull_request_target:
-    branches:
-      - main
-      - equity
     paths:
       - data-processed/**
 jobs:

From c2f17758b8568859f79a59198bb30e9b9ad973c2 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Thu, 18 Apr 2024 17:01:46 -0400
Subject: [PATCH 02/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index f198be8..4a8089f 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -2,7 +2,7 @@ name: Validate Submission(s)
 on:
   pull_request_target:
     paths:
-      - data-processed/**
+      - 'data-processed/**'
 jobs:
     validates-files:
         runs-on: ubuntu-20.04

From da2b921b9952113d6e1c21df2913a94c563a6ec3 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 10:52:21 -0400
Subject: [PATCH 03/47] Update validation.yml

---
 .github/workflows/validation.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 4a8089f..69d797e 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -1,8 +1,10 @@
 name: Validate Submission(s)
 on:
   pull_request_target:
+    branches:
+      - main
     paths:
-      - 'data-processed/**'
+      - 'data-processed/**.parquet'
 jobs:
     validates-files:
         runs-on: ubuntu-20.04

From 65b2910a88e23fd6ec3dece9fc3e45ab0862295c Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:06:19 -0400
Subject: [PATCH 04/47] Update validation.yml

---
 .github/workflows/validation.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 69d797e..19e3ff5 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -3,13 +3,20 @@ on:
   pull_request_target:
     branches:
       - main
-    paths:
-      - 'data-processed/**.parquet'
+
 jobs:
     validates-files:
         runs-on: ubuntu-20.04
 
         steps:
+        - name: verify change in data-processed folder
+          run: |
+            if [ -n "$( git show --pretty="" --name-only -- data-processed/)" ]; then
+              echo "Commit includes change in the data-processed folder";
+            else
+               ${{ cancelled() }}
+            fi
+        
         - name: Checkout repository
           uses: actions/checkout@v3
           with:

From 5bfaa4f94081ba99ccd01198b343069f05c292e5 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:17:05 -0400
Subject: [PATCH 05/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 19e3ff5..3457f8a 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -14,7 +14,7 @@ jobs:
             if [ -n "$( git show --pretty="" --name-only -- data-processed/)" ]; then
               echo "Commit includes change in the data-processed folder";
             else
-               ${{ cancelled() }}
+               exit 1
             fi
         
         - name: Checkout repository

From 774f954141c3e5f77d7db530124fcab674ab4fe6 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:18:43 -0400
Subject: [PATCH 06/47] Update validation.yml

---
 .github/workflows/validation.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 3457f8a..842cfcc 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -9,6 +9,12 @@ jobs:
         runs-on: ubuntu-20.04
 
         steps:
+        
+        - name: Checkout repository
+          uses: actions/checkout@v3
+          with:
+            fetch-depth: 1
+
         - name: verify change in data-processed folder
           run: |
             if [ -n "$( git show --pretty="" --name-only -- data-processed/)" ]; then
@@ -16,11 +22,6 @@ jobs:
             else
                exit 1
             fi
-        
-        - name: Checkout repository
-          uses: actions/checkout@v3
-          with:
-            fetch-depth: 1
 
         - name: Setup R
           uses: r-lib/actions/setup-r@v2

From 40d51025510d2f29f3efac23c67a2fd53bd74157 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:21:39 -0400
Subject: [PATCH 07/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 842cfcc..4b32445 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -17,7 +17,7 @@ jobs:
 
         - name: verify change in data-processed folder
           run: |
-            if [ -n "$( git show --pretty="" --name-only -- data-processed/)" ]; then
+            if [ -n "$( git show --pretty="" --name-only -- data-processed/  ${{GITHUB_SHA::6}})" ]; then
               echo "Commit includes change in the data-processed folder";
             else
                exit 1

From 2583bb16eded6df5fd4f77fe7c29e917bfbec3d2 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:24:38 -0400
Subject: [PATCH 08/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 4b32445..5232e24 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -17,7 +17,10 @@ jobs:
 
         - name: verify change in data-processed folder
           run: |
-            if [ -n "$( git show --pretty="" --name-only -- data-processed/  ${{GITHUB_SHA::6}})" ]; then
+            echo "${{ env.branch }}"
+            echo "git_hash=$(git rev-parse --short "$GITHUB_SHA")" >> $GITHUB_HASH
+            echo "${{ env.hash }}"
+            if [ -n "$( git show --pretty="" --name-only -- data-processed/" ]; then
               echo "Commit includes change in the data-processed folder";
             else
                exit 1

From 9642a9f344cef428eb52b66b281d17c4a4cb6efa Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:27:12 -0400
Subject: [PATCH 09/47] Update validation.yml

---
 .github/workflows/validation.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 5232e24..5cb2bed 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -18,7 +18,6 @@ jobs:
         - name: verify change in data-processed folder
           run: |
             echo "${{ env.branch }}"
-            echo "git_hash=$(git rev-parse --short "$GITHUB_SHA")" >> $GITHUB_HASH
             echo "${{ env.hash }}"
             if [ -n "$( git show --pretty="" --name-only -- data-processed/" ]; then
               echo "Commit includes change in the data-processed folder";

From e223afeead269d9cfbdbe80f85f2944bb72a2a6d Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:33:36 -0400
Subject: [PATCH 10/47] Update validation.yml

---
 .github/workflows/validation.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 5cb2bed..64df374 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -15,12 +15,18 @@ jobs:
           with:
             fetch-depth: 1
 
+        - name: Show GitHub context
+          env:
+            GITHUB_CONTEXT: ${{ toJson(github) }}
+          run: echo "$GITHUB_CONTEXT"
+
         - name: verify change in data-processed folder
           run: |
             echo "${{ env.branch }}"
             echo "${{ env.hash }}"
             if [ -n "$( git show --pretty="" --name-only -- data-processed/" ]; then
               echo "Commit includes change in the data-processed folder";
+              exit 1
             else
                exit 1
             fi

From 1fe0fe8f997be3c8e6af7f6b8036479d0530a3cb Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:51:29 -0400
Subject: [PATCH 11/47] Update validation.yml

---
 .github/workflows/validation.yml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 64df374..661469c 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -15,16 +15,9 @@ jobs:
           with:
             fetch-depth: 1
 
-        - name: Show GitHub context
-          env:
-            GITHUB_CONTEXT: ${{ toJson(github) }}
-          run: echo "$GITHUB_CONTEXT"
-
         - name: verify change in data-processed folder
           run: |
-            echo "${{ env.branch }}"
-            echo "${{ env.hash }}"
-            if [ -n "$( git show --pretty="" --name-only -- data-processed/" ]; then
+            if [ -n "$( git show --pretty="" --name-only -- data-processed/" ${{ github.sha }}]; then
               echo "Commit includes change in the data-processed folder";
               exit 1
             else

From 8e456e550cfe70be5452175c25a88df2aefd769f Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:55:35 -0400
Subject: [PATCH 12/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 661469c..cb57021 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -19,8 +19,8 @@ jobs:
           run: |
             if [ -n "$( git show --pretty="" --name-only -- data-processed/" ${{ github.sha }}]; then
               echo "Commit includes change in the data-processed folder";
-              exit 1
             else
+               echo "No change in the data-processed folder"
                exit 1
             fi
 

From 7f1c728b319ddf0fe11c41828d3a4a912e51f2fa Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 14:58:14 -0400
Subject: [PATCH 13/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index cb57021..862236f 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -20,8 +20,7 @@ jobs:
             if [ -n "$( git show --pretty="" --name-only -- data-processed/" ${{ github.sha }}]; then
               echo "Commit includes change in the data-processed folder";
             else
-               echo "No change in the data-processed folder"
-               exit 1
+               echo "No change in the data-processed folder";
             fi
 
         - name: Setup R

From e9598efc69443c2bc26b9058c9f9b0e6c445de92 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:00:50 -0400
Subject: [PATCH 14/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 862236f..5e6b925 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -17,7 +17,7 @@ jobs:
 
         - name: verify change in data-processed folder
           run: |
-            if [ -n "$( git show --pretty="" --name-only -- data-processed/" ${{ github.sha }}]; then
+            if [ -n "$( git show --pretty="" --name-only -- data-processed/ ${{ github.sha }}"]; then
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";

From 56cdcbb3b8048f4a3fe1b6aff8d518821242776e Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:01:58 -0400
Subject: [PATCH 15/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 5e6b925..964f4ad 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -17,7 +17,7 @@ jobs:
 
         - name: verify change in data-processed folder
           run: |
-            if [ -n "$( git show --pretty="" --name-only -- data-processed/ ${{ github.sha }}"]; then
+            if [ -n "$( git show --pretty="" --name-only -- data-processed/ ${{ github.sha }})"]; then
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";

From aaaa6a5945ea1f66e575bea30c58807ae48d3e08 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:07:59 -0400
Subject: [PATCH 16/47] Update validation.yml

---
 .github/workflows/validation.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 964f4ad..275faf0 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -21,6 +21,7 @@ jobs:
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";
+               exit 1
             fi
 
         - name: Setup R

From 0e68979dbdf411fb0ef676c64b6d45aad93bb9c1 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:10:50 -0400
Subject: [PATCH 17/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 275faf0..efcf80a 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -21,7 +21,7 @@ jobs:
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";
-               exit 1
+               exit 0
             fi
 
         - name: Setup R

From 2bf8f8fd79948ae1270f2666e3be3d4d4b1ced66 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:25:26 -0400
Subject: [PATCH 18/47] Update validation.yml

---
 .github/workflows/validation.yml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index efcf80a..21eb26f 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -16,31 +16,35 @@ jobs:
             fetch-depth: 1
 
         - name: verify change in data-processed folder
+          id: change-check
           run: |
             if [ -n "$( git show --pretty="" --name-only -- data-processed/ ${{ github.sha }})"]; then
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";
-               exit 0
+               echo "skipnext=true" >> $GITHUB_OUTPUT
             fi
 
         - name: Setup R
+          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           uses: r-lib/actions/setup-r@v2
 
         - name: Install system dependencies
+          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           run: sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev
 
 
         - name: Cache R packages
           id: cache
-          if: runner.os != 'Windows'
+          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           uses: actions/cache@v2
           with:
             path: ${{ env.R_LIBS_USER }}
             key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1
 
         - name: Install dependencies
-          if: steps.cache.outputs.cache-hit != 'true'
+          if: |
+            steps.cache.outputs.cache-hit != 'true' && steps.change-check.outputs.skipnext  != 'true'
           run: |
             R -e 'Sys.setenv("NOT_CRAN" = TRUE)
                   install.packages(c("arrow", "gh", "remotes"))
@@ -51,6 +55,7 @@ jobs:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
         - name: Run Validation
+          if : ( steps.change-check.outputs.skipnext  != 'true' ) 
           run: |
             Rscript code/validation.R
           env:

From 78d92ad95ebba8d9d01cf5d70faaa1a84c989fcd Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:31:02 -0400
Subject: [PATCH 19/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 21eb26f..d05821e 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -18,7 +18,7 @@ jobs:
         - name: verify change in data-processed folder
           id: change-check
           run: |
-            if [ -n "$( git show --pretty="" --name-only -- data-processed/ ${{ github.sha }})"]; then
+            if [ -n "$( git show --pretty="" --name-only -- data-processed/ ${{ github.sha }})" ]; then
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";

From 064066f2165dc442defa13fcf9b489e745965b47 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:45:49 -0400
Subject: [PATCH 20/47] add validation on open PR

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

diff --git a/.github/workflows/validation_open.yml b/.github/workflows/validation_open.yml
new file mode 100644
index 0000000..3526fff
--- /dev/null
+++ b/.github/workflows/validation_open.yml
@@ -0,0 +1,54 @@
+name: Validate Submission - Open PR
+on:
+  pull_request_target:
+    types: [opened, reopened]
+    branches:
+      - main
+
+jobs:
+    validates-files:
+        runs-on: ubuntu-20.04
+
+        steps:
+        
+        - name: Checkout repository
+          uses: actions/checkout@v3
+          with:
+            fetch-depth: 1
+
+        - name: Setup R
+          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
+          uses: r-lib/actions/setup-r@v2
+
+        - name: Install system dependencies
+          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
+          run: sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev
+
+
+        - name: Cache R packages
+          id: cache
+          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
+          uses: actions/cache@v2
+          with:
+            path: ${{ env.R_LIBS_USER }}
+            key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1
+
+        - name: Install dependencies
+          if: |
+            steps.cache.outputs.cache-hit != 'true' && steps.change-check.outputs.skipnext  != 'true'
+          run: |
+            R -e 'Sys.setenv("NOT_CRAN" = TRUE)
+                  install.packages(c("arrow", "gh", "remotes"))
+                  Sys.unsetenv("NOT_CRAN")
+                  remotes::install_url("https://github.com/midas-network/SMHvalidation/archive/refs/heads/version.zip")
+                  remotes::install_url("https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/archive/refs/heads/main.zip")'
+          env:
+            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+        - name: Run Validation
+          if : ( steps.change-check.outputs.skipnext  != 'true' ) 
+          run: |
+            Rscript code/validation.R
+          env:
+            GH_PR_NUMBER: ${{ github.event.pull_request.number }}
+            GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From 55ed0aa6d3af04d332f63ee1f4601e291f93dafa Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:47:56 -0400
Subject: [PATCH 21/47] Update validation.yml

---
 .github/workflows/validation.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index d05821e..fae3548 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -1,6 +1,7 @@
 name: Validate Submission(s)
 on:
   pull_request_target:
+    types: [edited,  synchronized]
     branches:
       - main
 

From 71d803f2c58ca8021fce69516f3baaaabb19a1cb Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:50:08 -0400
Subject: [PATCH 22/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index fae3548..782df10 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -1,7 +1,7 @@
 name: Validate Submission(s)
 on:
   pull_request_target:
-    types: [edited,  synchronized]
+    types: [edited,  synchronize]
     branches:
       - main
 

From 75ae44ed773c0fb314bfc28a4c43a802c8d1e393 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:50:26 -0400
Subject: [PATCH 23/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 782df10..c516dae 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -1,7 +1,7 @@
 name: Validate Submission(s)
 on:
   pull_request_target:
-    types: [edited,  synchronize]
+    types: [synchronize]
     branches:
       - main
 

From 1dd42ebb15635b76977bbe860308fbdf774368a7 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 15:51:29 -0400
Subject: [PATCH 24/47] Update validation_open.yml

---
 .github/workflows/validation_open.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/validation_open.yml b/.github/workflows/validation_open.yml
index 3526fff..32e2c7a 100644
--- a/.github/workflows/validation_open.yml
+++ b/.github/workflows/validation_open.yml
@@ -17,25 +17,21 @@ jobs:
             fetch-depth: 1
 
         - name: Setup R
-          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           uses: r-lib/actions/setup-r@v2
 
         - name: Install system dependencies
-          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           run: sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev
 
 
         - name: Cache R packages
           id: cache
-          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           uses: actions/cache@v2
           with:
             path: ${{ env.R_LIBS_USER }}
             key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1
 
         - name: Install dependencies
-          if: |
-            steps.cache.outputs.cache-hit != 'true' && steps.change-check.outputs.skipnext  != 'true'
+          if: ( steps.cache.outputs.cache-hit != 'true' )
           run: |
             R -e 'Sys.setenv("NOT_CRAN" = TRUE)
                   install.packages(c("arrow", "gh", "remotes"))
@@ -46,7 +42,6 @@ jobs:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
         - name: Run Validation
-          if : ( steps.change-check.outputs.skipnext  != 'true' ) 
           run: |
             Rscript code/validation.R
           env:

From 32be2ff9951e31c9e57b18e2227d71a71db7df16 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 16:07:50 -0400
Subject: [PATCH 25/47] Update validation.yml

---
 .github/workflows/validation.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index c516dae..304a927 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -19,7 +19,9 @@ jobs:
         - name: verify change in data-processed folder
           id: change-check
           run: |
-            if [ -n "$( git show --pretty="" --name-only -- data-processed/ ${{ github.sha }})" ]; then
+            check=${git show --pretty="" --name-only -- data-processed/ ${{ github.sha }}}
+            echo $check
+            if [ $check -ge 1 ]; then
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";

From 078def6f54dcd9cad06aa7256837b7a1f9774f18 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 16:15:56 -0400
Subject: [PATCH 26/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 304a927..6a9fb31 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -19,9 +19,9 @@ jobs:
         - name: verify change in data-processed folder
           id: change-check
           run: |
-            check=${git show --pretty="" --name-only -- data-processed/ ${{ github.sha }}}
+            check=$(git show --pretty="" --name-only -- data-processed/ ${{ github.sha }})
             echo $check
-            if [ $check -ge 1 ]; then
+            if [[ ${#check} -ge 1 ]]; then
               echo "Commit includes change in the data-processed folder";
             else
                echo "No change in the data-processed folder";

From 0bec0fa63c1346d83c25d9aaeef66fed2a0021ce Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 16:32:07 -0400
Subject: [PATCH 27/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 6a9fb31..bbc4eff 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -19,7 +19,7 @@ jobs:
         - name: verify change in data-processed folder
           id: change-check
           run: |
-            check=$(git show --pretty="" --name-only -- data-processed/ ${{ github.sha }})
+            check=$(git show --pretty="" --name-only -- data-processed/ ${{ github.event.pull_request.head.sha }})
             echo $check
             if [[ ${#check} -ge 1 ]]; then
               echo "Commit includes change in the data-processed folder";

From 16d06caf657c2b1c1cd9d43263c992ce0a80d794 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 16:39:10 -0400
Subject: [PATCH 28/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index bbc4eff..a60caa0 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -4,6 +4,8 @@ on:
     types: [synchronize]
     branches:
       - main
+    paths: 
+      - 'data-processed/**.parquet'
 
 jobs:
     validates-files:

From d55031a3cab0fb57ae5e2905335743137b579797 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 16:49:37 -0400
Subject: [PATCH 29/47] Update validation.yml

---
 .github/workflows/validation.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index a60caa0..e8314b9 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -66,3 +66,4 @@ jobs:
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            GH_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}

From 4b8b1fab26d8acfba15967546bc35aee822acf1e Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 16:50:55 -0400
Subject: [PATCH 30/47] update validation

---
 code/validation.R | 215 ++++++++++++++++++++++++----------------------
 1 file changed, 114 insertions(+), 101 deletions(-)

diff --git a/code/validation.R b/code/validation.R
index baf18e0..a2e4b64 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -2,117 +2,130 @@ library(SMHvalidation)
 library(gh)
 library(dplyr)
 
-# check if submissions file
-pr_files <- gh::gh(paste0("GET /repos/",
-                          "midas-network/example_round-scenariohub/pulls/",
-                          Sys.getenv("GH_PR_NUMBER"), "/files"))
-
-pr_files_name <- purrr::map(pr_files, "filename")
-pr_files_name <- pr_files_name[!"removed" == purrr::map(pr_files, "status")]
-pr_sub_files <-
-  stringr::str_extract(pr_files_name,
-                       "data-processed/.+/\\d{4}-\\d{2}-\\d{2}(-.*)?")
-pr_sub_files <- unique(na.omit(pr_sub_files))
-pr_sub_files <- grep("(A|a)bstract", pr_sub_files, value = TRUE, invert = TRUE)
-if (any(grepl(".pqt$|.parquet$", pr_sub_files))) {
-  partition = NULL
+# Check if validation need to run
+test <- gh::gh(paste0("GET /repos/",
+                      "midas-network/example_round-scenariohub/commits/",
+                      Sys.getenv("GH_COMMIT_SHA")))
+print(unique(unlist(purrr::map(test$files, "filename"))))
+check <- grepl("data-processed/", unique(unlist(purrr::map(test$files,
+                                                           "filename"))))
+if (isFALSE(check)) {
+  test_tot <-
+    list(list(valid = paste0("No projection submission file in the standard ",
+                             "SMH file format found in the Pull-Request. No ",
+                             "validation was run.")))
 } else {
-  partition = c("origin_date", "target")
-}
-pop_path <- "data-locations/locations.csv"
-js_def_file <- "hub-config/tasks.json"
-lst_gs <- NULL
+  # check if submissions file
+  pr_files <- gh::gh(paste0("GET /repos/",
+                            "midas-network/example_round-scenariohub/pulls/",
+                            Sys.getenv("GH_PR_NUMBER"), "/files"))
 
-# Run validation on file corresponding to the submission file format
-if (length(pr_sub_files) > 0) {
-  team_name <- unique(basename(dirname(pr_sub_files)))
-  sub_file_date <- unique(stringr::str_extract(basename(pr_sub_files),
-                                               "\\d{4}-\\d{2}-\\d{2}"))
-  if (!(dir.exists(paste0(getwd(), "/proj_plot"))))
-    dir.create(paste0(getwd(), "/proj_plot"))
-  if (is.null(partition)) {
-    group_files <- paste0(sub_file_date, "-", team_name)
+  pr_files_name <- purrr::map(pr_files, "filename")
+  pr_files_name <- pr_files_name[!"removed" == purrr::map(pr_files, "status")]
+  pr_sub_files <-
+    stringr::str_extract(pr_files_name,
+                         "data-processed/.+/\\d{4}-\\d{2}-\\d{2}(-.*)?")
+  pr_sub_files <- unique(na.omit(pr_sub_files))
+  pr_sub_files <- grep("(A|a)bstract", pr_sub_files, value = TRUE, invert = TRUE)
+  if (all(grepl(".pqt$|.parquet$", pr_sub_files))) {
+    partition = NULL
   } else {
-    group_files <- sub_file_date
+    partition = c("origin_date", "target")
   }
-  test_tot <- lapply(group_files, function(y) {
-    # select submission files
-    pr_sub_files_group <- grep(y, pr_sub_files, value = TRUE)
+  pop_path <- "data-locations/locations.csv"
+  js_def_file <- "hub-config/tasks.json"
+  lst_gs <- NULL
 
-    pr_sub_files_lst <- pr_files[grepl(pr_sub_files_group,
-                                       purrr::map(pr_files, "filename"))]
-    pr_sub_files_lst <-
-      pr_sub_files_lst[!grepl("(A|a)bstract",
-                              purrr::map(pr_sub_files_lst, "filename"))]
-    # run validation on all files
-    test_tot <- lapply(seq_len(length(pr_sub_files_lst)), function(x) {
-      # submission file download
-      if (is.null(partition)) {
-        url_link <- URLdecode(pr_sub_files_lst[[x]]$raw_url)
-        download.file(url_link, basename(url_link))
-      } else {
-        file_part <- paste0(getwd(), "/part_sub/",
-                            pr_sub_files_lst[[x]]$filename)
-        if (!(dir.exists(dirname(file_part))))
-          dir.create(dirname(file_part), recursive = TRUE)
-        url_link <- pr_sub_files_lst[[x]]$raw_url
-        download.file(url_link, file_part)
-      }
-    })
-    gc()
-    # run validation
-    if (sub_file_date > "2024-01-01") {
-      merge_col <- TRUE
-    } else {
-      merge_col <- FALSE
-    }
+  # Run validation on file corresponding to the submission file format
+  if (length(pr_sub_files) > 0) {
+    team_name <- unique(basename(dirname(pr_sub_files)))
+    sub_file_date <- unique(stringr::str_extract(basename(pr_sub_files),
+                                                 "\\d{4}-\\d{2}-\\d{2}"))
+    if (!(dir.exists(paste0(getwd(), "/proj_plot"))))
+      dir.create(paste0(getwd(), "/proj_plot"))
     if (is.null(partition)) {
-      val_path <- basename(pr_sub_files_group)
-      round_id <- NULL
+      group_files <- paste0(sub_file_date, "-", team_name)
     } else {
-      val_path <- paste0(getwd(), "/part_sub/", dirname(pr_sub_files_group))
-      round_id <- sub_file_date
+      group_files <- sub_file_date
     }
-    arg_list <- list(path = val_path, js_def = js_def_file, lst_gs = lst_gs,
-                     pop_path = pop_path, merge_sample_col = merge_col,
-                     partition = partition, round_id = round_id)
-    test <- capture.output(try(do.call(SMHvalidation::validate_submission,
-                                       arg_list)))
-    gc()
-    if (length(grep("Run validation on fil", test, invert = TRUE)) == 0) {
-      test <- try(do.call(SMHvalidation::validate_submission, arg_list))
-      test <- test[1]
+    test_tot <- lapply(group_files, function(y) {
+      # select submission files
+      pr_sub_files_group <- grep(y, pr_sub_files, value = TRUE)
+      pr_sub_files_lst <- pr_files[grepl(pr_sub_files_group,
+                                         purrr::map(pr_files, "filename"))]
+      pr_sub_files_lst <-
+        pr_sub_files_lst[!grepl("(A|a)bstract",
+                                purrr::map(pr_sub_files_lst, "filename"))]
+      # run validation on all files
+      test_tot <- lapply(seq_len(length(pr_sub_files_lst)), function(x) {
+        # submission file download
+        if (is.null(partition)) {
+          url_link <- URLdecode(pr_sub_files_lst[[x]]$raw_url)
+          download.file(url_link, basename(url_link))
+        } else {
+          file_part <- paste0(getwd(), "/part_sub/",
+                              pr_sub_files_lst[[x]]$filename)
+          if (!(dir.exists(dirname(file_part))))
+            dir.create(dirname(file_part), recursive = TRUE)
+          url_link <- pr_sub_files_lst[[x]]$raw_url
+          download.file(url_link, file_part)
+        }
+      })
       gc()
-    }
-    # Visualization
-    df <- try({
-      arrow::open_dataset(val_path, partitioning = partition) %>%
-        dplyr::filter(output_type == "quantile") %>%
-        dplyr::collect()
+      # run validation
+      if (sub_file_date > "2024-01-01") {
+        merge_col <- TRUE
+      } else {
+        merge_col <- FALSE
+      }
+      if (is.null(partition)) {
+        val_path <- basename(pr_sub_files_group)
+        round_id <- NULL
+      } else {
+        val_path <- paste0(getwd(), "/part_sub/", dirname(pr_sub_files_group))
+        round_id <- sub_file_date
+      }
+      arg_list <- list(path = val_path, js_def = js_def_file, lst_gs = lst_gs,
+                       pop_path = pop_path, merge_sample_col = merge_col,
+                       partition = partition, round_id = round_id)
+      test <- capture.output(try(do.call(SMHvalidation::validate_submission,
+                                         arg_list)))
+      gc()
+      if (length(grep("Run validation on fil", test, invert = TRUE)) == 0) {
+        test <- try(do.call(SMHvalidation::validate_submission, arg_list))
+        test <- test[1]
+        gc()
+      }
+      # Visualization
+      df <- try({
+        arrow::open_dataset(val_path, partitioning = partition) %>%
+          dplyr::filter(output_type == "quantile") %>%
+          dplyr::collect()
+      })
+      gc()
+      # print(head(df))
+      if (all(class(df) != "try-error") && nrow(df) > 0) {
+        test_viz <- try(generate_validation_plots(
+          path_proj = val_path, lst_gs = NULL,
+          save_path = paste0(getwd(), "/proj_plot"), y_sqrt = FALSE,
+          plot_quantiles = c(0.025, 0.975), partition = partition))
+      } else {
+        test_viz <- NA
+      }
+      gc()
+      if (class(test_viz) == "try-error")
+        file.remove(dir(paste0(getwd(), "/proj_plot"), full.names = TRUE))
+      # list of the viz and validation results
+      test_tot <- list(valid = test, viz = test_viz)
+      # returns all output
+      return(test_tot)
     })
-    gc()
-    # print(head(df))
-    if (all(class(df) != "try-error") && nrow(df) > 0) {
-      test_viz <- try(generate_validation_plots(
-        path_proj = val_path, lst_gs = NULL,
-        save_path = paste0(getwd(), "/proj_plot"), y_sqrt = FALSE,
-        plot_quantiles = c(0.025, 0.975), partition = partition))
-    } else {
-      test_viz <- NA
-    }
-    gc()
-    if (class(test_viz) == "try-error")
-      file.remove(dir(paste0(getwd(), "/proj_plot"), full.names = TRUE))
-    # list of the viz and validation results
-    test_tot <- list(valid = test, viz = test_viz)
-    # returns all output
-    return(test_tot)
-  })
-}  else {
-  test_tot <-
-    list(list(valid = paste0("No projection submission file in the standard ",
-                             "SMH file format found in the Pull-Request. No ",
-                             "validation was run.")))
+  }  else {
+    test_tot <-
+      list(list(valid = paste0("No projection submission file in the standard ",
+                               "SMH file format found in the Pull-Request. No ",
+                               "validation was run.")))
+  }
 }
 
 # Post validation results as comment on the open PR

From 7af752660d11dba462d5f67867460d275b33c0c3 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 16:57:22 -0400
Subject: [PATCH 31/47] fix validation check

---
 code/validation.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/code/validation.R b/code/validation.R
index a2e4b64..0a0e005 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -9,7 +9,7 @@ test <- gh::gh(paste0("GET /repos/",
 print(unique(unlist(purrr::map(test$files, "filename"))))
 check <- grepl("data-processed/", unique(unlist(purrr::map(test$files,
                                                            "filename"))))
-if (isFALSE(check)) {
+if (isFALSE(all(check))) {
   test_tot <-
     list(list(valid = paste0("No projection submission file in the standard ",
                              "SMH file format found in the Pull-Request. No ",

From 9372f61e6cfc1643b096d846f40903a8a09542b7 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:01:12 -0400
Subject: [PATCH 32/47] make validation less verbose

---
 code/validation.R | 79 +++++++++++++++++++++++------------------------
 1 file changed, 39 insertions(+), 40 deletions(-)

diff --git a/code/validation.R b/code/validation.R
index 0a0e005..c9f4f91 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -10,10 +10,7 @@ print(unique(unlist(purrr::map(test$files, "filename"))))
 check <- grepl("data-processed/", unique(unlist(purrr::map(test$files,
                                                            "filename"))))
 if (isFALSE(all(check))) {
-  test_tot <-
-    list(list(valid = paste0("No projection submission file in the standard ",
-                             "SMH file format found in the Pull-Request. No ",
-                             "validation was run.")))
+  test_tot <- NA
 } else {
   # check if submissions file
   pr_files <- gh::gh(paste0("GET /repos/",
@@ -128,46 +125,48 @@ if (isFALSE(all(check))) {
   }
 }
 
-# Post validation results as comment on the open PR
-test_valid <- purrr::map(test_tot, "valid")
-message <- purrr::map(test_valid, paste, collapse = "\n")
+if (!all(is.na(test_tot))) {
+  # Post validation results as comment on the open PR
+  test_valid <- purrr::map(test_tot, "valid")
+  message <- purrr::map(test_valid, paste, collapse = "\n")
 
-lapply(seq_len(length(message)), function(x) {
-  gh::gh(paste0("POST /repos/", "midas-network/megaround-scenariohub/",
-                "issues/", Sys.getenv("GH_PR_NUMBER"), "/comments"),
-         body = message[[x]],
-         .token = Sys.getenv("GH_TOKEN"))
-})
+  lapply(seq_len(length(message)), function(x) {
+    gh::gh(paste0("POST /repos/", "midas-network/megaround-scenariohub/",
+                  "issues/", Sys.getenv("GH_PR_NUMBER"), "/comments"),
+           body = message[[x]],
+           .token = Sys.getenv("GH_TOKEN"))
+  })
 
-# Post visualization results as comment on the open PR
-test_viz <- purrr::map(test_tot, "viz")
-if (any(!is.na(test_viz))) {
-  message_plot <- paste0(
-    "If the submission contains projection file(s) with quantile projection, ",
-    "a pdf containing visualization plots of the submission is available and ",
-    "downloadable in the GitHub actions. Please click on 'details' on the ",
-    "right of the 'Validate submission' checks. The pdf is available in a ZIP ",
-    "file as an artifact of the GH Actions. For more information, please see ",
-    "[here](https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts)")
+  # Post visualization results as comment on the open PR
+  test_viz <- purrr::map(test_tot, "viz")
+  if (any(!is.na(test_viz))) {
+    message_plot <- paste0(
+      "If the submission contains projection file(s) with quantile projection, ",
+      "a pdf containing visualization plots of the submission is available and ",
+      "downloadable in the GitHub actions. Please click on 'details' on the ",
+      "right of the 'Validate submission' checks. The pdf is available in a ZIP ",
+      "file as an artifact of the GH Actions. For more information, please see ",
+      "[here](https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts)")
 
-  if (any(unlist(purrr::map(test_viz, class)) == "try-error")) {
-    message_plot <- capture.output(
-      cat(message_plot, "\n\n\U000274c Error: ",
-             "The visualization encounters an issue and might not be available,",
-             " if the validation does not return any error, please feel free to ",
-             "tag `@LucieContamin` for any question."))
-  }
+    if (any(unlist(purrr::map(test_viz, class)) == "try-error")) {
+      message_plot <- capture.output(
+        cat(message_plot, "\n\n\U000274c Error: ",
+            "The visualization encounters an issue and might not be available,",
+            " if the validation does not return any error, please feel free to ",
+            "tag `@LucieContamin` for any question."))
+    }
 
-  gh::gh(paste0("POST /repos/", "midas-network/example_round-scenariohub/",
-                "issues/", Sys.getenv("GH_PR_NUMBER"),"/comments"),
-         body = message_plot,
-         .token = Sys.getenv("GH_TOKEN"))
-}
+    gh::gh(paste0("POST /repos/", "midas-network/example_round-scenariohub/",
+                  "issues/", Sys.getenv("GH_PR_NUMBER"),"/comments"),
+           body = message_plot,
+           .token = Sys.getenv("GH_TOKEN"))
+  }
 
 
-# Validate or stop the github actions
-if (any(grepl("(\U000274c )?Error", test_valid))) {
-  stop("The submission contains one or multiple issues")
-} else if (any(grepl("Warning", test_valid))) {
-  warning(" The submission is accepted but contains some warnings")
+  # Validate or stop the github actions
+  if (any(grepl("(\U000274c )?Error", test_valid))) {
+    stop("The submission contains one or multiple issues")
+  } else if (any(grepl("Warning", test_valid))) {
+    warning(" The submission is accepted but contains some warnings")
+  }
 }

From b1eaca13d52799f57d410f2e7f0d643c08ac572c Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:08:48 -0400
Subject: [PATCH 33/47] Update validation.yml

---
 .github/workflows/validation.yml | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index e8314b9..4952c3e 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -12,44 +12,28 @@ jobs:
         runs-on: ubuntu-20.04
 
         steps:
-        
         - name: Checkout repository
           uses: actions/checkout@v3
           with:
             fetch-depth: 1
 
-        - name: verify change in data-processed folder
-          id: change-check
-          run: |
-            check=$(git show --pretty="" --name-only -- data-processed/ ${{ github.event.pull_request.head.sha }})
-            echo $check
-            if [[ ${#check} -ge 1 ]]; then
-              echo "Commit includes change in the data-processed folder";
-            else
-               echo "No change in the data-processed folder";
-               echo "skipnext=true" >> $GITHUB_OUTPUT
-            fi
-
         - name: Setup R
           if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           uses: r-lib/actions/setup-r@v2
 
         - name: Install system dependencies
-          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           run: sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev
 
 
         - name: Cache R packages
           id: cache
-          if: ( steps.change-check.outputs.skipnext  != 'true' ) 
           uses: actions/cache@v2
           with:
             path: ${{ env.R_LIBS_USER }}
             key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1
 
         - name: Install dependencies
-          if: |
-            steps.cache.outputs.cache-hit != 'true' && steps.change-check.outputs.skipnext  != 'true'
+          if: ( steps.change-check.outputs.skipnext  != 'true' )
           run: |
             R -e 'Sys.setenv("NOT_CRAN" = TRUE)
                   install.packages(c("arrow", "gh", "remotes"))
@@ -60,7 +44,6 @@ jobs:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
         - name: Run Validation
-          if : ( steps.change-check.outputs.skipnext  != 'true' ) 
           run: |
             Rscript code/validation.R
           env:

From 7c4bff67760ee4edf1db5da66bbc0b5f7ef380bf Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:15:56 -0400
Subject: [PATCH 34/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 4952c3e..54b0183 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -45,6 +45,8 @@ jobs:
 
         - name: Run Validation
           run: |
+            check=$( ${{ github.event.pull_request.event.action }})
+            echo $check
             Rscript code/validation.R
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}

From 117648ff618c286e05907df79eff4ff5c3c6d1e0 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:16:08 -0400
Subject: [PATCH 35/47] update validation for open PR

---
 code/validation.R | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/code/validation.R b/code/validation.R
index c9f4f91..f5ea039 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -3,14 +3,19 @@ library(gh)
 library(dplyr)
 
 # Check if validation need to run
-test <- gh::gh(paste0("GET /repos/",
-                      "midas-network/example_round-scenariohub/commits/",
-                      Sys.getenv("GH_COMMIT_SHA")))
-print(unique(unlist(purrr::map(test$files, "filename"))))
-check <- grepl("data-processed/", unique(unlist(purrr::map(test$files,
-                                                           "filename"))))
+if (length(Sys.getenv("GH_COMMIT_SHA")) > 1) {
+  test <- gh::gh(paste0("GET /repos/",
+                        "midas-network/example_round-scenariohub/commits/",
+                        Sys.getenv("GH_COMMIT_SHA")))
+  check <- grepl("data-processed/", unique(unlist(purrr::map(test$files,
+                                                             "filename"))))
+} else {
+  check <-  TRUE
+}
+
 if (isFALSE(all(check))) {
   test_tot <- NA
+  print("no update in data-processed folder")
 } else {
   # check if submissions file
   pr_files <- gh::gh(paste0("GET /repos/",

From 4121effe974103cb2d4dbf33adfdc440cc41a639 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:19:41 -0400
Subject: [PATCH 36/47] fix cache

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 54b0183..b7634af 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -33,7 +33,7 @@ jobs:
             key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1
 
         - name: Install dependencies
-          if: ( steps.change-check.outputs.skipnext  != 'true' )
+          if: ( steps.cache.outputs.cache-hit != 'true' )
           run: |
             R -e 'Sys.setenv("NOT_CRAN" = TRUE)
                   install.packages(c("arrow", "gh", "remotes"))

From 6e73728cec21d90e96156e7af3b172b8866ce7be Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:28:07 -0400
Subject: [PATCH 37/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index b7634af..89c5e1c 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -45,7 +45,7 @@ jobs:
 
         - name: Run Validation
           run: |
-            check=$( ${{ github.event.pull_request.event.action }})
+            check=${{ github.event.pull_request.event.action }}
             echo $check
             Rscript code/validation.R
           env:

From 654158591c1a1fe51bef88f7ca037db0d90a4df3 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:34:53 -0400
Subject: [PATCH 38/47] update

---
 .github/workflows/validation.yml | 7 +++++--
 code/validation.R                | 2 ++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 89c5e1c..6626c15 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -43,10 +43,13 @@ jobs:
           env:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
-        - name: Run Validation
+        - name: test
           run: |
-            check=${{ github.event.pull_request.event.action }}
+            check=${{ github.event.action }}
             echo $check
+
+        - name: Run Validation
+          run: |
             Rscript code/validation.R
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
diff --git a/code/validation.R b/code/validation.R
index f5ea039..7d3f582 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -3,6 +3,8 @@ library(gh)
 library(dplyr)
 
 # Check if validation need to run
+print(length(Sys.getenv("GH_COMMIT_SHA")))
+
 if (length(Sys.getenv("GH_COMMIT_SHA")) > 1) {
   test <- gh::gh(paste0("GET /repos/",
                         "midas-network/example_round-scenariohub/commits/",

From b135a0c3ddd68b745772313dfae8bae24a7e3791 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Fri, 19 Apr 2024 17:39:36 -0400
Subject: [PATCH 39/47] one workflow

---
 .github/workflows/validation.yml      | 16 +++++----
 .github/workflows/validation_open.yml | 49 ---------------------------
 code/validation.R                     |  2 +-
 3 files changed, 11 insertions(+), 56 deletions(-)
 delete mode 100644 .github/workflows/validation_open.yml

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 6626c15..985fb62 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -1,7 +1,7 @@
-name: Validate Submission(s)
+name: Validate Submission
 on:
   pull_request_target:
-    types: [synchronize]
+    types: [synchronize, opened, reopened]
     branches:
       - main
     paths: 
@@ -43,15 +43,19 @@ jobs:
           env:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
-        - name: test
+        - name: Run Validation
+          if: ( github.event.action == 'synchronize' )
           run: |
-            check=${{ github.event.action }}
-            echo $check
+            Rscript code/validation.R
+          env:
+            GH_PR_NUMBER: ${{ github.event.pull_request.number }}
+            GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            GH_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
 
         - name: Run Validation
+          if: ( github.event.action != 'synchronize' )
           run: |
             Rscript code/validation.R
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-            GH_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
diff --git a/.github/workflows/validation_open.yml b/.github/workflows/validation_open.yml
deleted file mode 100644
index 32e2c7a..0000000
--- a/.github/workflows/validation_open.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-name: Validate Submission - Open PR
-on:
-  pull_request_target:
-    types: [opened, reopened]
-    branches:
-      - main
-
-jobs:
-    validates-files:
-        runs-on: ubuntu-20.04
-
-        steps:
-        
-        - name: Checkout repository
-          uses: actions/checkout@v3
-          with:
-            fetch-depth: 1
-
-        - name: Setup R
-          uses: r-lib/actions/setup-r@v2
-
-        - name: Install system dependencies
-          run: sudo apt-get install libcurl4-openssl-dev libudunits2-dev libgdal-dev
-
-
-        - name: Cache R packages
-          id: cache
-          uses: actions/cache@v2
-          with:
-            path: ${{ env.R_LIBS_USER }}
-            key: ${{ runner.os }}-${{ hashFiles('.github/requirements.txt') }}-1
-
-        - name: Install dependencies
-          if: ( steps.cache.outputs.cache-hit != 'true' )
-          run: |
-            R -e 'Sys.setenv("NOT_CRAN" = TRUE)
-                  install.packages(c("arrow", "gh", "remotes"))
-                  Sys.unsetenv("NOT_CRAN")
-                  remotes::install_url("https://github.com/midas-network/SMHvalidation/archive/refs/heads/version.zip")
-                  remotes::install_url("https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/archive/refs/heads/main.zip")'
-          env:
-            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-        - name: Run Validation
-          run: |
-            Rscript code/validation.R
-          env:
-            GH_PR_NUMBER: ${{ github.event.pull_request.number }}
-            GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/code/validation.R b/code/validation.R
index 7d3f582..b2a12ec 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -5,7 +5,7 @@ library(dplyr)
 # Check if validation need to run
 print(length(Sys.getenv("GH_COMMIT_SHA")))
 
-if (length(Sys.getenv("GH_COMMIT_SHA")) > 1) {
+if (length(Sys.getenv("GH_COMMIT_SHA")) > 0) {
   test <- gh::gh(paste0("GET /repos/",
                         "midas-network/example_round-scenariohub/commits/",
                         Sys.getenv("GH_COMMIT_SHA")))

From e2c079c34e8821105999b5c56fde3756f99e8ba8 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 13:09:19 -0400
Subject: [PATCH 40/47] Update ubuntu version

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

diff --git a/.github/workflows/install_cache_dependencies.yml b/.github/workflows/install_cache_dependencies.yml
index b8d034d..2d80820 100644
--- a/.github/workflows/install_cache_dependencies.yml
+++ b/.github/workflows/install_cache_dependencies.yml
@@ -8,7 +8,7 @@ on:
 
 jobs:
     cache-R-library:
-        runs-on: ubuntu-20.04
+        runs-on: ubuntu-latest
 
         steps:
         - name: Checkout repository

From 1272e050ad9e1a40ccd936278f67d97bfdd2edff Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 13:10:55 -0400
Subject: [PATCH 41/47] Update validation.yml

---
 .github/workflows/validation.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 985fb62..7f08313 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -9,7 +9,7 @@ on:
 
 jobs:
     validates-files:
-        runs-on: ubuntu-20.04
+        runs-on: ubuntu-latest
 
         steps:
         - name: Checkout repository
@@ -43,19 +43,20 @@ jobs:
           env:
             GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
-        - name: Run Validation
-          if: ( github.event.action == 'synchronize' )
+        - name: Run Validation - Open/reopen
+          if: ( github.event.action != 'synchronize' )
           run: |
             Rscript code/validation.R
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-            GH_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
 
-        - name: Run Validation
-          if: ( github.event.action != 'synchronize' )
+        - name: Run Validation - Synchronize
+          if: ( github.event.action == 'synchronize' )
           run: |
             Rscript code/validation.R
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            GH_COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
+

From f8402c6050d7c06fc6f9f7905ca489163be61f87 Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 13:49:34 -0400
Subject: [PATCH 42/47] Update validation.yml

---
 .github/workflows/validation.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 7f08313..92c6fe1 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -50,6 +50,7 @@ jobs:
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            GH_COMMIT_SHA: ""
 
         - name: Run Validation - Synchronize
           if: ( github.event.action == 'synchronize' )

From 6dca2dc55b279db4e3b9def4ad3459fa009a5eda Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 14:00:04 -0400
Subject: [PATCH 43/47] Update validation.yml

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

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 92c6fe1..95b01a8 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -50,7 +50,7 @@ jobs:
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-            GH_COMMIT_SHA: ""
+            GH_COMMIT_SHA: "none"
 
         - name: Run Validation - Synchronize
           if: ( github.event.action == 'synchronize' )

From bd8de72abaa4fba0a40e141c00129a2e3e7bd416 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 14:12:45 -0400
Subject: [PATCH 44/47] update validation - run check

---
 code/validation.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/code/validation.R b/code/validation.R
index b2a12ec..27d27ee 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -5,13 +5,14 @@ library(dplyr)
 # Check if validation need to run
 print(length(Sys.getenv("GH_COMMIT_SHA")))
 
-if (length(Sys.getenv("GH_COMMIT_SHA")) > 0) {
+if (length(Sys.getenv("GH_COMMIT_SHA")) > 1) {
   test <- gh::gh(paste0("GET /repos/",
                         "midas-network/example_round-scenariohub/commits/",
                         Sys.getenv("GH_COMMIT_SHA")))
   check <- grepl("data-processed/", unique(unlist(purrr::map(test$files,
                                                              "filename"))))
 } else {
+  print(Sys.getenv("GH_COMMIT_SHA"))
   check <-  TRUE
 }
 

From 16372e0e9116023b88f072946759e5d94ff45135 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 14:16:05 -0400
Subject: [PATCH 45/47] fix check run

---
 code/validation.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/code/validation.R b/code/validation.R
index 27d27ee..f0e6a1e 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -3,16 +3,15 @@ library(gh)
 library(dplyr)
 
 # Check if validation need to run
-print(length(Sys.getenv("GH_COMMIT_SHA")))
+print(nchar(Sys.getenv("GH_COMMIT_SHA")))
 
-if (length(Sys.getenv("GH_COMMIT_SHA")) > 1) {
+if (nchar(Sys.getenv("GH_COMMIT_SHA")) > 1) {
   test <- gh::gh(paste0("GET /repos/",
                         "midas-network/example_round-scenariohub/commits/",
                         Sys.getenv("GH_COMMIT_SHA")))
   check <- grepl("data-processed/", unique(unlist(purrr::map(test$files,
                                                              "filename"))))
 } else {
-  print(Sys.getenv("GH_COMMIT_SHA"))
   check <-  TRUE
 }
 

From 08d872f4320c425dd280321f34d507906872f9da Mon Sep 17 00:00:00 2001
From: Lucie Contamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 14:16:36 -0400
Subject: [PATCH 46/47] Update validation.yml

---
 .github/workflows/validation.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 95b01a8..7f08313 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -50,7 +50,6 @@ jobs:
           env:
             GH_PR_NUMBER: ${{ github.event.pull_request.number }}
             GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-            GH_COMMIT_SHA: "none"
 
         - name: Run Validation - Synchronize
           if: ( github.event.action == 'synchronize' )

From e4e4fba87c8fe697032ecf1dc7e9bd9012fe3a59 Mon Sep 17 00:00:00 2001
From: LucieContamin <CONTAMIN@pitt.edu>
Date: Mon, 22 Apr 2024 16:43:33 -0400
Subject: [PATCH 47/47] update validation

---
 code/validation.R | 39 +++++++++++++++++++++++++++------------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/code/validation.R b/code/validation.R
index f0e6a1e..fc0ca1f 100644
--- a/code/validation.R
+++ b/code/validation.R
@@ -19,6 +19,11 @@ if (isFALSE(all(check))) {
   test_tot <- NA
   print("no update in data-processed folder")
 } else {
+  # Prerequisite
+  pop_path <- "data-locations/locations.csv"
+  js_def_file <- "hub-config/tasks.json"
+  lst_gs <- NULL
+
   # check if submissions file
   pr_files <- gh::gh(paste0("GET /repos/",
                             "midas-network/example_round-scenariohub/pulls/",
@@ -30,32 +35,42 @@ if (isFALSE(all(check))) {
     stringr::str_extract(pr_files_name,
                          "data-processed/.+/\\d{4}-\\d{2}-\\d{2}(-.*)?")
   pr_sub_files <- unique(na.omit(pr_sub_files))
-  pr_sub_files <- grep("(A|a)bstract", pr_sub_files, value = TRUE, invert = TRUE)
-  if (all(grepl(".pqt$|.parquet$", pr_sub_files))) {
+  pr_sub_files <- grep("(A|a)bstract", pr_sub_files, value = TRUE,
+                       invert = TRUE)
+  round_id <- unique(stringr::str_extract(pr_sub_files,
+                                          "\\d{4}-\\d{2}-\\d{2}"))
+  config_json <- jsonlite::read_json(js_def_file)
+  rounds_ids <- unique(hubUtils::get_round_ids(config_json))
+  sel_round <- grepl(paste(round_id, collapse = "|"), rounds_ids)
+  if (all(isFALSE(sel_round))) {
+    stop("The round id in the submission file was not recognized, please ",
+         "verify")
+  }
+  if (is.null(unlist(purrr::map(config_json$rounds[sel_round], "partition")))) {
     partition = NULL
   } else {
-    partition = c("origin_date", "target")
-  }
-  pop_path <- "data-locations/locations.csv"
-  js_def_file <- "hub-config/tasks.json"
-  lst_gs <- NULL
+    partition = unlist(purrr::map(config_json$rounds[sel_round], "partition"))
 
+  }
   # Run validation on file corresponding to the submission file format
   if (length(pr_sub_files) > 0) {
-    team_name <- unique(basename(dirname(pr_sub_files)))
-    sub_file_date <- unique(stringr::str_extract(basename(pr_sub_files),
-                                                 "\\d{4}-\\d{2}-\\d{2}"))
     if (!(dir.exists(paste0(getwd(), "/proj_plot"))))
       dir.create(paste0(getwd(), "/proj_plot"))
+    sub_file_date <- unique(stringr::str_extract(basename(pr_sub_files),
+                                                 "\\d{4}-\\d{2}-\\d{2}"))
     if (is.null(partition)) {
+      team_name <- unique(basename(dirname(pr_sub_files)))
       group_files <- paste0(sub_file_date, "-", team_name)
     } else {
       group_files <- sub_file_date
+      file_paths <- stringr::str_extract(pr_sub_files,
+                                         "(?<=data-processed/)(.+\\/)?")
+      team_name <- unique(unlist(purrr::map(strsplit(file_paths, "/"),1)))
     }
     test_tot <- lapply(group_files, function(y) {
       # select submission files
       pr_sub_files_group <- grep(y, pr_sub_files, value = TRUE)
-      pr_sub_files_lst <- pr_files[grepl(pr_sub_files_group,
+      pr_sub_files_lst <- pr_files[grepl(paste(pr_sub_files_group, collapse = "|"),
                                          purrr::map(pr_files, "filename"))]
       pr_sub_files_lst <-
         pr_sub_files_lst[!grepl("(A|a)bstract",
@@ -86,7 +101,7 @@ if (isFALSE(all(check))) {
         val_path <- basename(pr_sub_files_group)
         round_id <- NULL
       } else {
-        val_path <- paste0(getwd(), "/part_sub/", dirname(pr_sub_files_group))
+        val_path <- paste0(getwd(), "/part_sub/data-processed/", team_name, "/")
         round_id <- sub_file_date
       }
       arg_list <- list(path = val_path, js_def = js_def_file, lst_gs = lst_gs,