From 2a587409aef6a794501794e558a27a81903bb5eb Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Wed, 4 Jun 2025 16:30:50 -0600
Subject: [PATCH 1/3] Update docker-compose.yml to fix virtuoso autoheal

need further changes to add autodial to frontend and backend
---
 docker-compose.yml | 44 +++++++++++++++++---------------------------
 1 file changed, 17 insertions(+), 27 deletions(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index 8de2f6d..9c48ca8 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,15 +1,8 @@
-version: '3.2'
-
 services:
-    autoheal: 
-        restart: always
-        image: willfarrell/autoheal
-        environment: 
-            - AUTOHEAL_CONTAINER_LABEL=all
-        volumes:
-            - /var/run/docker.sock:/var/run/docker.sock
     virtuoso:
-        image: tenforce/virtuoso:virtuoso7.2.5
+        build:
+            context: .
+            dockerfile: Dockerfile.virtuoso
         environment:
             - VIRT_SPARQL_MaxQueryCostEstimationTime=default
             - VIRT_SPARQL_MaxQueryExecutionTime=300
@@ -19,24 +12,18 @@ services:
             - type: volume
               source: virtuoso-db1
               target: /data
-        ports:
-            - "8890:8890"
-        restart: always  
-        labels:
-            - "autoheal=true"
-    synbiohubFrontend:
-        image: synbiohub/sbh3frontend:snapshot
-        ports:
-            - "3333:3333"
-        dns: 8.8.8.8
         restart: always
-        environment: 
-            - backend=http://localhost:7777
-            - backendSS=http://synbiohub:7777
+        healthcheck:
+            test: ["CMD-SHELL", "curl -f http://localhost:8890/sparql"]
+            interval: 15s
+            timeout: 10s
+            retries: 4
+    
     synbiohub:
         image: synbiohub/synbiohub:1.6.1-standalone
-        depends_on: 
-            - virtuoso
+        depends_on:
+            virtuoso:
+                condition: service_healthy
         ports:
             - "7777:7777"
         volumes:
@@ -46,10 +33,13 @@ services:
             - type: volume
               source: virtuoso-db1
               target: /virtuoso
-        dns: 8.8.8.8
         restart: always
 
+    synbiohubFrontend:
+        image: synbiohub/sbh3frontend:snapshot
+        ports:
+            - "3333:3333"
+        restart: always
 volumes:
     virtuoso-db1:
     sbh1:
-

From ea9512b1ac4380b917f9dda4671379a3b093d41e Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Wed, 4 Jun 2025 16:31:51 -0600
Subject: [PATCH 2/3] Create Dockerfile.virtuoso

completes last commit
---
 Dockerfile.virtuoso | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 Dockerfile.virtuoso

diff --git a/Dockerfile.virtuoso b/Dockerfile.virtuoso
new file mode 100644
index 0000000..6a0ab81
--- /dev/null
+++ b/Dockerfile.virtuoso
@@ -0,0 +1,3 @@
+FROM tenforce/virtuoso:virtuoso7.2.5
+
+RUN apt-get update && apt-get install -y curl && rm -rf /var/lib/apt/lists/*

From ebe9877b9eb220d791fa1009bd952e20de0b9216 Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Tue, 10 Jun 2025 15:24:07 -0600
Subject: [PATCH 3/3] Update Dockerfile.virtuoso

no install recommends

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 Dockerfile.virtuoso | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile.virtuoso b/Dockerfile.virtuoso
index 6a0ab81..77054ff 100644
--- a/Dockerfile.virtuoso
+++ b/Dockerfile.virtuoso
@@ -1,3 +1,3 @@
 FROM tenforce/virtuoso:virtuoso7.2.5
 
-RUN apt-get update && apt-get install -y curl && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y --no-install-recommends curl && rm -rf /var/lib/apt/lists/*