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thetechnocrat-dev
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[LAB-630] bacalhau 1.1.0 compose (#693)
Co-authored-by: thetechnocrat-dev <josh.mcmenemy@openzyme.bio>
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Lines changed: 220 additions & 39 deletions

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‎.github/actions/gateway-tests/action.yml‎

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name: 'Gateway Tests'
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description: 'Tests that gateway features work'
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runs:
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using: 'composite'
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steps:
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- name: Test healthcheck endpoint
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run: |
8+
response=$(curl --silent http://localhost:8080/healthcheck)
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if [[ "$response" != "Healthy" ]]; then
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echo "Test 1 failed: Expected 'Healthy' but got '$response'"
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exit 1
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else
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echo "Gateway Healthcheck passed"
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fi
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shell: bash
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- name: Test add Datafile endpoint
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run: |
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# upload first file
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response=$(curl --silent -X POST \
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-F "file=@testdata/binding/abl/7n9g.pdb;filename=7n9g.pdb" \
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-F "filename=7n9g.pdb" \
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-F "wallet_address=0xd8dA6BF26964aF9D7eEd9e03E53415D37aA96045" \
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http://localhost:8080/datafiles)
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if echo "$response" | jq -e '.cid' > /dev/null; then
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echo "File upload test passed"
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else
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echo "File upload test failed: 'cid' key not found in the response"
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exit 1
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fi
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# upload second file
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response=$(curl --silent -X POST \
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-F "file=@testdata/binding/abl/ZINC000003986735.sdf;filename=ZINC000003986735.sdf" \
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-F "filename=ZINC000003986735.sdf" \
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-F "wallet_address=0xd8dA6BF26964aF9D7eEd9e03E53415D37aA96045" \
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http://localhost:8080/datafiles)
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if echo "$response" | jq -e '.cid' > /dev/null; then
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echo "File upload test passed"
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else
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echo "File upload test failed: 'cid' key not found in the response"
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exit 1
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fi
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shell: bash
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- name: Test List Datafiles Endpoint
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run: |
48+
response=$(curl --silent http://localhost:8080/datafiles)
49+
length=$(echo "$response" | jq 'length')
50+
51+
if [ "$length" -eq 2 ]; then
52+
echo "Datafiles test passed"
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else
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echo "Datafiles test failed: Expected length of 2 but got '$length'"
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exit 1
56+
fi
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shell: bash
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- name: Test add Tool Endpoint
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run: |
61+
TOOL_JSON_CONTENT=$(jq -c . < tools/equibind.json)
62+
json_payload="{\"toolJson\": $TOOL_JSON_CONTENT, \"walletAddress\": \"0xab5801a7d398351b8be11c439e05c5b3259aec9b\"}"
63+
response=$(curl -s -X POST "http://localhost:8080/tools" \
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-H "Content-Type: application/json" \
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-d "$json_payload")
66+
67+
cid_value=$(echo "$response" | jq -r '.cid')
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if [ "$cid_value" == "QmTFMb527A3VDCmVNwC1d6yCM3eUdvLwHsEXwtRULeczZ2" ]; then
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echo "Add Tool upload test passed"
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else
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echo "Add Tool upload test failed: Expected 'QmTFMb527A3VDCmVNwC1d6yCM3eUdvLwHsEXwtRULeczZ2' but got '$cid_value'"
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exit 1
74+
fi
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shell: bash
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- name: Test list Tools Endpoint
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run: |
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response=$(curl --silent http://localhost:8080/tools)
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length=$(echo "$response" | jq 'length')
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if [ "$length" -eq 1 ]; then
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echo "List Tools test passed"
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else
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echo "List Tools test failed: Expected length of 1 but got '$length'"
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exit 1
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fi
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shell: bash
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- name: Test Add Flow Endpoint
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run: |
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payload='{
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"name": "testFlow",
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"walletAddress": "0xab5801a7d398351b8be11c439e05c5b3259aec9b",
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"toolCid": "QmTFMb527A3VDCmVNwC1d6yCM3eUdvLwHsEXwtRULeczZ2",
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"scatteringMethod": "dotProduct",
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"kwargs": {
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"protein": ["QmUWCBTqbRaKkPXQ3M14NkUuM4TEwfhVfrqLNoBB7syyyd/7n9g.pdb"],
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"small_molecule": ["QmV6qVzdQLNM6SyEDB3rJ5R5BYJsQwQTn1fjmPzvCCkCYz/ZINC000003986735.sdf"]
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}
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}'
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response=$(curl -s -X POST "http://localhost:8080/flows" \
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-H "Content-Type: application/json" \
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-d "$payload")
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# Extract the CID from the response
108+
cid_value=$(echo "$response" | jq -r '.cid')
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# Check if the CID exists
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if [[ ! -z "$cid_value" && "$cid_value" != "null" ]]; then
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echo "Create Flow test passed"
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else
114+
echo "Create Flow test failed: CID not found in the response"
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exit 1
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fi
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shell: bash

‎.github/workflows/ci.yml‎

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Original file line numberDiff line numberDiff line change
@@ -103,23 +103,24 @@ jobs:
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strategy:
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matrix:
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os: [ubuntu-22.04]
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bacalhau_version: [1.0.3, 1.1.0]
106107
runs-on: ${{ matrix.os }}
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environment: ci
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steps:
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- name: Download bacalhau
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run: |
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# Download bacalhau plugin
112113
if [[ "$OSTYPE" == "linux-gnu"* ]]; then
113-
curl -sSL https://github.com/bacalhau-project/bacalhau/releases/download/v1.0.3/bacalhau_v1.0.3_linux_amd64.tar.gz -o bacalhau.tgz
114+
curl -sSL https://github.com/bacalhau-project/bacalhau/releases/download/v${{ matrix.bacalhau_version }}/bacalhau_v${{ matrix.bacalhau_version }}_linux_amd64.tar.gz -o bacalhau.tgz
114115
elif [[ "$OSTYPE" == "darwin"* ]]; then
115-
curl -sSL https://github.com/bacalhau-project/bacalhau/releases/download/v1.0.3/bacalhau_v1.0.3_darwin_arm64.tar.gz -o bacalhau.tgz
116+
curl -sSL https://github.com/bacalhau-project/bacalhau/releases/download/v${{ matrix.bacalhau_version }}/bacalhau_v${{ matrix.bacalhau_version }}_darwin_arm64.tar.gz -o bacalhau.tgz
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fi
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tar -zxvf bacalhau.tgz
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- name: upload bacalhau plugin to be used later
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uses: actions/upload-artifact@v3
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with:
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name: bacalhau-binary-${{matrix.os}}
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name: bacalhau-binary-${{matrix.os}}-${{matrix.bacalhau_version}}
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path: ./bacalhau
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125126
ci-public:
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strategy:
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matrix:
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os: [ubuntu-22.04] # , macos-13]
134+
bacalhau_version: [1.0.3, 1.1.0]
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runs-on: ${{ matrix.os }}
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environment: ci
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env:
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- name: download bacalhau binary
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uses: actions/download-artifact@v3
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with:
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name: bacalhau-binary-${{matrix.os}}
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name: bacalhau-binary-${{matrix.os}}-${{matrix.bacalhau_version}}
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153155
- name: download docker compose plugin artifact
154156
if: runner.os != 'macos'
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NEXT_PUBLIC_PRIVY_APP_ID: ${{ secrets.NEXT_PUBLIC_PRIVY_APP_ID }}
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- name: Bring up the stack
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if: matrix.bacalhau_version == '1.0.3'
195198
run: |
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# Setup docker compose private
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# Setup docker compose
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docker compose up -d --wait
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- name: Bring up the stack
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if: matrix.bacalhau_version == '1.1.0'
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run: |
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# Setup docker compose 1.1.0
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docker compose -f docker-compose.yml -f docker-compose.1.1.0.yml up -d --wait
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- name: Run docker compose ps
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run: |
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# Inspect number of running containers
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docker compose ps
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- name: Run Equibind
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if: matrix.bacalhau_version == '1.0.3'
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run: |
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# Add execute permission
204217
chmod +x plex
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find . -name '*docked.sdf' | grep 'docked.sdf'
214227
fi
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- name: Run docker compose logs
217-
# run always even when
218-
if: always()
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run: |
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docker compose logs
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- name: Run bacalhau describe
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if: matrix.bacalhau_version == '1.0.3'
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# run always even when
224-
if: always()
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run: |
226233
# Execute permission
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chmod +x ./bacalhau
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./bacalhau version
228236
JOB_ID=$(./bacalhau list --output json | jq -r '.[0].State.JobID')
229237
./bacalhau describe ${JOB_ID}
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- name: Run Gateway Integration Tests
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uses: ./.github/actions/gateway-tests
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- name: Run docker compose logs
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# run always even when
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if: always()
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run: |
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docker compose logs
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231248
- name: upload outputs
232249
# run always even when
233250
if: always()
234251
uses: actions/upload-artifact@v3
235252
with:
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name: ci-public-output-${{matrix.os}}
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name: ci-public-output-${{matrix.os}}-${{matrix.bacalhau_version}}
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path: |
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job-*
239256
jobs/
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strategy:
248265
matrix:
249266
os: [ubuntu-22.04] # , macos-13]
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bacalhau_version: [1.0.3, 1.1.0]
250268
runs-on: ${{ matrix.os }}
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environment: ci
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env:
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# Setting it at workflow level to be used by all the steps
254272
BACALHAU_API_HOST: "127.0.0.1"
255-
NEXT_PUBLIC_PRIVY_APP_ID: "{{ secrets.NEXT_PUBLIC_PRIVY_APP_ID }}"
273+
NEXT_PUBLIC_PRIVY_APP_ID: "${{ secrets.NEXT_PUBLIC_PRIVY_APP_ID }}"
256274
steps:
257275
- name: Checkout code
258276
uses: actions/checkout@v4
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270288
- name: download bacalhau binary
271289
uses: actions/download-artifact@v3
272290
with:
273-
name: bacalhau-binary-${{matrix.os}}
291+
name: bacalhau-binary-${{matrix.os}}-${{matrix.bacalhau_version}}
274292

275293
- name: download docker compose plugin artifact
276294
if: runner.os != 'macos'
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314332
NEXT_PUBLIC_PRIVY_APP_ID: ${{ secrets.NEXT_PUBLIC_PRIVY_APP_ID }}
315333

316334
- name: Bring up the stack
335+
if: matrix.bacalhau_version == '1.0.3'
317336
run: |
318337
# Setup docker compose private
319338
docker compose -f docker-compose.yml -f docker-compose.private.yml up -d --wait
339+
340+
- name: Bring up the stack
341+
if: matrix.bacalhau_version == '1.1.0'
342+
run: |
343+
# Setup docker compose private
344+
docker compose -f docker-compose.yml -f docker-compose.1.1.0.yml -f docker-compose.private.yml up -d --wait
345+
346+
- name: Run docker compose ps
347+
run: |
320348
# Inspect number of running containers
321349
docker compose ps
322350
323351
- name: Run Equibind
352+
if: matrix.bacalhau_version == '1.0.3'
324353
run: |
325354
set -x
326355
# Add execute permission
@@ -351,27 +380,30 @@ jobs:
351380
find . -name '*docked.sdf' | grep 'docked.sdf'
352381
fi
353382
354-
- name: Run docker compose logs
355-
# run always even when
356-
if: always()
357-
run: |
358-
docker compose logs
359-
360383
- name: Run bacalhau describe
361-
# run always even when
362-
if: always()
384+
if: matrix.bacalhau_version == '1.0.3'
363385
run: |
364386
# Execute permission
365387
chmod +x ./bacalhau
388+
./bacalhau version
366389
JOB_ID=$(./bacalhau list --output json | jq -r '.[0].State.JobID')
367390
./bacalhau describe ${JOB_ID}
368391
392+
- name: Run Gateway Integration Tests
393+
uses: ./.github/actions/gateway-tests
394+
395+
- name: Run docker compose logs
396+
# run always even when
397+
if: always()
398+
run: |
399+
docker compose logs
400+
369401
- name: upload outputs
370402
# run always even when
371403
if: always()
372404
uses: actions/upload-artifact@v3
373405
with:
374-
name: ci-private-output-${{matrix.os}}
406+
name: ci-private-output-${{matrix.os}}-${{matrix.bacalhau_version}}
375407
path: |
376408
job-*
377409
jobs/

‎docker-compose.1.1.0.yml‎

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---
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3+
version: "3.7"
4+
5+
services:
6+
# sidecar container for setting up required key material
7+
requester_setup:
8+
image: "alpine"
9+
command: >
10+
sh -c '
11+
mkdir -p /home/nonroot/.bacalhau &&
12+
echo 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 > /home/nonroot/.bacalhau/libp2p_private_key &&
13+
chown -R 65532:65532 /home/nonroot/'
14+
15+
requester:
16+
image: "ghcr.io/bacalhau-project/bacalhau:v1.1.0"
17+
18+
# sidecar container for requester healthcheck
19+
requester_health:
20+
healthcheck:
21+
test: curl -f http://requester:1234/api/v1/healthz
22+
interval: 10s
23+
timeout: 10s
24+
retries: 10
25+
start_period: 10s
26+
27+
compute:
28+
image: "ghcr.io/bacalhau-project/bacalhau:v1.1.0"
29+
30+
# sidecar container for compute healthcheck
31+
compute_health:
32+
healthcheck:
33+
test: curl -f http://requester:1234/api/v1/healthz
34+
interval: 10s
35+
timeout: 10s
36+
retries: 10
37+
start_period: 10s

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