Merge pull request #1506 from MIT-LCP/gh_action_debug

fix gh actions
MIT-LCP · Mar 23, 2023 · 176be33 · 176be33
2 parents 68cf860 + eae7580
commit 176be33
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Showing 4 changed files with 10 additions and 14 deletions.
diff --git a/.github/workflows/duckdb.yml b/.github/workflows/duckdb.yml
@@ -4,7 +4,7 @@ on:
  types: [submitted]
 
 jobs:
- mimic-iv-sqlite:
+ mimic-iv-duckdb:
  # only run if PR is approved
  if: github.event.review.state == 'approved'
  runs-on: ubuntu-20.04
@@ -13,11 +13,13 @@ jobs:
  - name: Check out repository code
  uses: actions/checkout@v3
 
- - name: Install dependencies and download CLI
+ - name: Download duckdb CLI
  run: |
- apt-get install unzip
  wget https://github.com/duckdb/duckdb/releases/download/v0.6.1/duckdb_cli-linux-amd64.zip
  unzip duckdb_cli-linux-amd64.zip
+ echo "$HOME/.local/bin" >> $GITHUB_PATH
+ mkdir -p "$HOME/.local/bin"
+ mv duckdb "$HOME/.local/bin/duckdb"
 
  - name: Download demo data
  uses: ./.github/actions/download-demo

diff --git a/.github/workflows/mysql.yml b/.github/workflows/mysql.yml
@@ -21,9 +21,9 @@ jobs:
 
  - name: Extract demo data to local folder
  run: |
- mv demo/hosp/*.csv.gz ./
- mv demo/icu/*.csv.gz ./
- mv demo/ed/*.csv.gz ./
+ mv hosp/*.csv.gz ./
+ mv icu/*.csv.gz ./
+ mv ed/*.csv.gz ./
  gzip -d *.csv.gz
 
  - name: Start MySQL service

diff --git a/.github/workflows/psql.yml b/.github/workflows/psql.yml
@@ -30,9 +30,6 @@ jobs:
 
  - name: Download demo data
  uses: ./.github/actions/download-demo
- with:
- gcp-project-id: ${{ secrets.GCP_PROJECT_ID }}
- gcp-sa-key: ${{ secrets.GCP_SA_KEY }}
 
  - name: Install postgresql-client
  run: |
@@ -43,7 +40,7 @@ jobs:
  run: |
  echo "Loading data into psql."
  psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql
- psql -q -h $POSTGRES_HOST -U postgres -v mimic_data_dir=demo -f ${BUILDCODE_PATH}/load_gz.sql
+ psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/load_gz.sql
  echo "Validating build."
  psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results
  
@@ -76,7 +73,7 @@ jobs:
  run: |
  echo "Loading data into psql."
  psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql
- psql -q -h $POSTGRES_HOST -U postgres -v mimic_data_dir=demo/ed -f ${BUILDCODE_PATH}/load_gz.sql
+ psql -q -h $POSTGRES_HOST -U postgres -v mimic_data_dir=ed/ -f ${BUILDCODE_PATH}/load_gz.sql
  echo "Validating build."
  psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results
  

diff --git a/.github/workflows/sqlite.yml b/.github/workflows/sqlite.yml
@@ -24,9 +24,6 @@ jobs:
 
  - name: Download demo data
  uses: ./.github/actions/download-demo
- with:
- gcp-project-id: ${{ secrets.GCP_PROJECT_ID }}
- gcp-sa-key: ${{ secrets.GCP_SA_KEY }}
 
  - name: Load icu/hosp data into SQLite
  run: |