Fix/linting (#1060)

* Fix `golangci-lint` linting issues

* Update deprecated functions

* Update deprecated GitHub Actions

* Update Nextflow and Compliance Tests

* Fix `golangci-lint` issues

* Update GitHub Actions

* Fix test errors

.github/workflows/build.yml

@@ -0,0 +1,44 @@
+name: Funnel Build and Cache
+
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Set up Go 1.x
+      uses: actions/setup-go@v5
+      with:
+        go-version: 1.21
+
+    - name: Check out code
+      uses: actions/checkout@v2
+
+    - name: Cache Funnel binary
+      uses: actions/cache@v3
+      with:
+        path: ./funnel
+        key: ${{ runner.os }}-funnel-bin-${{ hashFiles('**/go.sum') }}-${{ github.ref }}
+        restore-keys: |
+          ${{ runner.os }}-funnel-bin-${{ github.ref }}
+          ${{ runner.os }}-funnel-bin-
+
+    - name: Build Funnel (if cache doesn't exist)
+      run: |
+        if [ ! -f ./funnel ]; then
+          make build
+        fi
+    
+    - name: Cache Funnel binary (after build)
+      uses: actions/cache@v3
+      with:
+        path: ./funnel
+        key: ${{ runner.os }}-funnel-bin-${{ hashFiles('**/go.sum') }}-${{ github.ref }}
+
+    - name: Upload Funnel binary as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: funnel
+        path: funnel

.github/workflows/compliance.yaml

@@ -0,0 +1,85 @@
+# Workflow for running the TES compliance suite against Funnel
+#
+# This includes the following steps:
+#  1. Build Funnel and store the resulting binary artifact
+#  2. Install tes-compliance-suite and run against every version of TES simultaneously
+#  3. start-report-deployment: Send a dispatch to the funnel-compliance repository to generate and publish
+#     the tes-compliance-suite report to https://ohsu-comp-bio.github.io/funnel-compliance/
+#
+# Optionally debug via SSH
+# Ref: https://fleetdm.com/engineering/tips-for-github-actions-usability
+#
+# To use this step uncomment and place anywhere in the build steps. The build will pause on this step and
+# output a ssh address associated with the Github action worker. Helpful for debugging build steps and
+# and intermediary files/artifacts.
+#
+# - name: "Debug: Package dependancies for tmate (CentOS)"
+#   run: |
+#     yum install -y xz
+#     ln -s /bin/true /bin/apt-get
+#
+# - name: Setup tmate session
+#   uses: mxschmitt/action-tmate@v3
+
+name: Compliance Test
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+    uses: ./.github/workflows/build.yml
+
+  compliance:
+    strategy:
+      fail-fast: false
+      matrix:
+        version: [1.0.0, 1.1.0]
+        db: ["boltdb", "mongodb"]
+        compute: ["local", "kubernetes"]
+        storage: ["local", "s3"]
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      # Required to access the 'tests/mongo.config.yml' file
+      # Perhaps uploading it as an artifact would be more efficient?
+      - name: Check out code
+        uses: actions/checkout@v2
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: funnel
+
+      - name: Start Funnel server
+        run: |
+          touch config.yml
+
+          if [ ${{ matrix.db }} = "mongodb" ]; then
+            make start-mongodb
+            cat `pwd`/tests/mongo.config.yml >> config.yml
+          fi
+
+          if [ ${{ matrix.storage }} = "s3" ]; then
+            docker run -d -p 9000:9000 --name minio \
+                       -e "MINIO_ROOT_USER=minioadmin" \
+                       -e "MINIO_ROOT_PASSWORD=minioadmin" \
+                       -v /tmp/data:/data \
+                       -v /tmp/config:/root/.minio \
+                       minio/minio server /data
+            cat `pwd`/tests/s3.config.yml >> config.yml
+          fi
+
+          chmod +x funnel
+          ./funnel server run --config `pwd`/config.yml &> funnel.logs &
+
+      - name: Run OpenAPI Test Runner
+        run: |
+          git clone https://github.com/elixir-cloud-aai/openapi-test-runner
+          cd openapi-test-runner
+          python3 -m venv venv
+          source venv/bin/activate
+          pip install -r requirements.txt
+          python setup.py install  
+          openapi-test-runner report --version "${{ matrix.version }}" --server "http://localhost:8000/"
+

.github/workflows/nextflow.yaml

@@ -2,55 +2,34 @@ name: Nextflow Test
 
 on:
   push:
+  pull_request:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Set up Go 1.x
-      uses: actions/setup-go@v2
-      with:
-        go-version: 1.21
-
-    - name: Check out code
-      uses: actions/checkout@v2
-
-    - name: Build Funnel (if cache does not exist)
-      run: make build
+    uses: ./.github/workflows/build.yml
 
-    - name: Store Funnel
-      uses: actions/upload-artifact@v2
-      with:
-        name: funnelBin
-        path: funnel
-
   nextflow:
-    runs-on: ubuntu-latest
     needs: build
+    runs-on: ubuntu-latest
     steps:
     - name: Download Funnel
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
-        name: funnelBin
-        path: funnel
+        name: funnel
 
     - name: Start Funnel
-      working-directory: 
       run: |
-        cd funnel/
         chmod +x ./funnel
         ./funnel server --LocalStorage.AllowedDirs $HOME run &
 
     - name: Install Nextflow
       run: |
-        cd ..
-        git clone https://github.com/nextflow-io/nextflow/ -b tes-update-1.1
+        git clone https://github.com/nextflow-io/nextflow
         cd nextflow
         make compile
 
     - name: Install nf-canary and GA4GH-TES plugin
       run: |
-        cd ..
         git clone https://github.com/seqeralabs/nf-canary
         cd nf-canary
         cat <<EOF >> nextflow.config
@@ -60,8 +39,7 @@ jobs:
           process.executor = 'tes'
           tes.endpoint = 'http://localhost:8000'
         EOF
-  
+
     - name: Run nf-canary tests
       run: |
-        cd ../nf-canary
-        ../nextflow/launch.sh run main.nf
+        ./nextflow/nextflow run nf-canary/main.nf