fix some issues preventing the docker container from starting

docker/Dockerfile

@@ -1,14 +1,15 @@
 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 . . 
 
+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 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 && \
@@ -30,7 +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
 
-HEALTHCHECK --start-period=60s CMD ["node", "healthcheck.js"] 
-ENTRYPOINT ["./entry.sh"]
-
+ENTRYPOINT ["./docker/entry.sh"]

docker/saveconfig.sh

@@ -0,0 +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!"

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)
+}

lib/config.js

@@ -1,4 +1,3 @@
-
 var fs = require('fs')
 var extend = require('xtend')
 var deepmerge = require('deepmerge')

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)
+  return updateQuery(sparql, graphUri, 'application/sparql-results+json')
+    .then(parseResult)
+    .catch(handleError)
 
   function parseResult (res) {
     // timer()
@@ -71,6 +73,12 @@ 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 +208,10 @@ function deleteStaggered (sparql, graphUri) {
       } else {
         return performQuery()
       }
+    }).catch((error) => {
+      console.error('Delete operation failed')
+      console.error(error.stack)
+      return Promise.reject(error)
     })
   }
 }

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()