From 1c0919634d927f8b84d7a8f4444e66f565ff1091 Mon Sep 17 00:00:00 2001
From: Maxime Mulder <maxime-mulder@outlook.com>
Date: Fri, 18 Oct 2024 15:53:38 -0400
Subject: [PATCH] add s3fs in docker

---
 .github/workflows/integration.yml | 30 ++++++++++++++++++++++++-
 test/mri.Dockerfile               | 37 +++++++++++++++++++++----------
 2 files changed, 54 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml
index 0191801fc..ffec1a578 100644
--- a/.github/workflows/integration.yml
+++ b/.github/workflows/integration.yml
@@ -11,12 +11,35 @@ env:
   DATABASE_NAME: TestDatabase
   DATABASE_USERNAME: TestUsername
   DATABASE_PASSWORD: TestPassword
+  BUCKET_URL: https://ace-minio-1.loris.ca:9000
+  BUCKET_NAME: loris-rb-data
+  BUCKET_ACCESS_KEY: lorisadmin
+  BUCKET_SECRET_KEY: dmwCdAZJ=9HwMte
 
 jobs:
   docker:
     name: Docker
     runs-on: ubuntu-latest
     steps:
+    - name: Mount raisinbread data
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y s3fs fuse kmod
+        echo "AAA"
+        sudo modprobe fuse
+        echo "BBB"
+        sudo mkdir /data-imaging
+        echo "CCC"
+        touch .passwd-s3fs
+        chmod 600 .passwd-s3fs
+        echo "DDD"
+        sudo echo ${{ env.BUCKET_ACCESS_KEY }}:${{ env.BUCKET_SECRET_KEY }} > .passwd-s3fs
+        echo "EEE"
+        sudo s3fs ${{ env.BUCKET_NAME }} /data-imaging -o passwd_file=.passwd-s3fs -o url=${{ env.BUCKET_URL }} -o use_path_request_style -o allow_other
+        echo "FFF"
+        sudo ls /data-imaging
+        echo "GGG"
+
     - name: Check out LORIS-MRI
       uses: actions/checkout@v4
 
@@ -52,10 +75,15 @@ jobs:
           DATABASE_NAME=${{ env.DATABASE_NAME }}
           DATABASE_USER=${{ env.DATABASE_USERNAME }}
           DATABASE_PASS=${{ env.DATABASE_PASSWORD }}
+          BUCKET_URL=${{ env.BUCKET_URL }}
+          BUCKET_NAME=${{ env.BUCKET_NAME }}
+          BUCKET_ACCESS_KEY=${{ env.BUCKET_ACCESS_KEY }}
+          BUCKET_SECRET_KEY=${{ env.BUCKET_SECRET_KEY }}
         tags: loris-mri
         load: true
         cache-from: type=gha,scope=loris-mri
-        cache-to: type=gha,scope=loris-mri
+        allow: security.insecure
+        cache-to: type=gha,mode=max,scope=loris-mri
 
     - name: Run integration tests
       run: docker compose --file ./test/docker-compose.yml run mri pytest python/tests/integration
diff --git a/test/mri.Dockerfile b/test/mri.Dockerfile
index f4eb90c48..6bc253aca 100644
--- a/test/mri.Dockerfile
+++ b/test/mri.Dockerfile
@@ -7,21 +7,29 @@ RUN apt-get update
 # Install utilities #
 #####################
 
-# Update the package list and install build-essential, checkinstall, and cmake
-# Install some general dependencies
-RUN apt-get install -y build-essential checkinstall cmake libzip-dev mariadb-client
-
-# Install Perl and update CPAN
-RUN apt-get install -y perl && \
-    cpan CPAN
+# Install the dependencies of LORIS-MRI
+RUN apt-get install -y build-essential checkinstall cmake dcmtk libzip-dev mariadb-client perl
 
 # Install utilities
-# - `wget` is used by some installation commands
 # - `sudo` is used by the imaging install script
-RUN apt-get install -y wget sudo
+# - `s3fs` is used to mount the imaging files on the file system
+# - `wget` is used by some installation commands
+RUN apt-get install -y s3fs fuse sudo wget kmod
 
-# Install the DICOM Toolkit
-RUN apt-get install -y dcmtk
+ARG BUCKET_URL
+ARG BUCKET_NAME
+ARG BUCKET_ACCESS_KEY
+ARG BUCKET_SECRET_KEY
+
+# Connect to the imaging S3 bucket and mount in the LORIS-MRI image
+RUN modprobe fuse && \
+    mkdir /data-imaging && \
+    touch .passwd-s3fs && \
+    chmod 600 .passwd-s3fs && \
+    echo $BUCKET_ACCESS_KEY:$BUCKET_SECRET_KEY > .passwd-s3fs && \
+    s3fs $BUCKET_NAME /data-imaging -o passwd_file=.passwd-s3fs -o url=$BUCKET_URL -o use_path_request_style -o allow_other
+
+RUN ls /data-imaging
 
 ########################
 # Install MINC Toolkit #
@@ -70,7 +78,8 @@ RUN dpkg -i /tmp/bic-mni-models-0.1.1-20120421.deb && \
 RUN apt-get install -y libmariadb-dev libmariadb-dev-compat
 
 # Install the Perl libraries
-RUN cpan install Math::Round && \
+RUN cpan CPAN && \
+    cpan install Math::Round && \
     cpan install DBI && \
     cpan install DBD::mysql@4.052 && \
     cpan install Getopt::Tabular && \
@@ -117,3 +126,7 @@ ENV LORIS_MRI=/opt/${PROJECT}/bin/mri
 ENV PYTHONPATH=$PYTHONPATH:/opt/${PROJECT}/bin/mri/python:/opt/${PROJECT}/bin/mri/python/react-series-data-viewer
 ENV BEASTLIB=${MINC_TOOLKIT_DIR}/../share/beast-library-1.1
 ENV MNI_MODELS=${MINC_TOOLKIT_DIR}/../share/icbm152_model_09c
+
+#######################
+# Mount imaging files #
+#######################