diff --git a/.github/workflows/after-validate-submission.yaml b/.github/workflows/after-validate-submission.yaml index df7e98a6..98792001 100644 --- a/.github/workflows/after-validate-submission.yaml +++ b/.github/workflows/after-validate-submission.yaml @@ -5,7 +5,7 @@ on: # workflows: ["Hub Submission Validation (R)"] # The name of the workflow we want to trigger from # types: # - completed - pull_request: + pull_request_target: types: - closed @@ -23,11 +23,12 @@ jobs: - name: Checkout and push to another repository uses: actions/checkout@v2 with: - repository: HopkinsIDD/rsv-forecast-hub_data #repository: kjsato/rsv-forecast-hub_data + repository: HopkinsIDD/rsv-forecast-hub_data token: ${{ secrets.KJ3_PATC }} path: ./rsv-forecast-hub_data fetch-depth: 2 + ref: main - name: Copy new files run: | diff --git a/.github/workflows/copy_data.yaml b/.github/workflows/copy_data.yaml new file mode 100644 index 00000000..0413872d --- /dev/null +++ b/.github/workflows/copy_data.yaml @@ -0,0 +1,47 @@ +name: copy data for maintenance + +on: + workflow_dispatch: + +jobs: + copy-files-to-rsv-data-repo: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v2 + with: + fetch-depth: 2 + + - name: Checkout and push to another repository + uses: actions/checkout@v2 + with: + #repository: kjsato/rsv-forecast-hub_data + repository: HopkinsIDD/rsv-forecast-hub_data + token: ${{ secrets.KJ3_PATC }} + path: ./rsv-forecast-hub_data + fetch-depth: 2 + ref: main + + - name: Copy new files + run: | + for FILE in model-output/**/* model-metadata/*; do + if [ -f "$FILE" ]; then + mkdir -p ./rsv-forecast-hub_data/$(dirname $FILE) + cp $FILE ./rsv-forecast-hub_data/$FILE + fi + done + + - name: Commit and push new files + run: | + cd ./rsv-forecast-hub_data + git config user.name "github-actions[bot]" + git config user.email "41898282+github-actions[bot]@users.noreply.github.com" + if [ -n "$(git status --porcelain)" ]; then + git add . + git commit -m "Upload new files to RSV data repo" + git push + echo "RSV data uploaded"; + else + echo "no upload"; + fi + shell: bash diff --git a/.github/workflows/token_test.yaml b/.github/workflows/token_test.yaml new file mode 100644 index 00000000..3c9a983f --- /dev/null +++ b/.github/workflows/token_test.yaml @@ -0,0 +1,21 @@ +name: Test Token + +on: + workflow_dispatch: + +jobs: + test: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository with KJ3_PATC token + uses: actions/checkout@v2 + with: + repository: HopkinsIDD/rsv-forecast-hub_data + token: ${{ secrets.KJ3_PATC }} + path: ./rsv-forecast-hub_data + fetch-depth: 2 + ref: main + + - name: List files in the repository + run: ls -la diff --git a/model-metadata/PSI-PROF.yaml b/model-metadata/PSI-PROF.yaml new file mode 100644 index 00000000..18680ac7 --- /dev/null +++ b/model-metadata/PSI-PROF.yaml @@ -0,0 +1,32 @@ +schema_version: "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/admin-schema.json" +team_name: "Predictive Science Inc." +team_abbr: "PSI" +model_name: "Package for Respiratory Disease Open-source Forecasting" +model_abbr: "PROF" +model_version: "1.0" +model_contributors: [ + { + "name": "Michal Ben-Nun", + "affiliation": "Predictive Science Inc", + "email": "mbennun@predsci.com" + }, + { + "name": "James Turtle", + "affiliation": "Predictive Science Inc", + "email": "jturtle@predsci.com" + }, + { + "name": "Pete Riley", + "affiliation": "Predictive Science Inc", + "email": "pete@predsci.com" + } +] +website_url: "https://www.predsci.com/usa-flu-hosp/" +license: "CC-BY-4.0" +citation: "https://doi.org/10.1371/journal.pcbi.1010375" +team_funding: "CSTE/CDC: Development of Forecasts and/or Scenario Projections for Influenza to Inform Public Health Decision Making (Cooperative Agreement number NU38OT000297)." +methods: "We fit and extrapolate an age-stratified SIR compartmental model with four levels of natural immunity as well as infant/elder vaccination." +data_inputs: "Weekly incident flu hospital admissions from RSV-NET. US Census population totals and age distributions by state. Estimated vaccination rates from the Scenario Modeling Hub-RSV Round 1." +methods_long: "Model parameters are determined by a three-phase fitting procedure. 1) Pre-pandemic data is used to determine parameters that characterize the pathogen transmission characteristics. 2) 2020-2023 season data are used to estimate the age-stratified number of susceptibles entering the current season. 3) Fit the timing of each model trajectory to the current late-season data and then filter trajectories for best alignment with the entire season. The model uses 14 age strata (highly concentrated in the very young) so that we can properly account for maternally-conferred immunity in infants." + + diff --git a/model-output/CU-RSV_SVIRS/2024-03-10-CU-RSV_SVIRS.parquet b/model-output/CU-RSV_SVIRS/2024-03-10-CU-RSV_SVIRS.parquet new file mode 100644 index 00000000..c1ad9344 Binary files /dev/null and b/model-output/CU-RSV_SVIRS/2024-03-10-CU-RSV_SVIRS.parquet differ diff --git a/model-output/PSI-PROF/2024-03-03-PSI-PROF.parquet b/model-output/PSI-PROF/2024-03-03-PSI-PROF.parquet new file mode 100644 index 00000000..1ac21447 Binary files /dev/null and b/model-output/PSI-PROF/2024-03-03-PSI-PROF.parquet differ diff --git a/model-output/PSI-PROF/2024-03-10-PSI-PROF.parquet b/model-output/PSI-PROF/2024-03-10-PSI-PROF.parquet new file mode 100644 index 00000000..3e56ddfe Binary files /dev/null and b/model-output/PSI-PROF/2024-03-10-PSI-PROF.parquet differ diff --git a/model-output/UGA_flucast-INFLAenza/2024-03-03-UGA_flucast-INFLAenza.parquet b/model-output/UGA_flucast-INFLAenza/2024-03-03-UGA_flucast-INFLAenza.parquet index 9b7afbee..96fbda2a 100644 Binary files a/model-output/UGA_flucast-INFLAenza/2024-03-03-UGA_flucast-INFLAenza.parquet and b/model-output/UGA_flucast-INFLAenza/2024-03-03-UGA_flucast-INFLAenza.parquet differ diff --git a/model-output/UGA_flucast-INFLAenza/2024-03-10-UGA_flucast-INFLAenza.parquet b/model-output/UGA_flucast-INFLAenza/2024-03-10-UGA_flucast-INFLAenza.parquet new file mode 100644 index 00000000..23522d2e Binary files /dev/null and b/model-output/UGA_flucast-INFLAenza/2024-03-10-UGA_flucast-INFLAenza.parquet differ