Choim troll.flags troll.logfiles logfiles.fill

.github/workflows/build_push_troll.flags.yml

@@ -0,0 +1,47 @@
+name: "Build-push_flow.troll.flags"
+
+on:
+  push:
+    branches:
+      - 'master'
+    paths:
+      - 'flow/flow.troll.flags/**'
+  workflow_dispatch: {} # Allows trigger of workflow from web interface
+
+env:
+  GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
+  # Use github and google registries
+  GHCR_REGISTRY: ghcr.io
+  GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev
+  GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }}
+  GCP_PROVIDER:  ${{ vars.SHARED_WIF_PROVIDER }}
+  GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }}
+  GHCR_NS: battelleecology
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # Get just the repo name from the event, i.e., NEON-IS-data-processing
+  REPO_NAME: ${{ github.event.repository.name }}
+  # IS module name
+  MODULE_PATH: ./flow/flow.troll.flags
+  IMAGE_NAME: neon-is-troll-flags
+
+jobs:
+  build-push:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: 'write'
+        id-token: 'write'
+    steps:
+      - name: "Checkout"
+        uses: "actions/[email protected]"
+        with:
+          fetch-depth: '0'
+
+      - name: Get short SHA
+        run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV
+
+      - name: Build and push
+        uses: ./.github/actions/build-push
+        with:
+            image-tag: "${short_sha}"
+

.github/workflows/build_push_troll.logfiles.fill.yml

@@ -0,0 +1,47 @@
+name: "Build-push_flow.troll.logfiles.fill"
+
+on:
+  push:
+    branches:
+      - 'master'
+    paths:
+      - 'flow/flow.troll.logfiles.fill/**'
+  workflow_dispatch: {} # Allows trigger of workflow from web interface
+
+env:
+  GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
+  # Use github and google registries
+  GHCR_REGISTRY: ghcr.io
+  GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev
+  GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }}
+  GCP_PROVIDER:  ${{ vars.SHARED_WIF_PROVIDER }}
+  GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }}
+  GHCR_NS: battelleecology
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # Get just the repo name from the event, i.e., NEON-IS-data-processing
+  REPO_NAME: ${{ github.event.repository.name }}
+  # IS module name
+  MODULE_PATH: ./flow/flow.troll.logfiles.fill
+  IMAGE_NAME: neon-is-troll-logfiles-fill
+
+jobs:
+  build-push:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: 'write'
+        id-token: 'write'
+    steps:
+      - name: "Checkout"
+        uses: "actions/[email protected]"
+        with:
+          fetch-depth: '0'
+
+      - name: Get short SHA
+        run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV
+
+      - name: Build and push
+        uses: ./.github/actions/build-push
+        with:
+            image-tag: "${short_sha}"
+

.github/workflows/build_push_troll.logfiles.yml

@@ -0,0 +1,47 @@
+name: "Build-push_flow.troll.logfiles"
+
+on:
+  push:
+    branches:
+      - 'master'
+    paths:
+      - 'flow/flow.troll.logfiles/**'
+  workflow_dispatch: {} # Allows trigger of workflow from web interface
+
+env:
+  GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
+  # Use github and google registries
+  GHCR_REGISTRY: ghcr.io
+  GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev
+  GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }}
+  GCP_PROVIDER:  ${{ vars.SHARED_WIF_PROVIDER }}
+  GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }}
+  GHCR_NS: battelleecology
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # Get just the repo name from the event, i.e., NEON-IS-data-processing
+  REPO_NAME: ${{ github.event.repository.name }}
+  # IS module name
+  MODULE_PATH: ./flow/flow.troll.logfiles
+  IMAGE_NAME: neon-is-troll-logfiles
+
+jobs:
+  build-push:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: 'write'
+        id-token: 'write'
+    steps:
+      - name: "Checkout"
+        uses: "actions/[email protected]"
+        with:
+          fetch-depth: '0'
+
+      - name: Get short SHA
+        run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV
+
+      - name: Build and push
+        uses: ./.github/actions/build-push
+        with:
+            image-tag: "${short_sha}"
+

.github/workflows/build_push_update_troll.flags.yml

@@ -0,0 +1,51 @@
+name: "Build-push-update_flow.troll.flags"
+
+on:
+  push:
+    # branches:
+    #   - 'master'
+    tags:
+      - "flow.troll.flags/v*.*.*"
+env:
+  GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
+  GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # Use github and google registries
+  GHCR_REGISTRY: ghcr.io
+  GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev
+  GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }}
+  GCP_PROVIDER:  ${{ vars.SHARED_WIF_PROVIDER }}
+  GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }}
+  GHCR_NS: battelleecology
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  # IMAGE_NAME: ${{ github.repository }}
+  # Get just the repo name from the event, i.e., NEON-IS-data-processing
+  REPO_NAME: ${{ github.event.repository.name }}
+  # IS module name
+  MODULE_PATH: ./flow/flow.troll.flags
+  IMAGE_NAME: neon-is-troll-flags
+
+jobs:
+  build-push-update:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: 'write'
+        id-token: 'write'
+        pull-requests: 'write'
+
+    steps:
+      - name: "Checkout"
+        uses: "actions/[email protected]"
+        with:
+          ref: 'master'
+          fetch-depth: '0'
+
+      - name: Get short SHA
+        run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV
+
+      - name: Get semver
+        run:  echo "semver=$(git describe --tags --abbrev=0 --match=flow.troll.flags/v*.*.* | awk -F "/" '{print $2}')" >> $GITHUB_ENV 
+
+      - name: Build push and update
+        uses: ./.github/actions/build-push-update

.github/workflows/build_push_update_troll.logfiles.fill.yml

@@ -0,0 +1,51 @@
+name: "Build-push-update_flow.troll.logfiles.fill"
+
+on:
+  push:
+    # branches:
+    #   - 'master'
+    tags:
+      - "flow.troll.logfiles.fill/v*.*.*"
+env:
+  GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
+  GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # Use github and google registries
+  GHCR_REGISTRY: ghcr.io
+  GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev
+  GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }}
+  GCP_PROVIDER:  ${{ vars.SHARED_WIF_PROVIDER }}
+  GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }}
+  GHCR_NS: battelleecology
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  # IMAGE_NAME: ${{ github.repository }}
+  # Get just the repo name from the event, i.e., NEON-IS-data-processing
+  REPO_NAME: ${{ github.event.repository.name }}
+  # IS module name
+  MODULE_PATH: ./flow/flow.troll.logfiles.fill
+  IMAGE_NAME: neon-is-troll-logfiles-fill
+
+jobs:
+  build-push-update:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: 'write'
+        id-token: 'write'
+        pull-requests: 'write'
+
+    steps:
+      - name: "Checkout"
+        uses: "actions/[email protected]"
+        with:
+          ref: 'master'
+          fetch-depth: '0'
+
+      - name: Get short SHA
+        run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV
+
+      - name: Get semver
+        run:  echo "semver=$(git describe --tags --abbrev=0 --match=flow.troll.logfiles.fill/v*.*.* | awk -F "/" '{print $2}')" >> $GITHUB_ENV 
+
+      - name: Build push and update
+        uses: ./.github/actions/build-push-update

.github/workflows/build_push_update_troll.logfiles.yml

@@ -0,0 +1,51 @@
+name: "Build-push-update_flow.troll.logfiles"
+
+on:
+  push:
+    # branches:
+    #   - 'master'
+    tags:
+      - "flow.troll.logfiles/v*.*.*"
+env:
+  GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}
+  GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # Use github and google registries
+  GHCR_REGISTRY: ghcr.io
+  GCP_ARTIFACT_HOST: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev
+  GCP_REGISTRY: ${{ vars.SHARED_WIF_LOCATON }}-docker.pkg.dev/${{ vars.SHARED_WIF_PROJECT }}/${{ vars.SHARED_WIF_REPO }}
+  GCP_PROVIDER:  ${{ vars.SHARED_WIF_PROVIDER }}
+  GCP_SERVICE_ACCOUNT: ${{ vars.SHARED_WIF_SERVICE_ACCOUNT }}
+  GHCR_NS: battelleecology
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  # IMAGE_NAME: ${{ github.repository }}
+  # Get just the repo name from the event, i.e., NEON-IS-data-processing
+  REPO_NAME: ${{ github.event.repository.name }}
+  # IS module name
+  MODULE_PATH: ./flow/flow.troll.logfiles
+  IMAGE_NAME: neon-is-troll-logfiles
+
+jobs:
+  build-push-update:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: 'write'
+        id-token: 'write'
+        pull-requests: 'write'
+
+    steps:
+      - name: "Checkout"
+        uses: "actions/[email protected]"
+        with:
+          ref: 'master'
+          fetch-depth: '0'
+
+      - name: Get short SHA
+        run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_ENV
+
+      - name: Get semver
+        run:  echo "semver=$(git describe --tags --abbrev=0 --match=flow.troll.logfiles/v*.*.* | awk -F "/" '{print $2}')" >> $GITHUB_ENV 
+
+      - name: Build push and update
+        uses: ./.github/actions/build-push-update

flow/flow.troll.flags/Dockerfile

@@ -3,12 +3,15 @@
 # Start with the neon-is-base-r image.
 FROM us-central1-docker.pkg.dev/neon-shared-service/neonscience/neon-is-pack-base-r:v1.4.7
 
+ARG FLOW_DIR="./flow"
+ARG APP_DIR="flow.troll.flags"
+
 # maintainer handle
 MAINTAINER "Nora Catolico" [email protected]
 
 # Copy the lockfile and restore known working versions of R dependency packages
 # ENSURE that the renv.lock file is up-to-date and thus has all listed dependencies prior to creating this docker image
-COPY ./renv.lock /renv.lock
+COPY ${FLOW_DIR}/${APP_DIR}/renv.lock /renv.lock
 RUN R -e 'renv::restore(lockfile="/renv.lock")'
 
 # Create app user
@@ -17,8 +20,8 @@ RUN groupadd app && \
 WORKDIR /home/app
 
 # Copy in troll flag workflow
-COPY ./flow.troll.flags.R .
-COPY ./wrap.troll.flags.R .
+COPY ${FLOW_DIR}/${APP_DIR}/flow.troll.flags.R .
+COPY ${FLOW_DIR}/${APP_DIR}/wrap.troll.flags.R .
 
 # Run as app user
 RUN chown app:app -R /home/app

flow/flow.troll.logfiles.fill/Dockerfile

@@ -3,15 +3,18 @@
 # Start with the neon-is-base-r image.
 FROM us-central1-docker.pkg.dev/neon-shared-service/neonscience/neon-is-pack-base-r:v1.4.7
 
+ARG FLOW_DIR="./flow"
+ARG APP_DIR="flow.troll.logfiles.fill"
+
 # maintainer handle
 MAINTAINER "Nora Catolico" [email protected]
 
 # Copy the lockfile and restore known working versions of R dependency packages
 # ENSURE that the renv.lock file is up-to-date and thus has all listed dependencies prior to creating this docker image
-COPY ./renv.lock /renv.lock
+COPY ${FLOW_DIR}/${APP_DIR}/renv.lock /renv.lock
 RUN R -e 'renv::restore(lockfile="/renv.lock")'
 
 # Copy in troll flag workflow
-COPY ./flow.troll.logfiles.fill.R .
-COPY ./wrap.troll.logfiles.fill.R .
+COPY ${FLOW_DIR}/${APP_DIR}/flow.troll.logfiles.fill.R .
+COPY ${FLOW_DIR}/${APP_DIR}/wrap.troll.logfiles.fill.R .