From 6eed01a8829048d1ef68636354acc1bec7446670 Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Wed, 2 Jul 2025 10:23:38 -0600
Subject: [PATCH 1/8] fix some issues preventing the docker container from
 starting

---
 docker/Dockerfile     |  8 +++-----
 docker/healthcheck.js | 10 ----------
 docker/saveconfig.sh  |  7 +++++++
 gitrevupdate.js       | 18 ++++++++++++++++++
 lib/config.js         |  1 -
 lib/sparql/sparql.js  | 12 +++++++++++-
 synbiohub.js          |  3 ---
 7 files changed, 39 insertions(+), 20 deletions(-)
 delete mode 100644 docker/healthcheck.js
 create mode 100755 docker/saveconfig.sh
 create mode 100644 gitrevupdate.js

diff --git a/docker/Dockerfile b/docker/Dockerfile
index f47f1e89a..99d1c5bd1 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -5,10 +5,11 @@ RUN apk add nss git openjdk8-jre openjdk8 maven python alpine-sdk libxml2-dev ya
 WORKDIR /synbiohub
 COPY . . 
 
+RUN git config --global url."https://".insteadOf git://
+RUN docker/saveconfig.sh
 RUN rm -rf .git
 
 RUN cd java && mvn package
-RUN git config --global url."https://".insteadOf git://
 RUN yarn install
 
 RUN mkdir /mnt/data && \
@@ -19,8 +20,6 @@ RUN mkdir /mnt/data && \
     mkdir /mnt/config
 
 COPY docker/config.local.json /mnt/config/config.local.json
-COPY docker/healthcheck.js healthcheck.js
-COPY docker/entry.sh entry.sh
 
 RUN ln -s /mnt/config/config.local.json ./config.local.json && \
     touch /mnt/data/synbiohub.sqlite && ln -s /mnt/data/synbiohub.sqlite ./synbiohub.sqlite && \
@@ -31,6 +30,5 @@ RUN ln -s /mnt/config/config.local.json ./config.local.json && \
 
 EXPOSE 7777
 
-HEALTHCHECK --start-period=60s CMD ["node", "healthcheck.js"] 
-ENTRYPOINT ["./entry.sh"]
+ENTRYPOINT ["./docker/entry.sh"]
 
diff --git a/docker/healthcheck.js b/docker/healthcheck.js
deleted file mode 100644
index b193f8135..000000000
--- a/docker/healthcheck.js
+++ /dev/null
@@ -1,10 +0,0 @@
-const axios = require('axios')
-const config = require('./lib/config')
-
-const url = 'http://localhost:' + config.get('port') + '/'
-
-axios.get(url).then(response => {
-  return process.exit(0)
-}).catch(error => {
-  return process.exit(1)
-})
diff --git a/docker/saveconfig.sh b/docker/saveconfig.sh
new file mode 100755
index 000000000..236eb5fb9
--- /dev/null
+++ b/docker/saveconfig.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+# Save git revision to config before removing .git folder
+echo "Saving git revision to configuration..."
+node gitrevupdate.js
+
+echo "Git revision saved successfully!"
\ No newline at end of file
diff --git a/gitrevupdate.js b/gitrevupdate.js
new file mode 100644
index 000000000..eb2aed785
--- /dev/null
+++ b/gitrevupdate.js
@@ -0,0 +1,18 @@
+#!/usr/bin/env node
+
+const config = require('./lib/config')
+const gitRev = require('./lib/gitRevision')
+
+console.log('Updating git revision in configuration...')
+
+// Get the current git revision
+const revision = gitRev()
+
+if (revision) {
+  // Set the revision in the config
+  config.set('revision', revision)
+  console.log(`Git revision updated to: ${revision}`)
+} else {
+  console.error('Failed to get git revision')
+  process.exit(1)
+}
\ No newline at end of file
diff --git a/lib/config.js b/lib/config.js
index 1f7652c09..3953c4a3a 100644
--- a/lib/config.js
+++ b/lib/config.js
@@ -1,4 +1,3 @@
-
 var fs = require('fs')
 var extend = require('xtend')
 var deepmerge = require('deepmerge')
diff --git a/lib/sparql/sparql.js b/lib/sparql/sparql.js
index 3c31ed128..da7455c8f 100644
--- a/lib/sparql/sparql.js
+++ b/lib/sparql/sparql.js
@@ -60,7 +60,7 @@ function updateQuery (sparql, graphUri, accept) {
 function updateQueryJson (sparql, graphUri) {
 // const timer = Timer('sparql query')
 
-  return updateQuery(sparql, graphUri, 'application/sparql-results+json').then(parseResult)
+  return updateQuery(sparql, graphUri, 'application/sparql-results+json').then(parseResult, handleError)
 
   function parseResult (res) {
     // timer()
@@ -71,6 +71,12 @@ function updateQueryJson (sparql, graphUri) {
 
     return Promise.resolve(sparqlResultsToArray(results))
   }
+
+  function handleError (error) {
+    console.error('SPARQL update query failed')
+    console.error(error.stack)
+    return Promise.reject(error)
+  }
 }
 
 function query (sparql, graphUri, accept, explorer = false) {
@@ -200,6 +206,10 @@ function deleteStaggered (sparql, graphUri) {
       } else {
         return performQuery()
       }
+    }).catch((error) => {
+      console.error('Delete operation failed')
+      console.error(error.stack)
+      return Promise.reject(error)
     })
   }
 }
diff --git a/synbiohub.js b/synbiohub.js
index d4f1feff6..cd8861643 100644
--- a/synbiohub.js
+++ b/synbiohub.js
@@ -4,7 +4,6 @@ const db = require('./lib/db')
 const fs = require('fs')
 const jobUtils = require('./lib/jobs/job-utils')
 const java = require('./lib/java')
-const gitRev = require('./lib/gitRevision')
 const logger = require('./lib/logger')
 const theme = require('./lib/theme')
 
@@ -22,8 +21,6 @@ if (!fs.existsSync('synbiohub.sqlite') || fs.statSync('synbiohub.sqlite').size =
   db.umzug.up().then(startServer)
 }
 
-config.set('revision', gitRev())
-
 async function startServer () {
   await java.init()
   await theme.setCurrentThemeFromConfig()

From b068ad539879b2b6439c84cbfd6596ca7bac125a Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Wed, 9 Jul 2025 12:22:58 -0600
Subject: [PATCH 2/8] Update Dockerfile

---
 docker/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 99d1c5bd1..1336deae2 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -29,6 +29,7 @@ RUN ln -s /mnt/config/config.local.json ./config.local.json && \
     ln -s /mnt/data/icons public/. 
 
 EXPOSE 7777
+HEALTHCHECK --interval=10s --timeout=10s --start-period=30s --retries=5 \
+  CMD curl -f http://localhost:7777/ || exit 1
 
 ENTRYPOINT ["./docker/entry.sh"]
-

From 7adf2e4b5ae3b8875d7ab890dfbdfb97442e8e8b Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Mon, 14 Jul 2025 10:34:14 -0600
Subject: [PATCH 3/8] Apply suggestion from @Copilot

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

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 1336deae2..afc64e439 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -6,7 +6,7 @@ WORKDIR /synbiohub
 COPY . . 
 
 RUN git config --global url."https://".insteadOf git://
-RUN docker/saveconfig.sh
+RUN chmod +x docker/saveconfig.sh && ./docker/saveconfig.sh
 RUN rm -rf .git
 
 RUN cd java && mvn package

From 7cbdc733003b7315104dacbd69b41c7f81a01957 Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Mon, 14 Jul 2025 10:34:36 -0600
Subject: [PATCH 4/8] Update Dockerfile

---
 docker/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index afc64e439..bd4c4f56e 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,6 +1,6 @@
 FROM node:11.1.0-alpine
 
-RUN apk add nss git openjdk8-jre openjdk8 maven python alpine-sdk libxml2-dev yarn g++ gcc bash raptor2 jq
+RUN apk add nss git openjdk8-jre openjdk8 maven python alpine-sdk libxml2-dev yarn g++ gcc bash raptor2 jq curl
 
 WORKDIR /synbiohub
 COPY . . 

From 2a67205c0294a99cc046bdc5017250355889a6de Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Mon, 14 Jul 2025 10:36:46 -0600
Subject: [PATCH 5/8] Apply suggestion from @Copilot

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 lib/sparql/sparql.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/sparql/sparql.js b/lib/sparql/sparql.js
index da7455c8f..55461aeed 100644
--- a/lib/sparql/sparql.js
+++ b/lib/sparql/sparql.js
@@ -60,7 +60,9 @@ function updateQuery (sparql, graphUri, accept) {
 function updateQueryJson (sparql, graphUri) {
 // const timer = Timer('sparql query')
 
-  return updateQuery(sparql, graphUri, 'application/sparql-results+json').then(parseResult, handleError)
+  return updateQuery(sparql, graphUri, 'application/sparql-results+json')
+    .then(parseResult)
+    .catch(handleError)
 
   function parseResult (res) {
     // timer()

From 2fdb18d34d2493782b383b07433d2072d2d6ee24 Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Mon, 14 Jul 2025 10:39:43 -0600
Subject: [PATCH 6/8] Update saveconfig.sh

---
 docker/saveconfig.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docker/saveconfig.sh b/docker/saveconfig.sh
index 236eb5fb9..25782e637 100755
--- a/docker/saveconfig.sh
+++ b/docker/saveconfig.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
+set -o errexit
 
 # Save git revision to config before removing .git folder
 echo "Saving git revision to configuration..."
 node gitrevupdate.js
 
-echo "Git revision saved successfully!"
\ No newline at end of file
+echo "Git revision saved successfully!"

From 77c0f57f53196e66e2e72219ca414d7e3e6dfa80 Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Mon, 14 Jul 2025 10:43:53 -0600
Subject: [PATCH 7/8] Update Dockerfile

---
 docker/Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index bd4c4f56e..7cd6ab7bd 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -6,12 +6,13 @@ WORKDIR /synbiohub
 COPY . . 
 
 RUN git config --global url."https://".insteadOf git://
-RUN chmod +x docker/saveconfig.sh && ./docker/saveconfig.sh
-RUN rm -rf .git
 
 RUN cd java && mvn package
 RUN yarn install
 
+RUN chmod +x docker/saveconfig.sh && ./docker/saveconfig.sh
+RUN rm -rf .git
+
 RUN mkdir /mnt/data && \
     mkdir /mnt/data/backup && \
     mkdir /mnt/data/uploads && \

From dabe66aac33e410db9e361815153cea136146605 Mon Sep 17 00:00:00 2001
From: Peter Hindes <19994487+PeterHindes@users.noreply.github.com>
Date: Wed, 13 Aug 2025 11:51:24 -0600
Subject: [PATCH 8/8] simplify changes

---
 docker/Dockerfile    |  9 +++++----
 docker/saveconfig.sh |  8 --------
 lib/sparql/sparql.js | 14 +-------------
 3 files changed, 6 insertions(+), 25 deletions(-)
 delete mode 100755 docker/saveconfig.sh

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 7cd6ab7bd..50319bd0f 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -10,8 +10,8 @@ RUN git config --global url."https://".insteadOf git://
 RUN cd java && mvn package
 RUN yarn install
 
-RUN chmod +x docker/saveconfig.sh && ./docker/saveconfig.sh
-RUN rm -rf .git
+RUN node gitrevupdate.js
+RUN rm -rf .git ; apk del git
 
 RUN mkdir /mnt/data && \
     mkdir /mnt/data/backup && \
@@ -30,7 +30,8 @@ RUN ln -s /mnt/config/config.local.json ./config.local.json && \
     ln -s /mnt/data/icons public/. 
 
 EXPOSE 7777
-HEALTHCHECK --interval=10s --timeout=10s --start-period=30s --retries=5 \
-  CMD curl -f http://localhost:7777/ || exit 1
+
+HEALTHCHECK --interval=10s --timeout=10s --start-period=20s --retries=5 \
+  CMD ["node", "healthcheck.js"]
 
 ENTRYPOINT ["./docker/entry.sh"]
diff --git a/docker/saveconfig.sh b/docker/saveconfig.sh
deleted file mode 100755
index 25782e637..000000000
--- a/docker/saveconfig.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-set -o errexit
-
-# Save git revision to config before removing .git folder
-echo "Saving git revision to configuration..."
-node gitrevupdate.js
-
-echo "Git revision saved successfully!"
diff --git a/lib/sparql/sparql.js b/lib/sparql/sparql.js
index 55461aeed..3c31ed128 100644
--- a/lib/sparql/sparql.js
+++ b/lib/sparql/sparql.js
@@ -60,9 +60,7 @@ function updateQuery (sparql, graphUri, accept) {
 function updateQueryJson (sparql, graphUri) {
 // const timer = Timer('sparql query')
 
-  return updateQuery(sparql, graphUri, 'application/sparql-results+json')
-    .then(parseResult)
-    .catch(handleError)
+  return updateQuery(sparql, graphUri, 'application/sparql-results+json').then(parseResult)
 
   function parseResult (res) {
     // timer()
@@ -73,12 +71,6 @@ function updateQueryJson (sparql, graphUri) {
 
     return Promise.resolve(sparqlResultsToArray(results))
   }
-
-  function handleError (error) {
-    console.error('SPARQL update query failed')
-    console.error(error.stack)
-    return Promise.reject(error)
-  }
 }
 
 function query (sparql, graphUri, accept, explorer = false) {
@@ -208,10 +200,6 @@ function deleteStaggered (sparql, graphUri) {
       } else {
         return performQuery()
       }
-    }).catch((error) => {
-      console.error('Delete operation failed')
-      console.error(error.stack)
-      return Promise.reject(error)
     })
   }
 }