Evaluate the use of sbol-db in SynBioHub as a replacement for Virtuoso

docker/Dockerfile

@@ -3,21 +3,27 @@ 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
 
 WORKDIR /synbiohub
-COPY . . 
 
-# RUN rm -rf .git
-
-RUN cd java && mvn package
 RUN git config --global url."https://".insteadOf git://
+
+# Install Node dependencies from the manifest + lockfile alone, in their own
+# cached layer, so application source changes don't re-run yarn install.
+# node_modules is excluded from the build context (.dockerignore), so this
+# install is what populates it.
+COPY package.json yarn.lock ./
 RUN yarn install
 
+# Application source and build. The yarn layer above stays cached across source
+# edits, so only the copy and the Java build below re-run on a code change.
+COPY . .
+RUN cd java && mvn package
+
 COPY docker/config.local.json config.initial.local.json
 COPY docker/healthcheck.js healthcheck.js
 COPY docker/entry.sh entry.sh
 COPY docker/first_run.sh first_run.sh
 
 EXPOSE 7777
 
-HEALTHCHECK --start-period=60s CMD ["node", "healthcheck.js"] 
+HEALTHCHECK --start-period=60s CMD ["node", "healthcheck.js"]
 ENTRYPOINT ["./entry.sh"]
-

lib/actions/makePublic.js

@@ -228,7 +228,7 @@ module.exports = function (req, res) {
         newRootCollectionDisplayId: collectionId + '_collection',
         newRootCollectionVersion: version,
         ownedByURI: config.get('databasePrefix') + 'user/' + req.params.userId,
-        creatorName: '',
+        creatorName: req.user.name,
         citationPubmedIDs: citations,
         overwrite_merge: overwriteMerge,
         user: apiTokens.createToken(req.user)

lib/fetch/local/fetch-sbol-object-recursive.js

@@ -349,7 +349,14 @@ return [
 '}'
 ]).join('\n') */
 
-  var from = 'FROM <' + config.get('databasePrefix') + 'public>' + ' FROM <' + graphUri + '>'
+  var from = 'FROM <' + config.get('databasePrefix') + 'public>'
+
+  // graphUri is null when resolving a purely public object. Only add the
+  // user-graph dataset clause when there is one; emitting `FROM <null>`
+  // produces an invalid (relative) IRI that a strict SPARQL parser rejects.
+  if (graphUri) {
+    from += ' FROM <' + graphUri + '>'
+  }
 
   var query = [
     isCount

lib/views/admin/graphs.js

@@ -9,7 +9,8 @@ module.exports = function (req, res) {
   const query = [
     'SELECT DISTINCT ?graph WHERE {',
     'GRAPH ?graph { ?s ?a ?t }',
-    '}'
+    '}',
+    'ORDER BY ?graph'
   ].join('\n')
 
   sparql.queryJson(query, null).then((results) => {

sparql/AttachUpload.sparql

@@ -3,7 +3,7 @@ PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX sbol: <http://sbols.org/v2#>
 
-INSERT {
+INSERT DATA {
     <$topLevel> sbol:attachment <$attachmentURI> .
 
     <$collectionUri> sbol:member <$attachmentURI> .

sparql/AttachUrl.sparql

@@ -2,7 +2,7 @@ PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
 PREFIX sbol: <http://sbols.org/v2#>
 
-INSERT {
+INSERT DATA {
     <$topLevel> sbol:attachment <$uri> .
 
     <$collectionUri> sbol:member <$uri> .

sparql/searchCount.sparql

@@ -16,10 +16,11 @@ PREFIX so: <http://identifiers.org/so/>
 PREFIX bench: <http://wiki.synbiohub.org/wiki/Terms/benchling#>
 PREFIX genbank: <http://www.ncbi.nlm.nih.gov/genbank#>
 
-select (sum(?tempcount) as ?count) WHERE {
+select (sum(?tempcount) as ?count)
+$from
+WHERE {
 {
     SELECT (count(distinct ?subject) as ?tempcount)
-    $from
     WHERE {
         $criteria
 

tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml

@@ -44,4 +44,4 @@ try {
 <a href="https://github.com/SynBioHub/synbiohub">View Source on Github</a>
 |
 <a href="https://github.com/synbiohub/synbiohub/issues">Report an Issue</a>
- <div class="testignore" style="display:inline-block">| v1.6.1 (6d694887)</div></span></div></body><script src="/js/saveSvgAsPng.js"></script><script src="/js/jquery/jquery-2.1.3.min.js"></script><script src="/js/bootstrap/bootstrap-3.3.4.js"></script><script src="/js/typeahead.bundle.js"></script><script src="/js/typeahead.jquery.min.js"></script><script src="/datatables.min.js"></script><script src="/js/pathseg.js"></script><script src="/js/chosen.jquery.js"></script><script src="/js/dropzone.js"></script><script src="/js/BootstrapMenu.js"></script><script src="/bundle.js"></script></head></html>
+ <div class="testignore" style="display:inline-block">| v1.6.1 (aa5056eb)</div></span></div></body><script src="/js/saveSvgAsPng.js"></script><script src="/js/jquery/jquery-2.1.3.min.js"></script><script src="/js/bootstrap/bootstrap-3.3.4.js"></script><script src="/js/typeahead.bundle.js"></script><script src="/js/typeahead.jquery.min.js"></script><script src="/datatables.min.js"></script><script src="/js/pathseg.js"></script><script src="/js/chosen.jquery.js"></script><script src="/js/dropzone.js"></script><script src="/js/BootstrapMenu.js"></script><script src="/bundle.js"></script></head></html>

tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbol_.xml

@@ -87,17 +87,6 @@
     <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
     <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
-    <sbol:component>
-      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012/1">
-        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012"/>
-        <sbol:displayId>BBa_C0012</sbol:displayId>
-        <sbol:version>1</sbol:version>
-        <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/1"/>
-        <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
-        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0012/1"/>
-        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
-      </sbol:Component>
-    </sbol:component>
     <sbol:component>
       <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/ECK120029600/1">
         <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/ECK120029600"/>
@@ -131,6 +120,17 @@
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012/1">
+        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012"/>
+        <sbol:displayId>BBa_C0012</sbol:displayId>
+        <sbol:version>1</sbol:version>
+        <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/1"/>
+        <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
+        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0012/1"/>
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+      </sbol:Component>
+    </sbol:component>
     <sbol:sequenceAnnotation>
       <sbol:SequenceAnnotation rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/anno1/1">
         <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/anno1"/>
@@ -231,68 +231,68 @@
     <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
     <sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
     <sbol:component>
-      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120/1">
-        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120"/>
-        <sbol:displayId>BBa_J61120</sbol:displayId>
+      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736/1">
+        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736"/>
+        <sbol:displayId>ECK120033736</sbol:displayId>
         <sbol:version>1</sbol:version>
         <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
         <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
-        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61120/1"/>
+        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/ECK120033736/1"/>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
     <sbol:component>
-      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040/1">
-        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040"/>
-        <sbol:displayId>BBa_E0040</sbol:displayId>
+      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010/1">
+        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010"/>
+        <sbol:displayId>BBa_R0010</sbol:displayId>
         <sbol:version>1</sbol:version>
         <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
         <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
-        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_E0040/1"/>
+        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_R0010/1"/>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
     <sbol:component>
-      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040/1">
-        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040"/>
-        <sbol:displayId>BBa_C0040</sbol:displayId>
+      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130/1">
+        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130"/>
+        <sbol:displayId>BBa_J61130</sbol:displayId>
         <sbol:version>1</sbol:version>
         <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
         <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
-        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0040/1"/>
+        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61130/1"/>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
     <sbol:component>
-      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736/1">
-        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736"/>
-        <sbol:displayId>ECK120033736</sbol:displayId>
+      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120/1">
+        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120"/>
+        <sbol:displayId>BBa_J61120</sbol:displayId>
         <sbol:version>1</sbol:version>
         <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
         <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
-        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/ECK120033736/1"/>
+        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61120/1"/>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
     <sbol:component>
-      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010/1">
-        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010"/>
-        <sbol:displayId>BBa_R0010</sbol:displayId>
+      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040/1">
+        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040"/>
+        <sbol:displayId>BBa_E0040</sbol:displayId>
         <sbol:version>1</sbol:version>
         <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
         <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
-        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_R0010/1"/>
+        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_E0040/1"/>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>
     <sbol:component>
-      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130/1">
-        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130"/>
-        <sbol:displayId>BBa_J61130</sbol:displayId>
+      <sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040/1">
+        <sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040"/>
+        <sbol:displayId>BBa_C0040</sbol:displayId>
         <sbol:version>1</sbol:version>
         <sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
         <sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
-        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61130/1"/>
+        <sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0040/1"/>
         <sbol:access rdf:resource="http://sbols.org/v2#public"/>
       </sbol:Component>
     </sbol:component>