Merge branch 'master' into PeterHindes-patch-1

Author: cjmyers

.github/workflows/test.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Package image
         run: |
           docker save synbiohub/synbiohub:snapshot-standalone | gzip > sbh.tar.gz
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         name: Upload Docker image
         with:
           name: sbh-image
@@ -30,7 +30,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
         name: Checkout source tree
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         name: Download Docker image
         with:
           name: sbh-image
@@ -57,7 +57,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
         name: Checkout source tree
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         name: Download Docker image
         with:
           name: sbh-image
@@ -80,7 +80,7 @@ jobs:
     runs-on: ubuntu-latest
     if: endsWith(github.ref, 'master')
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         name: Download Docker iamge
         with:
           name: sbh-image

java/src/main/java/org/synbiohub/ConvertToGenBankJob.java

@@ -21,9 +21,7 @@ public void execute() throws Exception
     {
             ByteArrayOutputStream logOutputStream = new ByteArrayOutputStream();
             ByteArrayOutputStream errorOutputStream = new ByteArrayOutputStream();
-            
-            System.err.println("GFF3="+gff3Out);
-            
+             
             SBOLDocument doc = SBOLValidate.validate(
             		new PrintStream(logOutputStream),
             		new PrintStream(errorOutputStream),
@@ -45,9 +43,11 @@ public void execute() throws Exception
             		false,
             		false,
             		gff3Out,
+            		false,
             		"",
             		false,
             		false,
+            		false,
             		false);
 
 		String log = new String(logOutputStream.toByteArray(), StandardCharsets.UTF_8);

java/src/main/java/org/synbiohub/PrepareSubmissionJob.java

@@ -87,6 +87,7 @@ public class PrepareSubmissionJob extends Job {
 	public String tempDirPath;
 	public boolean useSBOLExplorer;
 	public String SBOLExplorerEndpoint;
+	public String user;
 
 	private boolean readCOMBINEArchive(String initialFilename, Map<String, String> attachments) {
 		CombineArchive combine = null;
@@ -481,6 +482,7 @@ public void visit(Identified identified, TopLevel topLevel) {
 				// Check if the object is already in the collection
 				for (String registry : webOfRegistries.keySet()) {
 					SynBioHubFrontend sbh = new SynBioHubFrontend(webOfRegistries.get(registry), registry);
+					sbh.setUser(user);
 					if (topLevel.getIdentity().toString().startsWith(registry)) {
 
 						// Fetch the object from SynBioHub

lib/actions/addOwnedBy.js

@@ -4,10 +4,20 @@ const config = require('../config')
 const getOwnedBy = require('../query/ownedBy')
 const retrieveUris = require('../retrieveUris')
 const getUrisFromReq = require('../getUrisFromReq')
+const db = require('../db')
 
-module.exports = function (req, res) {
+module.exports = async function (req, res) {
   const userUri = req.body.user
 
+  var userId = ''
+  if (req.body.user.lastIndexOf('/') >= 0) {
+    userId = req.body.user.substring(req.body.user.lastIndexOf('/') + 1)
+  }
+
+  const user = await db.model.User.findOne({
+    where: db.sequelize.or({ email: userId }, { username: userId })
+  })
+
   const { graphUri, uri } = getUrisFromReq(req, res)
 
   const sharedAdditionQuery = loadTemplate('./sparql/AddToSharedCollection.sparql', {
@@ -23,6 +33,12 @@ module.exports = function (req, res) {
       })
     }
 
+    if (!user) {
+      return new Promise(function (resolve, reject) {
+        reject(new Error('user ' + userId + ' not recognized'))
+      })
+    }
+
     return sparql.updateQuery(sharedAdditionQuery, userUri).then(() => {
       return retrieveUris(uri, graphUri)
     }).then((uris) => {

lib/actions/makePublic.js

@@ -26,6 +26,8 @@ var fs = require('mz/fs')
 
 const prepareSubmission = require('../prepare-submission')
 
+const apiTokens = require('../apiTokens')
+
 module.exports = function (req, res) {
   req.setTimeout(0) // no timeout
 
@@ -225,10 +227,11 @@ module.exports = function (req, res) {
         rootCollectionIdentity: config.get('databasePrefix') + 'public/' + collectionId + '/' + collectionId + '_collection' + '/' + version,
         newRootCollectionDisplayId: collectionId + '_collection',
         newRootCollectionVersion: version,
-        ownedByURI: config.get('databasePrefix') + 'user/' + req.user.username,
+        ownedByURI: config.get('databasePrefix') + 'user/' + req.params.userId,
         creatorName: '',
         citationPubmedIDs: citations,
-        overwrite_merge: overwriteMerge
+        overwrite_merge: overwriteMerge,
+        user: apiTokens.createToken(req.user)
 
       })
     }).then((result) => {

lib/actions/removeOwnedBy.js

@@ -6,20 +6,19 @@ const loadTemplate = require('../loadTemplate')
 const getOwnedBy = require('../query/ownedBy')
 
 module.exports = function (req, res) {
-  const { graphUri, uri, share } = getUrisFromReq(req, res)
+  const { graphUri, uri, url } = getUrisFromReq(req, res)
 
   return getOwnedBy(uri, graphUri).then((ownedBy) => {
     if (ownedBy.indexOf(config.get('databasePrefix') + 'user/' + req.user.username) === -1) {
-      res.status(401).send('not authorized to remove an owner')
+      return res.status(401).send('Not authorized to remove an owner')
     }
 
-    return retrieveUris(uri, graphUri).then(uris => {
+    return retrieveUris(uri, graphUri).then((uris) => {
       let chunks = []
       let offset = config.get('resolveBatch')
 
       for (let i = 0; i < uris.length; i += offset) {
         let end = i + offset < uris.length ? i + offset : uris.length
-
         chunks.push(uris.slice(i, end))
       }
 
@@ -30,22 +29,33 @@ module.exports = function (req, res) {
 
       console.log(sharedRemovalQuery)
 
-      return sparql.updateQuery(sharedRemovalQuery, req.body.userUri).then(result => {
-        return Promise.all(chunks.map(chunk => {
-          let uris = chunk.map(uri => {
-            return '<' + uri + '> sbh:ownedBy <' + req.body.userUri + '>'
-          }).join(' . \n')
-
-          const updateQuery = loadTemplate('./sparql/RemoveOwnedBy.sparql', {
-            uris: uris
-          })
-          console.log(updateQuery)
-
-          return sparql.updateQuery(updateQuery, graphUri).then(() => {
-            res.redirect(share)
-          })
-        }))
-      })
+      return sparql.updateQuery(sharedRemovalQuery, req.body.userUri)
+        .then(() => {
+          return Promise.all(
+            chunks.map((chunk) => {
+              let uris = chunk
+                .map((uri) => `<${uri}> sbh:ownedBy <${req.body.userUri}>`)
+                .join(' . \n')
+
+              const updateQuery = loadTemplate('./sparql/RemoveOwnedBy.sparql', { uris })
+              console.log(updateQuery)
+
+              return sparql.updateQuery(updateQuery, graphUri)
+            })
+          )
+        })
+        .then(() => {
+          // Redirect only once after all promises resolve
+          if (!req.accepts('text/html')) {
+            res.status(200).send('Success')
+          } else {
+            res.redirect(url)
+          }
+        })
+        .catch((err) => {
+          console.error('Error:', err)
+          res.status(500).send(`Error removing ownership: ${err.message}`)
+        })
     })
   })
 }

lib/actions/upload.js

@@ -31,6 +31,13 @@ module.exports = function (req, res) {
       return res.status(401).send('not authorized to edit this submission')
     }
 
+    let formFields = {} // Object to store parsed form fields
+
+    form.on('field', (name, value) => {
+      // Capture the form fields, such as `id`
+      formFields[name] = value
+    })
+
     form.on('part', (partStream) => {
       if (partStream.filename) {
         uploads.createUpload(partStream).then((uploadInfo) => {
@@ -41,7 +48,7 @@ module.exports = function (req, res) {
 
           return attachments.addAttachmentToTopLevel(
             graphUri, baseUri, uri, partStream.filename, hash, size,
-            mime, req.user.username)
+            mime, req.user.username, formFields.id)
         }).then(() => {
           var templateParams = {
             uri: uri

lib/api/attachUrl.js

@@ -11,11 +11,18 @@ async function serve (req, res) {
   let typeString = req.body.type
   let name = req.body.name || uuid()
 
-  let displayId = name
+  // Replace non-alphanumeric characters and spaces with underscores
+  let displayId = name.replace(/[^a-zA-Z0-9]/g, '_')
+  // Ensure it does not start with a number by prefixing an underscore if needed
+  if (/^\d/.test(displayId)) {
+    displayId = '_' + displayId
+  }
+
   let version = '1'
   let attachmentUri = `${baseUri}/${displayId}/${version}`
   let persistentIdentity = `${baseUri}/${displayId}`
   let ownedBy = await getOwnedBy(uri, graphUri)
+  const collectionUri = baseUri + baseUri.slice(baseUri.lastIndexOf('/')) + '_collection/' + version
 
   if (ownedBy.indexOf(config.get('databasePrefix') + 'user/' + req.user.username) === -1) {
     if (!req.accepts('text/html')) {
@@ -52,7 +59,8 @@ async function serve (req, res) {
     ownedBy: ownedBy,
     uri: attachmentUri,
     source: source,
-    type: typeString
+    type: typeString,
+    collectionUri: collectionUri
   })
 
   console.log('attachUrl: ' + graphUri)

lib/api/datatables.js

@@ -56,11 +56,16 @@ function collectionMembersDatatable (req, res) {
   ]).then((result) => {
     const [count, filterCount, members] = result
 
+    const uniqueMembers = members.filter(
+      (item, index, self) =>
+        index === self.findIndex((t) => t.uri === item.uri)
+    )
+
     res.header('content-type', 'application/json').send(JSON.stringify({
       draw: parseInt(req.query.draw),
       recordsTotal: count,
       recordsFiltered: filterCount,
-      data: members.map((member) => {
+      data: uniqueMembers.map((member) => {
         var memberUrl = uriToUrl(member.uri)
         if (member.uri.toString().startsWith(config.get('databasePrefix') + 'user/')) {
           if (req.headers.referer.toString().endsWith('/share')) {

lib/api/shareLink.js

@@ -0,0 +1,15 @@
+
+var getUrisFromReq = require('../getUrisFromReq')
+
+function shareLink (req, res) {
+  const { graphUri, uri, share } = getUrisFromReq(req, res)
+
+  if (share && uri.startsWith(graphUri)) {
+    res.status(200).type('text/plain')
+    res.header('content-type', 'text/plain').send(share)
+  } else {
+    res.status(404).send(uri + ' not found')
+  }
+}
+
+module.exports = shareLink

lib/api/sparql.js

@@ -6,6 +6,8 @@ const SparqlGenerator = require('sparqljs').Generator
 
 const checkQuery = require('../checkSparqlQuery')
 
+const getUrisFromReq = require('../getUrisFromReq')
+
 module.exports = function (req, res) {
   if (req.method === 'POST') {
     query(req, res, req.body.query, req.body['default-graph-uri'])
@@ -15,8 +17,6 @@ module.exports = function (req, res) {
 }
 
 function query (req, res, rawQuery, graphUri) {
-  graphUri = graphUri || null
-
   const parser = new SparqlParser()
   const generator = new SparqlGenerator()
 
@@ -33,8 +33,19 @@ function query (req, res, rawQuery, graphUri) {
 
     queryString = generator.stringify(query)
 
+    var baseUri
+
+    if (req.url.toString().indexOf('?') >= 0 &&
+        req.url.toString().substring(0, req.url.toString().indexOf('?')).endsWith('/share/sparql')) {
+      ({ graphUri,
+        baseUri
+      } = getUrisFromReq(req, res))
+    } else {
+      graphUri = graphUri || null
+    }
+
     try {
-      checkQuery(query, req.user)
+      checkQuery(query, req.user, baseUri)
     } catch (e) {
       res.status(400).send(e.stack.split('\n')[0])
       return