Merge branch 'european-modelling-hubs:main' into main

sfiandrino · Mar 12, 2024 · 9b6d183 · 9b6d183
2 parents bd19cdc + f1a8ab0
commit 9b6d183
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diff --git a/.github/data-storage/changes_db.json b/.github/data-storage/changes_db.json
@@ -1,9 +1,29 @@
 {
+    "ISI": [
+        {
+            "model": "AriABCaster",
+            "changes": [
+                "model-output/ISI-AriABCaster/2024-03-13-ISI-AriABCaster.csv"
+            ]
+        },
+        {
+            "model": "GenLogModelAri",
+            "changes": [
+                "model-output/ISI-GenLogModelAri/2024-03-13-ISI-GenLogModelAri.csv"
+            ]
+        }
+    ],
     "ECDC": [
         {
-            "model": "ARI2MA",
+            "model": "norrsken_blue",
+            "changes": [
+                "model-output/ECDC-norrsken_blue/2024-03-13-ECDC-norrsken_blue.csv"
+            ]
+        },
+        {
+            "model": "norrsken_green",
             "changes": [
-                "model-output/ECDC-ARI2MA/2024-03-06-ECDC-ARI2MA.csv"
+                "model-output/ECDC-norrsken_green/2024-03-13-ECDC-norrsken_green.csv"
             ]
         }
     ]

diff --git a/.github/data-storage/target_db.json b/.github/data-storage/target_db.json
@@ -1,8 +1,8 @@
 {
     "ARI incidence": {
         "changes": [
-            "target-data/ERVISS/snapshots/2024-03-01-ARI_incidence.csv",
-            "target-data/FluID/snapshots/2024-03-01-ARI_incidence.csv"
+            "target-data/FluID/snapshots/2024-03-08-ARI_incidence.csv",
+            "target-data/ERVISS/snapshots/2024-03-08-ARI_incidence.csv"
         ]
     }
 }
diff --git a/.github/logs/ensemble-members/2024-03-06-respicast-hubEnsemble-ensemble_models.json b/.github/logs/ensemble-members/2024-03-06-respicast-hubEnsemble-ensemble_models.json
@@ -0,0 +1 @@
+[{"target":["ARI incidence"],"countries":[{"id":["BG"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["CZ"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["DE"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["EE"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["ES"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["FI"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["FR"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]}]},{"id":["GB-ENG"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA"]},{"horizon":[2],"models":["ECDC-ARI2MA"]},{"horizon":[3],"models":["ECDC-ARI2MA"]},{"horizon":[4],"models":["ECDC-ARI2MA"]}]},{"id":["GB-NIR"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA"]},{"horizon":[2],"models":["ECDC-ARI2MA"]},{"horizon":[3],"models":["ECDC-ARI2MA"]},{"horizon":[4],"models":["ECDC-ARI2MA"]}]},{"id":["GB-SCT"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA"]},{"horizon":[2],"models":["ECDC-ARI2MA"]},{"horizon":[3],"models":["ECDC-ARI2MA"]},{"horizon":[4],"models":["ECDC-ARI2MA"]}]},{"id":["HU"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]}]},{"id":["LT"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["RO"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["SI"],"members":[{"horizon":[1],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[2],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[3],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]},{"horizon":[4],"models":["ECDC-ARI2MA","ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri","fjordhest-ensemble"]}]},{"id":["LV"],"members":[{"horizon":[1],"models":["ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[2],"models":["ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[3],"models":["ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]},{"horizon":[4],"models":["ECDC-norrsken_blue","ECDC-norrsken_green","ECDC-soca_simplex","ISI-AriABCaster","ISI-EpiNowARI","ISI-GenLogModelAri"]}]},{"id":["LU"],"members":[{"horizon":[1],"models":["ECDC-norrsken_green","ISI-EpiNowARI"]},{"horizon":[2],"models":["ECDC-norrsken_green","ISI-EpiNowARI"]},{"horizon":[3],"models":["ECDC-norrsken_green","ISI-EpiNowARI"]},{"horizon":[4],"models":["ECDC-norrsken_green","ISI-EpiNowARI"]}]},{"id":["BE"],"members":[{"horizon":[1],"models":["fjordhest-ensemble"]},{"horizon":[2],"models":["fjordhest-ensemble"]},{"horizon":[3],"models":["fjordhest-ensemble"]},{"horizon":[4],"models":["fjordhest-ensemble"]}]}]}]
diff --git a/.github/workflows/ensemble.yml b/.github/workflows/ensemble.yml
@@ -41,7 +41,7 @@ jobs:
     - name: Installing dependencies
       run: |
         install.packages("remotes")
-        remotes::install_github("Infectious-Disease-Modeling-Hubs/hubUtils")
+        remotes::install_github("Infectious-Disease-Modeling-Hubs/hubData")
         remotes::install_github("Infectious-Disease-Modeling-Hubs/hubEnsembles")
         install.packages("dplyr")
         install.packages("jsonlite")

diff --git a/.github/workflows/scoring.yml b/.github/workflows/scoring.yml
@@ -51,8 +51,9 @@ jobs:
     - name: Installing dependencies
       run: |
         install.packages("remotes")
-        remotes::install_github("Infectious-Disease-Modeling-Hubs/hubUtils")
+        remotes::install_github("Infectious-Disease-Modeling-Hubs/hubData")
         install.packages("dplyr")
+        install.packages('jsonlite')
         install.packages("optparse")
         install.packages("scoringutils")
       shell: Rscript {0}

diff --git a/.github/workflows/upload_baseline_and_ensemble.yml b/.github/workflows/upload_baseline_and_ensemble.yml
@@ -12,8 +12,8 @@ on:
 
 jobs:
   scheduled-submit:
-    # if: ${{ github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'european-modelling-hubs' }}
-    if: ${{ github.repository_owner == 'european-modelling-hubs' }}
+    if: ${{ github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'european-modelling-hubs' }}
+    # if: ${{ github.repository_owner == 'european-modelling-hubs' }}
     runs-on: ubuntu-latest
 
     steps:

diff --git a/.github/workflows/upload_scoring.yml b/.github/workflows/upload_scoring.yml
@@ -14,11 +14,15 @@ on:
 
 jobs:
   scheduled-submit:
-    #if: ${{ github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'european-modelling-hubs' }}
+    if: ${{ github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'european-modelling-hubs' }}
     runs-on: ubuntu-latest
 
     steps:
-
+      # Introduce some delay to complete DB write 
+      - name: Sleep for 90 seconds
+        run: sleep 90s
+        shell: bash
+
       # Checkout the python tools repo
       # used to authenticate and validate the PR
       # -------------------------------------------
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
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