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fix gh actions #1506

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merged 1 commit into from
Mar 23, 2023
Merged

fix gh actions #1506

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fix gh actions
  • Loading branch information
@alistairewj
alistairewj committed Mar 23, 2023
commit eae758000e6b40e7643919c1fe6d4d5ddac9d678
8 changes: 5 additions & 3 deletions .github/workflows/duckdb.yml
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Expand Up @@ -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
Expand All @@ -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
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6 changes: 3 additions & 3 deletions .github/workflows/mysql.yml
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Expand Up @@ -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
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7 changes: 2 additions & 5 deletions .github/workflows/psql.yml
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Expand Up @@ -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: |
Expand All @@ -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

Expand Down Expand Up @@ -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

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3 changes: 0 additions & 3 deletions .github/workflows/sqlite.yml
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Expand Up @@ -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: |
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