From da934d2c39e86c27b70dbbd5eb3a03bbd663dab8 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 25 Apr 2024 14:26:35 -0600
Subject: [PATCH 01/61] adding a new github action for building and pushing
 slim images

---
 .github/workflows/image_build_push_slim.yaml | 183 +++++++++++++++++++
 1 file changed, 183 insertions(+)
 create mode 100644 .github/workflows/image_build_push_slim.yaml

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
new file mode 100644
index 00000000..415cbebf
--- /dev/null
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -0,0 +1,183 @@
+name: Build Slim Image and Push to Registries
+
+on:
+  workflow_call:
+    inputs:
+      DOCKERFILE_LOCATION:
+        required: false
+        type: string
+        default: "./Dockerfile"
+      AWS_REGION:
+        required: false
+        type: string
+        default: "us-east-1"
+      AWS_ECR_REGISTRY:
+        required: false
+        type: string
+        default: "707767160287.dkr.ecr.us-east-1.amazonaws.com"
+      DOCKERFILE_BUILD_CONTEXT:
+        required: false
+        type: string
+        default: "."
+      OVERRIDE_REPO_NAME:
+        required: false
+        type: string
+        default: ""
+      OVERRIDE_TAG_NAME:
+        required: false
+        type: string
+        default: ""
+      USE_QUAY_ONLY:
+        required: false
+        type: boolean
+        default: false
+      BUILD_PLATFORMS:
+        required: false
+        type: string
+        default: "linux/amd64, linux/arm64"
+    secrets:
+      ECR_AWS_ACCESS_KEY_ID:
+        required: true
+      ECR_AWS_SECRET_ACCESS_KEY:
+        required: true
+      QUAY_USERNAME:
+        required: true
+      QUAY_ROBOT_TOKEN:
+        required: true
+
+jobs:
+  ci:
+    name: Build Image and Push
+    runs-on: ubuntu-latest
+    steps:
+      # https://github.com/docker/login-action#quayio
+      - name: Login to Quay.io
+        uses: docker/login-action@v2
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
+
+      # https://github.com/docker/login-action#aws-public-elastic-container-registry-ecr
+      - name: Login to ECR
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ inputs.AWS_ECR_REGISTRY }}
+          username: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
+          password: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
+        env:
+          AWS_REGION: ${{ inputs.AWS_REGION }}
+
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set Variables
+        shell: bash
+        run: |
+          echo "OVERRIDE_REPO_NAME = ${{ inputs.OVERRIDE_REPO_NAME }}"
+          echo "OVERRIDE_TAG_NAME = ${{ inputs.OVERRIDE_TAG_NAME }}"
+
+          if [[ -z "${{ inputs.OVERRIDE_TAG_NAME }}" ]]
+          then
+            echo "No OVERRIDE_TAG_NAME input provided, defaulting to current branch/tag name..."
+            echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)"
+            echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)" >> $GITHUB_ENV
+          else
+            echo "OVERRIDE_TAG_NAME provided, using it for IMAGE_TAG..."
+            echo "IMAGE_TAG=${{ inputs.OVERRIDE_TAG_NAME }}"
+            echo "IMAGE_TAG=${{ inputs.OVERRIDE_TAG_NAME }}" >> $GITHUB_ENV
+          fi
+
+          if [[ -z "${{ inputs.OVERRIDE_REPO_NAME }}" ]]
+          then
+            echo "No OVERRIDE_REPO_NAME input provided, defaulting to repo name..."
+            echo "REPO_NAME=$(echo $GITHUB_REPOSITORY | awk -F / '{print $2}')"
+            echo "REPO_NAME=$(echo $GITHUB_REPOSITORY | awk -F / '{print $2}')" >> $GITHUB_ENV
+          else
+            echo "OVERRIDE_REPO_NAME provided, using it for REPO_NAME..."
+            echo "REPO_NAME=${{ inputs.OVERRIDE_REPO_NAME }}"
+            echo "REPO_NAME=${{ inputs.OVERRIDE_REPO_NAME }}" >> $GITHUB_ENV
+          fi
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v3
+        with:
+          images: |
+            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+            ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+
+      # - name: Build
+      #   if: ${{ !inputs.USE_QUAY_ONLY }}
+      #   uses: docker/build-push-action@v3
+      #   # You may get ECR-push errors when first adding the workflow to a github repo.
+      #   # If so, run the following in dev/qa to create the ECR repository:
+      #   # qaplanetv1@cdistest_dev_admin:~$ aws ecr create-repository --repository-name "gen3/<repo name>" --image-scanning-configuration scanOnPush=true
+      #   with:
+      #     context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+      #     file: ${{ inputs.DOCKERFILE_LOCATION }}
+      #     push: false
+      #     tags: |
+      #       quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #       ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #     labels: ${{ steps.meta.outputs.labels }}
+      #     cache-from: type=registry,ref=${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #     cache-to: type=inline
+      #     platforms: ${{ inputs.BUILD_PLATFORMS }}
+
+      # - name: Slim
+      #   if: ${{ !inputs.USE_QUAY_ONLY }}
+      #   uses: kitabisa/docker-slim-action@v1
+      #   with:
+      #     target: ${{ github.repository }}:latest
+      #     tag: "slim"
+      #   env:
+      #     DSLIM_HTTP_PROBE: false
+
+      # - name: Push
+      #   if: ${{ !inputs.USE_QUAY_ONLY }}
+      #   run: |
+      #     docker image push "${{ github.repository }}" --all-tags
+
+      - name: Build (Quay only)
+        # if: ${{ inputs.USE_QUAY_ONLY }}
+        uses: docker/build-push-action@v3
+        with:
+          context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+          file: ${{ inputs.DOCKERFILE_LOCATION }}
+          push: false
+          tags: |
+            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          cache-to: type=inline
+          platforms: ${{ inputs.BUILD_PLATFORMS }}
+
+      - name: Slim (Quay only)
+        # if: ${{ inputs.USE_QUAY_ONLY }}
+        uses: kitabisa/docker-slim-action@v1
+        with:
+          target: quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          tag: "slim"
+        env:
+          DSLIM_HTTP_PROBE: false
+
+      - name: Push (Quay only)
+        # if: ${{ inputs.USE_QUAY_ONLY }}
+        run: |
+          docker image push "${{ github.repository }}" --all-tags
+
+      # Dump the report
+      - name: Report
+        run: echo "${REPORT}"
+        env:
+          REPORT: ${{ steps.slim.outputs.report }}

From 7b0b85c2f666fa064d4d50af64e63589c3b7ed3c Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 09:22:44 -0600
Subject: [PATCH 02/61] testing a few changes to build-push-action for Slim
 Workflow

---
 .github/workflows/image_build_push_slim.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 415cbebf..4f4e201f 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -157,10 +157,11 @@ jobs:
           push: false
           tags: |
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=registry,ref=quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          cache-to: type=inline
-          platforms: ${{ inputs.BUILD_PLATFORMS }}
+          load: true
+          # labels: ${{ steps.meta.outputs.labels }}
+          # cache-from: type=registry,ref=quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          # cache-to: type=inline
+          # platforms: ${{ inputs.BUILD_PLATFORMS }}
 
       - name: Slim (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 298e93d7676e07861c74eb277e87f1c8bbb8b439 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 09:27:21 -0600
Subject: [PATCH 03/61] testing with "push" enabled

---
 .github/workflows/image_build_push_slim.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 4f4e201f..1181a1e1 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -154,10 +154,9 @@ jobs:
         with:
           context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
           file: ${{ inputs.DOCKERFILE_LOCATION }}
-          push: false
+          push: true
           tags: |
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          load: true
           # labels: ${{ steps.meta.outputs.labels }}
           # cache-from: type=registry,ref=quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           # cache-to: type=inline

From 7eded2b5cd761f1664c130ff22dbdc2be674348a Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 09:30:09 -0600
Subject: [PATCH 04/61] adding back old configuration

---
 .github/workflows/image_build_push_slim.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 1181a1e1..31bf5978 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -157,10 +157,10 @@ jobs:
           push: true
           tags: |
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          # labels: ${{ steps.meta.outputs.labels }}
-          # cache-from: type=registry,ref=quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          # cache-to: type=inline
-          # platforms: ${{ inputs.BUILD_PLATFORMS }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          cache-to: type=inline
+          platforms: ${{ inputs.BUILD_PLATFORMS }}
 
       - name: Slim (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 610b4dea21c89828014a93ba97e1db32922ab113 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 09:34:12 -0600
Subject: [PATCH 05/61] modifying build and push for testing

---
 .github/workflows/image_build_push_slim.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 31bf5978..1b70df35 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -148,9 +148,9 @@ jobs:
       #   run: |
       #     docker image push "${{ github.repository }}" --all-tags
 
-      - name: Build (Quay only)
+      - name: Build and push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
           file: ${{ inputs.DOCKERFILE_LOCATION }}
@@ -158,8 +158,6 @@ jobs:
           tags: |
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=registry,ref=quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          cache-to: type=inline
           platforms: ${{ inputs.BUILD_PLATFORMS }}
 
       - name: Slim (Quay only)

From 8e547145505dcf164f5ca553c88801fbe01a0513 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 09:38:12 -0600
Subject: [PATCH 06/61] test

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 1b70df35..31a50d98 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -160,7 +160,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           platforms: ${{ inputs.BUILD_PLATFORMS }}
 
-      - name: Slim (Quay only)
+      - name: Slimmm (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
         uses: kitabisa/docker-slim-action@v1
         with:

From 9a9210aba018ffa12235fdf74cc53e1c6d9616a7 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 10:28:29 -0600
Subject: [PATCH 07/61] modifying workflow to append "slim" to the original
 image name. Also, adding "load" "true" instead of "push" "true", so the image
 is not pushed twice.

---
 .github/workflows/image_build_push_slim.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 31a50d98..c63b5310 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -154,25 +154,26 @@ jobs:
         with:
           context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
           file: ${{ inputs.DOCKERFILE_LOCATION }}
-          push: true
+          push: false
+          load: true
           tags: |
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           labels: ${{ steps.meta.outputs.labels }}
           platforms: ${{ inputs.BUILD_PLATFORMS }}
 
-      - name: Slimmm (Quay only)
+      - name: Slim (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
         uses: kitabisa/docker-slim-action@v1
         with:
           target: quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          tag: "slim"
+          tag: ${{ env.IMAGE_TAG }}-Slim
         env:
           DSLIM_HTTP_PROBE: false
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
         run: |
-          docker image push "${{ github.repository }}" --all-tags
+          docker image push ${{ github.repository }}${{ env.IMAGE_TAG }}-Slim
 
       # Dump the report
       - name: Report

From 6663a26c4d9315a9f8fc45998081a7919029c470 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 13:38:04 -0600
Subject: [PATCH 08/61] cannot use "load: true" due to building the image for
 multiple architectures

---
 .github/workflows/image_build_push_slim.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index c63b5310..1cafc404 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -154,8 +154,7 @@ jobs:
         with:
           context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
           file: ${{ inputs.DOCKERFILE_LOCATION }}
-          push: false
-          load: true
+          push: true
           tags: |
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           labels: ${{ steps.meta.outputs.labels }}

From f02c6956c18e553bd44a07aac50aa6e529389ef3 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 13:46:45 -0600
Subject: [PATCH 09/61] changing to lowercase

---
 .github/workflows/image_build_push_slim.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 1cafc404..aa513936 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -165,14 +165,14 @@ jobs:
         uses: kitabisa/docker-slim-action@v1
         with:
           target: quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          tag: ${{ env.IMAGE_TAG }}-Slim
+          tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: false
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
         run: |
-          docker image push ${{ github.repository }}${{ env.IMAGE_TAG }}-Slim
+          docker image push ${{ github.repository }}${{ env.IMAGE_TAG }}-slim
 
       # Dump the report
       - name: Report

From ba7b83ee801e01dfca915eba601bb5a6726bbe9a Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 13:53:11 -0600
Subject: [PATCH 10/61] updating push command

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index aa513936..eb581649 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -172,7 +172,7 @@ jobs:
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
         run: |
-          docker image push ${{ github.repository }}${{ env.IMAGE_TAG }}-slim
+          docker image push quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}-slim
 
       # Dump the report
       - name: Report

From 5b35d7b18e51b2129850871940114c7ae65aafaa Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 15:19:36 -0600
Subject: [PATCH 11/61] testing the "include_path_file" variable

---
 .github/workflows/image_build_push_slim.yaml | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index eb581649..6769e60a 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -167,15 +167,10 @@ jobs:
           target: quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
-          DSLIM_HTTP_PROBE: false
+          DSLIM_HTTP_PROBE: true
+          DSLIM_INCLUDE_PATH_FILE: "/usr/bin/sort:/usr/bin/find:/bin/rm:/bin/tar
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
         run: |
           docker image push quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}-slim
-
-      # Dump the report
-      - name: Report
-        run: echo "${REPORT}"
-        env:
-          REPORT: ${{ steps.slim.outputs.report }}

From 901c2c8a7faa7e957afc176dddaaee3ef32ce7aa Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 15:25:48 -0600
Subject: [PATCH 12/61] fixing syntax error

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 6769e60a..dfbdf4d6 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_INCLUDE_PATH_FILE: "/usr/bin/sort:/usr/bin/find:/bin/rm:/bin/tar
+          DSLIM_INCLUDE_PATH_FILE: "/usr/bin/sort:/usr/bin/find:/bin/rm:/bin/tar"
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From c70a79411182e61fe551c38ffeebe226d834e24d Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 15:34:35 -0600
Subject: [PATCH 13/61] trying the "include_bin_file" var instead

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index dfbdf4d6..44878d6e 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_INCLUDE_PATH_FILE: "/usr/bin/sort:/usr/bin/find:/bin/rm:/bin/tar"
+          DSLIM_INCLUDE_BIN_FILE: "/usr/bin/sort:/usr/bin/find:/bin/rm:/bin/tar"
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 25bef947fcf0621cd6d43698f4e30936d1f840e4 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 26 Apr 2024 15:38:54 -0600
Subject: [PATCH 14/61] trying just one path

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 44878d6e..e3df3d19 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_INCLUDE_BIN_FILE: "/usr/bin/sort:/usr/bin/find:/bin/rm:/bin/tar"
+          DSLIM_INCLUDE_BIN_FILE: "/usr/bin/sort"
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From f4c038061d8117a96509ae2a6194d2ec892c2daa Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 09:11:40 -0600
Subject: [PATCH 15/61] creating a file with the list of binaries to include

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 .github/workflows/include-binaries.txt       | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/include-binaries.txt

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index e3df3d19..789104f7 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_INCLUDE_BIN_FILE: "/usr/bin/sort"
+          DSLIM_INCLUDE_BIN_FILE: include-binaries.txt
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
diff --git a/.github/workflows/include-binaries.txt b/.github/workflows/include-binaries.txt
new file mode 100644
index 00000000..ebf715e0
--- /dev/null
+++ b/.github/workflows/include-binaries.txt
@@ -0,0 +1,6 @@
+/usr/bin/sort
+/usr/bin/curl
+/usr/bin/find
+/bin/rm
+/usr/local/bin/python
+/bin/tar

From 3c3b4f701b5e1d14ebccbf1ddc0e9e0c7b66a422 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 09:17:59 -0600
Subject: [PATCH 16/61] modifying the directory name for include-binaries.txt

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 789104f7..33bf9321 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_INCLUDE_BIN_FILE: include-binaries.txt
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From f403e0caef38005ea91f0710792092157da9d026 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 09:32:21 -0600
Subject: [PATCH 17/61] testing to see if failures are from
 DSLIM_INCLUDE_BIN_FILE environment var

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 33bf9321..36a5f5bc 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
+          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 3e4728c933545d6e7ab7e613236b90a3b1480824 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 09:40:47 -0600
Subject: [PATCH 18/61] adding some steps for debugging

---
 .github/workflows/image_build_push_slim.yaml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 36a5f5bc..b4f1a76b 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -74,6 +74,15 @@ jobs:
           persist-credentials: false
           fetch-depth: 0
 
+      - name: List files in the repository
+        run: ls -alh
+      - name: Show contents of the include-binaries.txt
+        run: cat include-binaries.txt
+      - name: Run DockerSlim
+        run: docker-slim build --http-probe=false my-app
+        env:
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
 

From 606274dbadf253ca731af583562bb794eb583fcd Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 09:49:35 -0600
Subject: [PATCH 19/61] adding the include bin file environment var back

---
 .github/workflows/image_build_push_slim.yaml | 11 +----------
 .github/workflows/include-binaries.txt       |  6 ------
 2 files changed, 1 insertion(+), 16 deletions(-)
 delete mode 100644 .github/workflows/include-binaries.txt

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index b4f1a76b..33bf9321 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -74,15 +74,6 @@ jobs:
           persist-credentials: false
           fetch-depth: 0
 
-      - name: List files in the repository
-        run: ls -alh
-      - name: Show contents of the include-binaries.txt
-        run: cat include-binaries.txt
-      - name: Run DockerSlim
-        run: docker-slim build --http-probe=false my-app
-        env:
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
-
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
 
@@ -177,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
diff --git a/.github/workflows/include-binaries.txt b/.github/workflows/include-binaries.txt
deleted file mode 100644
index ebf715e0..00000000
--- a/.github/workflows/include-binaries.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-/usr/bin/sort
-/usr/bin/curl
-/usr/bin/find
-/bin/rm
-/usr/local/bin/python
-/bin/tar

From 8a4be3068fbf9507957a58ca3d0fd2bbc6a50234 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 10:14:16 -0600
Subject: [PATCH 20/61] adding "SLIM_PRESERVE_PATH_FILE" env var

---
 .github/workflows/image_build_push_slim.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 33bf9321..0085e5cf 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,8 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/include-binaries.txt
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From d8e262b16a40dcd9ac0e8a37e24b9574e1c51223 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 11:06:30 -0600
Subject: [PATCH 21/61] adding a path to preserve to slim GH action

---
 .github/workflows/image_build_push_slim.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 0085e5cf..dfb623a8 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,6 +170,8 @@ jobs:
           DSLIM_HTTP_PROBE: true
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
+          DSLIM_PRESERVE_PATH: /var/run/gen3/
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 266606e60cd9ed9a55cfa624151712bf69efffb2 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 11:07:10 -0600
Subject: [PATCH 22/61] commenting out include exec files for gh action

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index dfb623a8..91622c97 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,7 +170,7 @@ jobs:
           DSLIM_HTTP_PROBE: true
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
-          DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
+          # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_PRESERVE_PATH: /var/run/gen3/
 
       - name: Push (Quay only)

From ab53b4a245fa36ad5004fa62cde077ee5ae27c3b Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 11:22:01 -0600
Subject: [PATCH 23/61] changing environment variable to "include" instead of
 "preserce"

---
 .github/workflows/image_build_push_slim.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 91622c97..bca7d049 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -169,9 +169,8 @@ jobs:
         env:
           DSLIM_HTTP_PROBE: true
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
-          DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
-          DSLIM_PRESERVE_PATH: /var/run/gen3/
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 73d3f8eaae452f524fb88c3a54f2ec188e777fad Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 11:33:31 -0600
Subject: [PATCH 24/61] keeping flask metrics path

---
 .github/workflows/image_build_push_slim.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index bca7d049..2b920e29 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -171,6 +171,7 @@ jobs:
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
+          DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 21c6e9fb8c5a18b52bfe91d8eb29eb0be9f858b4 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 13:13:44 -0600
Subject: [PATCH 25/61] testing "DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS	"
 environment var

---
 .github/workflows/image_build_push_slim.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 2b920e29..9dbf4e30 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -172,6 +172,7 @@ jobs:
           DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
+          DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 2f9783c6e3417f12708606c52e5a9985fc8fa9a5 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 13:59:35 -0600
Subject: [PATCH 26/61] adding fence app as a path to preserve

---
 .github/workflows/image_build_push_slim.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 9dbf4e30..7fe06b4d 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -173,6 +173,7 @@ jobs:
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
+          DSLIM_PRESERVE_PATH: /var/www/fence/
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From aba37ec5e2fb860a7c17f806f4904a0eecd75b54 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 14:05:24 -0600
Subject: [PATCH 27/61] testing out setting the working dir

---
 .github/workflows/image_build_push_slim.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 7fe06b4d..0a7fad89 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -174,6 +174,7 @@ jobs:
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           DSLIM_PRESERVE_PATH: /var/www/fence/
+          DSLIM_NEW_WORKDIR: /var/www/fence/
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 14933537652b9e4dc192af9870d7fea55ffe3abd Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 14:08:33 -0600
Subject: [PATCH 28/61] preserving fence path

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 0a7fad89..ac3102c8 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -173,7 +173,7 @@ jobs:
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
-          DSLIM_PRESERVE_PATH: /var/www/fence/
+          DSLIM_PRESERVE_PATH: /fence
           DSLIM_NEW_WORKDIR: /var/www/fence/
 
       - name: Push (Quay only)

From 60061de3155b8ad60b6f320ba842e199aaebc4da Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 14:18:28 -0600
Subject: [PATCH 29/61] adding "preserve-files"

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index ac3102c8..ec186cc4 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,10 +170,10 @@ jobs:
           DSLIM_HTTP_PROBE: true
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
-          DSLIM_PRESERVE_PATH: /fence
           DSLIM_NEW_WORKDIR: /var/www/fence/
 
       - name: Push (Quay only)

From f0ee5a29c891c0e65a5231ae6b74822bf7a51775 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 15:16:54 -0600
Subject: [PATCH 30/61] removing working dir var

---
 .github/workflows/image_build_push_slim.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index ec186cc4..d4b4536d 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -169,12 +169,12 @@ jobs:
         env:
           DSLIM_HTTP_PROBE: true
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
-          DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
-          DSLIM_NEW_WORKDIR: /var/www/fence/
+          # DSLIM_NEW_WORKDIR: /var/www/fence/
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From e3fd76d0c36f86e5fccb960b79f60efd06472ac8 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 15:23:36 -0600
Subject: [PATCH 31/61] setting the working dir

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index d4b4536d..8f826d0e 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -174,7 +174,7 @@ jobs:
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
-          # DSLIM_NEW_WORKDIR: /var/www/fence/
+          DSLIM_NEW_WORKDIR: /fence
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 84c2db7cea80d21603883ebfa8a159c012c15bba Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Tue, 30 Apr 2024 15:49:56 -0600
Subject: [PATCH 32/61] testing an environment var to change the user the
 container runs with

---
 .github/workflows/image_build_push_slim.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 8f826d0e..af37592b 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -175,6 +175,7 @@ jobs:
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           DSLIM_NEW_WORKDIR: /fence
+          DSLIM_RUN_TAS_USER: false
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From c72f1cdc841e11eb5729925bc6d8047a3c0339c6 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 12:55:52 -0600
Subject: [PATCH 33/61] commenting out "build" step so the actions runs quickly
 for testing

---
 .github/workflows/image_build_push_slim.yaml | 22 ++++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index af37592b..162de3a6 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -148,17 +148,17 @@ jobs:
       #   run: |
       #     docker image push "${{ github.repository }}" --all-tags
 
-      - name: Build and push (Quay only)
-        # if: ${{ inputs.USE_QUAY_ONLY }}
-        uses: docker/build-push-action@v5
-        with:
-          context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
-          file: ${{ inputs.DOCKERFILE_LOCATION }}
-          push: true
-          tags: |
-            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          labels: ${{ steps.meta.outputs.labels }}
-          platforms: ${{ inputs.BUILD_PLATFORMS }}
+      # - name: Build and push (Quay only)
+      #   # if: ${{ inputs.USE_QUAY_ONLY }}
+      #   uses: docker/build-push-action@v5
+      #   with:
+      #     context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+      #     file: ${{ inputs.DOCKERFILE_LOCATION }}
+      #     push: true
+      #     tags: |
+      #       quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #     labels: ${{ steps.meta.outputs.labels }}
+      #     platforms: ${{ inputs.BUILD_PLATFORMS }}
 
       - name: Slim (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From e893ac665a1b8a9b6a491a2e71f42c4253882821 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 12:59:52 -0600
Subject: [PATCH 34/61] test

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 162de3a6..352f81fc 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -174,7 +174,7 @@ jobs:
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
-          DSLIM_NEW_WORKDIR: /fence
+          # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false
 
       - name: Push (Quay only)

From d57af41d4842f0c8037f2b4ac1957de483405a1a Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 13:02:18 -0600
Subject: [PATCH 35/61] disabling HTTP PROBE

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 352f81fc..bf5c9333 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -167,7 +167,7 @@ jobs:
           target: quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
-          DSLIM_HTTP_PROBE: true
+          DSLIM_HTTP_PROBE: false
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt

From dd69289a8868f2d70d3e7fb9c424aad75ac80652 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 13:08:08 -0600
Subject: [PATCH 36/61] temporarily getting rid of include-binaries for testing

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index bf5c9333..da690c7d 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: false
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt

From fe574ed644ed23c45b9fe4eb9c0c8d9bf1934293 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 13:14:52 -0600
Subject: [PATCH 37/61] adding back include binaries

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index da690c7d..bf5c9333 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,7 +168,7 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: false
-          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt

From 24fa37ff8fd8bf5447242d2072da1b7dfdf06561 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 13:32:16 -0600
Subject: [PATCH 38/61] uncommenting build for testing

---
 .github/workflows/image_build_push_slim.yaml | 22 ++++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index bf5c9333..4cf827b2 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -148,17 +148,17 @@ jobs:
       #   run: |
       #     docker image push "${{ github.repository }}" --all-tags
 
-      # - name: Build and push (Quay only)
-      #   # if: ${{ inputs.USE_QUAY_ONLY }}
-      #   uses: docker/build-push-action@v5
-      #   with:
-      #     context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
-      #     file: ${{ inputs.DOCKERFILE_LOCATION }}
-      #     push: true
-      #     tags: |
-      #       quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-      #     labels: ${{ steps.meta.outputs.labels }}
-      #     platforms: ${{ inputs.BUILD_PLATFORMS }}
+      - name: Build and push (Quay only)
+        # if: ${{ inputs.USE_QUAY_ONLY }}
+        uses: docker/build-push-action@v5
+        with:
+          context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+          file: ${{ inputs.DOCKERFILE_LOCATION }}
+          push: true
+          tags: |
+            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          platforms: ${{ inputs.BUILD_PLATFORMS }}
 
       - name: Slim (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From d3600f19c680b11270bb0c6b3bd4434b59bc0fe1 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 14:19:37 -0600
Subject: [PATCH 39/61] including shell

---
 .github/workflows/image_build_push_slim.yaml | 29 ++++++++++++--------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 4cf827b2..c2e9e81f 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -148,17 +148,17 @@ jobs:
       #   run: |
       #     docker image push "${{ github.repository }}" --all-tags
 
-      - name: Build and push (Quay only)
-        # if: ${{ inputs.USE_QUAY_ONLY }}
-        uses: docker/build-push-action@v5
-        with:
-          context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
-          file: ${{ inputs.DOCKERFILE_LOCATION }}
-          push: true
-          tags: |
-            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          labels: ${{ steps.meta.outputs.labels }}
-          platforms: ${{ inputs.BUILD_PLATFORMS }}
+      # - name: Build and push (Quay only)
+      #   # if: ${{ inputs.USE_QUAY_ONLY }}
+      #   uses: docker/build-push-action@v5
+      #   with:
+      #     context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+      #     file: ${{ inputs.DOCKERFILE_LOCATION }}
+      #     push: true
+      #     tags: |
+      #       quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #     labels: ${{ steps.meta.outputs.labels }}
+      #     platforms: ${{ inputs.BUILD_PLATFORMS }}
 
       - name: Slim (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
@@ -176,8 +176,15 @@ jobs:
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false
+          DSLIM_INCLUDE_SHELL: true
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
         run: |
           docker image push quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}-slim
+
+      # Dump the report
+      - name: Report
+        run: echo "${REPORT}"
+        env:
+          REPORT: ${{ steps.slim.outputs.report }}

From 4f99d4ae20da436a66056d4e30c2c1b3102c61eb Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 14:49:20 -0600
Subject: [PATCH 40/61] adding back include-files

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index c2e9e81f..2abe9b76 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -169,7 +169,7 @@ jobs:
         env:
           DSLIM_HTTP_PROBE: false
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
-          # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics

From fd77c79208f918f41925ed3f8611554a683712d9 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 15:59:07 -0600
Subject: [PATCH 41/61] adding new path for include path

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 2abe9b76..a3ee1ac8 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -172,7 +172,7 @@ jobs:
           DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
-          DSLIM_INCLUDE_PATH: /var/tmp/uwsgi_flask_metrics
+          DSLIM_INCLUDE_PATH: /usr/bin/
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false

From c3ad25d69b3949861b301ed8e13efebef0e0da2f Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 16:05:05 -0600
Subject: [PATCH 42/61] including all paths for debugging

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index a3ee1ac8..e56d3f4d 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -172,7 +172,7 @@ jobs:
           DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
-          DSLIM_INCLUDE_PATH: /usr/bin/
+          DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false

From 304c3875954697e1c356dfba4a5370b465300ecf Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Wed, 1 May 2024 16:08:40 -0600
Subject: [PATCH 43/61] testing

---
 .github/workflows/image_build_push_slim.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index e56d3f4d..77617a08 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,15 +168,15 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: false
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
-          DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
-          DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
+          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          # DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false
-          DSLIM_INCLUDE_SHELL: true
+          # DSLIM_INCLUDE_SHELL: true
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From dce23751d2715c38f0f7ca2b6bec252a58af6f9f Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 10:30:51 -0600
Subject: [PATCH 44/61] adding back preserve and include files

---
 .github/workflows/image_build_push_slim.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 77617a08..e8761307 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,11 +168,11 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: false
-          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
-          # DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
+          DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
-          DSLIM_INCLUDE_PATH: /
+          # DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false

From fd812fd5db839adbc2a14f708c2adf3a09ce9c0f Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 11:49:21 -0600
Subject: [PATCH 45/61] adding additional environment variables

---
 .github/workflows/image_build_push_slim.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index e8761307..80983c25 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -167,7 +167,9 @@ jobs:
           target: quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
-          DSLIM_HTTP_PROBE: false
+          DSLIM_HTTP_PROBE: true
+          DSLIM_NEW_EXPOSE: 8080
+          DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt

From 9dc30e514b4cfb7cc98b152fa2e931f1dcc856a0 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 11:57:50 -0600
Subject: [PATCH 46/61] revert

---
 .github/workflows/image_build_push_slim.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 80983c25..0d366f18 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -168,8 +168,8 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: true
-          DSLIM_NEW_EXPOSE: 8080
-          DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
+          # DSLIM_NEW_EXPOSE: 8080
+          # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt

From fcc17331e1d54ab90ea3fbf010b4b8019f150bb3 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 12:03:55 -0600
Subject: [PATCH 47/61] revert to false

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 0d366f18..3b087a33 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -167,7 +167,7 @@ jobs:
           target: quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
-          DSLIM_HTTP_PROBE: true
+          DSLIM_HTTP_PROBE: false
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt

From 3ed63fe300f4713ac91ecb09be8571ec9196cca4 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 12:46:57 -0600
Subject: [PATCH 48/61] adding back include shell

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 3b087a33..b3284af8 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -178,7 +178,7 @@ jobs:
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false
-          # DSLIM_INCLUDE_SHELL: true
+          DSLIM_INCLUDE_SHELL: true
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 51563276a6eef8a12b6303046cfde1699c6ea933 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 12:59:59 -0600
Subject: [PATCH 49/61] removing bin files

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index b3284af8..4aeeacec 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,7 +170,7 @@ jobs:
           DSLIM_HTTP_PROBE: false
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt

From 53f049c2bb4aa75548f7d8b67c7a33c9c4754894 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 13:07:55 -0600
Subject: [PATCH 50/61] adding it back

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 4aeeacec..b3284af8 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,7 +170,7 @@ jobs:
           DSLIM_HTTP_PROBE: false
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
-          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt

From 1c0b2171381e9593868f865686f9b6aae425fecb Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 13:13:46 -0600
Subject: [PATCH 51/61] adding include files

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index b3284af8..7c5a4109 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -171,7 +171,7 @@ jobs:
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
-          # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
           # DSLIM_INCLUDE_PATH: /

From a22ab773f0dea3e826f40b8e6c1a612c458097d6 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 13:15:33 -0600
Subject: [PATCH 52/61] testing include executables

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 7c5a4109..ef0dcb92 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -173,7 +173,7 @@ jobs:
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
-          # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-executables.txt
+          DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           # DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence

From 34141c5ece39f6dac861c581ca0ff07068ff907b Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 13:17:34 -0600
Subject: [PATCH 53/61] test

---
 .github/workflows/image_build_push_slim.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index ef0dcb92..99d81d50 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -171,9 +171,9 @@ jobs:
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
-          DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
-          DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           # DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence

From a12418b259307ffb406111c7a5a6294ca57eb7bd Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 14:23:38 -0600
Subject: [PATCH 54/61] test

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 99d81d50..763eaeea 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -173,7 +173,7 @@ jobs:
           DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
-          # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           # DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence

From ea5ab2638818f016a0fc64b9bdaf21dc0388136a Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 15:05:47 -0600
Subject: [PATCH 55/61] test

---
 .github/workflows/image_build_push_slim.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 763eaeea..8768857e 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,10 +170,10 @@ jobs:
           DSLIM_HTTP_PROBE: false
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
-          DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
+          # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           # DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence

From 8d3a24b37092356fbc87b37fef0670ef88984586 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 15:17:44 -0600
Subject: [PATCH 56/61] test

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 8768857e..99d81d50 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,7 +170,7 @@ jobs:
           DSLIM_HTTP_PROBE: false
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
-          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt

From dfa4bec70ab2d72d6a0fce05bc2ed9674a482ca9 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Thu, 2 May 2024 15:21:24 -0600
Subject: [PATCH 57/61] test

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 99d81d50..7ea00d8b 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -178,7 +178,7 @@ jobs:
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false
-          DSLIM_INCLUDE_SHELL: true
+          # DSLIM_INCLUDE_SHELL: true
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From 6cd0b90d2e8fe882fba8c1c24c6e9410009b77aa Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 3 May 2024 08:57:46 -0600
Subject: [PATCH 58/61] test

---
 .github/workflows/image_build_push_slim.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 7ea00d8b..8768857e 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -170,7 +170,7 @@ jobs:
           DSLIM_HTTP_PROBE: false
           # DSLIM_NEW_EXPOSE: 8080
           # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
-          DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
+          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
           # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
@@ -178,7 +178,7 @@ jobs:
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false
-          # DSLIM_INCLUDE_SHELL: true
+          DSLIM_INCLUDE_SHELL: true
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From ee3444e60d79d89daf968961ab5b8b28a19f0a53 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 3 May 2024 10:21:44 -0600
Subject: [PATCH 59/61] cleaning up PR

---
 .github/workflows/image_build_push_slim.yaml | 99 +++++++++-----------
 1 file changed, 43 insertions(+), 56 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 8768857e..d34f79af 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -116,49 +116,49 @@ jobs:
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
             ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
 
-      # - name: Build
-      #   if: ${{ !inputs.USE_QUAY_ONLY }}
-      #   uses: docker/build-push-action@v3
-      #   # You may get ECR-push errors when first adding the workflow to a github repo.
-      #   # If so, run the following in dev/qa to create the ECR repository:
-      #   # qaplanetv1@cdistest_dev_admin:~$ aws ecr create-repository --repository-name "gen3/<repo name>" --image-scanning-configuration scanOnPush=true
-      #   with:
-      #     context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
-      #     file: ${{ inputs.DOCKERFILE_LOCATION }}
-      #     push: false
-      #     tags: |
-      #       quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-      #       ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-      #     labels: ${{ steps.meta.outputs.labels }}
-      #     cache-from: type=registry,ref=${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-      #     cache-to: type=inline
-      #     platforms: ${{ inputs.BUILD_PLATFORMS }}
-
-      # - name: Slim
-      #   if: ${{ !inputs.USE_QUAY_ONLY }}
-      #   uses: kitabisa/docker-slim-action@v1
-      #   with:
-      #     target: ${{ github.repository }}:latest
-      #     tag: "slim"
-      #   env:
-      #     DSLIM_HTTP_PROBE: false
-
-      # - name: Push
-      #   if: ${{ !inputs.USE_QUAY_ONLY }}
-      #   run: |
-      #     docker image push "${{ github.repository }}" --all-tags
-
-      # - name: Build and push (Quay only)
-      #   # if: ${{ inputs.USE_QUAY_ONLY }}
-      #   uses: docker/build-push-action@v5
-      #   with:
-      #     context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
-      #     file: ${{ inputs.DOCKERFILE_LOCATION }}
-      #     push: true
-      #     tags: |
-      #       quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-      #     labels: ${{ steps.meta.outputs.labels }}
-      #     platforms: ${{ inputs.BUILD_PLATFORMS }}
+      - name: Build
+        if: ${{ !inputs.USE_QUAY_ONLY }}
+        uses: docker/build-push-action@v3
+        # You may get ECR-push errors when first adding the workflow to a github repo.
+        # If so, run the following in dev/qa to create the ECR repository:
+        # qaplanetv1@cdistest_dev_admin:~$ aws ecr create-repository --repository-name "gen3/<repo name>" --image-scanning-configuration scanOnPush=true
+        with:
+          context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+          file: ${{ inputs.DOCKERFILE_LOCATION }}
+          push: false
+          tags: |
+            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+            ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          cache-to: type=inline
+          platforms: ${{ inputs.BUILD_PLATFORMS }}
+
+      - name: Slim
+        if: ${{ !inputs.USE_QUAY_ONLY }}
+        uses: kitabisa/docker-slim-action@v1
+        with:
+          target: ${{ github.repository }}:latest
+          tag: "slim"
+        env:
+          DSLIM_HTTP_PROBE: false
+
+      - name: Push
+        if: ${{ !inputs.USE_QUAY_ONLY }}
+        run: |
+          docker image push "${{ github.repository }}" --all-tags
+
+      - name: Build and push (Quay only)
+        # if: ${{ inputs.USE_QUAY_ONLY }}
+        uses: docker/build-push-action@v5
+        with:
+          context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+          file: ${{ inputs.DOCKERFILE_LOCATION }}
+          push: true
+          tags: |
+            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          platforms: ${{ inputs.BUILD_PLATFORMS }}
 
       - name: Slim (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}
@@ -168,15 +168,8 @@ jobs:
           tag: ${{ env.IMAGE_TAG }}-slim
         env:
           DSLIM_HTTP_PROBE: false
-          # DSLIM_NEW_EXPOSE: 8080
-          # DSLIM_HTTP_PROBE_CMD: "gunicorn -c deployment/wsgi/gunicorn.conf.py"
-          # DSLIM_INCLUDE_BIN_FILE: ${{ github.workspace }}/.github/workflows/include-binaries.txt
-          # DSLIM_INCLUDE_PATH_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
-          # DSLIM_INCLUDE_EXE_FILE: ${{ github.workspace }}/.github/workflows/include-files.txt
-          # DSLIM_INCLUDE_PATH: /
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
-          # DSLIM_NEW_WORKDIR: /fence
           DSLIM_RUN_TAS_USER: false
           DSLIM_INCLUDE_SHELL: true
 
@@ -184,9 +177,3 @@ jobs:
         # if: ${{ inputs.USE_QUAY_ONLY }}
         run: |
           docker image push quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}-slim
-
-      # Dump the report
-      - name: Report
-        run: echo "${REPORT}"
-        env:
-          REPORT: ${{ steps.slim.outputs.report }}

From 5d17d924160fdaeef323878d34dfa169b255365c Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 3 May 2024 11:07:20 -0600
Subject: [PATCH 60/61] setting "include-shell" to fale

---
 .github/workflows/image_build_push_slim.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index d34f79af..2b02660b 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -171,7 +171,7 @@ jobs:
           DSLIM_PRESERVE_PATH_FILE: ${{ github.workspace }}/.github/workflows/preserve-files.txt
           DSLIM_DEP_INCLUDE_COMPOSE_SVC_DEPS: true
           DSLIM_RUN_TAS_USER: false
-          DSLIM_INCLUDE_SHELL: true
+          DSLIM_INCLUDE_SHELL: false
 
       - name: Push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}

From cef639001344b89516a492466aee8870457b7713 Mon Sep 17 00:00:00 2001
From: EliseCastle23 <elisemcastle@uchicago.edu>
Date: Fri, 3 May 2024 13:27:54 -0600
Subject: [PATCH 61/61] disabling ECR push for now

---
 .github/workflows/image_build_push_slim.yaml | 62 ++++++++++----------
 1 file changed, 31 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/image_build_push_slim.yaml b/.github/workflows/image_build_push_slim.yaml
index 2b02660b..83086e7f 100644
--- a/.github/workflows/image_build_push_slim.yaml
+++ b/.github/workflows/image_build_push_slim.yaml
@@ -116,37 +116,37 @@ jobs:
             quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
             ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
 
-      - name: Build
-        if: ${{ !inputs.USE_QUAY_ONLY }}
-        uses: docker/build-push-action@v3
-        # You may get ECR-push errors when first adding the workflow to a github repo.
-        # If so, run the following in dev/qa to create the ECR repository:
-        # qaplanetv1@cdistest_dev_admin:~$ aws ecr create-repository --repository-name "gen3/<repo name>" --image-scanning-configuration scanOnPush=true
-        with:
-          context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
-          file: ${{ inputs.DOCKERFILE_LOCATION }}
-          push: false
-          tags: |
-            quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-            ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=registry,ref=${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
-          cache-to: type=inline
-          platforms: ${{ inputs.BUILD_PLATFORMS }}
-
-      - name: Slim
-        if: ${{ !inputs.USE_QUAY_ONLY }}
-        uses: kitabisa/docker-slim-action@v1
-        with:
-          target: ${{ github.repository }}:latest
-          tag: "slim"
-        env:
-          DSLIM_HTTP_PROBE: false
-
-      - name: Push
-        if: ${{ !inputs.USE_QUAY_ONLY }}
-        run: |
-          docker image push "${{ github.repository }}" --all-tags
+      # - name: Build
+      #   if: ${{ !inputs.USE_QUAY_ONLY }}
+      #   uses: docker/build-push-action@v3
+      #   # You may get ECR-push errors when first adding the workflow to a github repo.
+      #   # If so, run the following in dev/qa to create the ECR repository:
+      #   # qaplanetv1@cdistest_dev_admin:~$ aws ecr create-repository --repository-name "gen3/<repo name>" --image-scanning-configuration scanOnPush=true
+      #   with:
+      #     context: ${{ inputs.DOCKERFILE_BUILD_CONTEXT }}
+      #     file: ${{ inputs.DOCKERFILE_LOCATION }}
+      #     push: false
+      #     tags: |
+      #       quay.io/cdis/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #       ${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #     labels: ${{ steps.meta.outputs.labels }}
+      #     cache-from: type=registry,ref=${{ inputs.AWS_ECR_REGISTRY }}/gen3/${{ env.REPO_NAME }}:${{ env.IMAGE_TAG }}
+      #     cache-to: type=inline
+      #     platforms: ${{ inputs.BUILD_PLATFORMS }}
+
+      # - name: Slim
+      #   if: ${{ !inputs.USE_QUAY_ONLY }}
+      #   uses: kitabisa/docker-slim-action@v1
+      #   with:
+      #     target: ${{ github.repository }}:latest
+      #     tag: "slim"
+      #   env:
+      #     DSLIM_HTTP_PROBE: false
+
+      # - name: Push
+      #   if: ${{ !inputs.USE_QUAY_ONLY }}
+      #   run: |
+      #     docker image push "${{ github.repository }}" --all-tags
 
       - name: Build and push (Quay only)
         # if: ${{ inputs.USE_QUAY_ONLY }}