Merge branch 'master' into fixRemoveOwner

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/attachments.js

@@ -8,9 +8,20 @@ const sha1 = require('sha1')
 const uuid = require('uuid/v4')
 const { fetchSBOLObjectRecursive } = require('./fetch/fetch-sbol-object-recursive')
 
-function addAttachmentToTopLevel (graphUri, baseUri, topLevelUri, name, uploadHash, size, attachmentType, owner) {
-// console.log('Adding:'+name+' to:'+topLevelUri)
-  const displayId = 'attachment_' + uuid().replace(/-/g, '')
+function addAttachmentToTopLevel (graphUri, baseUri, topLevelUri, name, uploadHash, size, attachmentType, owner, id) {
+  // console.log('Adding:'+name+' to:'+topLevelUri)
+
+  // Replace non-alphanumeric characters and spaces with underscores
+  var cleanId = id
+  if (cleanId) {
+    cleanId = id.replace(/[^a-zA-Z0-9]/g, '_')
+    // Ensure it does not start with a number by prefixing an underscore if needed
+    if (/^\d/.test(cleanId)) {
+      cleanId = '_' + cleanId
+    }
+  }
+
+  const displayId = cleanId || 'attachment_' + uuid().replace(/-/g, '')
   const persistentIdentity = baseUri + '/' + displayId
   // TODO: should get version from topLevelUri
   const version = '1'
@@ -130,6 +141,7 @@ function getAttachmentsFromTopLevel (sbol, topLevel, share) {
           type: attachmentType,
           image: attachmentIsImage,
           url: url,
+          source: attachment.source.toString(),
           size: attachment.size,
           sizeString: attachment.size === -1 ? null : filesize(attachment.size)
         })
@@ -143,6 +155,7 @@ function getAttachmentsFromTopLevel (sbol, topLevel, share) {
           name: metaData.name,
           type: 'unknown',
           url: url,
+          source: 'unknown',
           size: -1,
           sizeString: 'unknown'
         })
@@ -194,6 +207,7 @@ function getAttachmentsFromList (graphUri, attachmentList, share) {
             name: attachment.name,
             type: format || 'Other',
             url: url,
+            source: attachment.source.toString(),
             size: size,
             sizeString: size === -1 ? null : filesize(size)
           })
@@ -204,6 +218,7 @@ function getAttachmentsFromList (graphUri, attachmentList, share) {
           name: 'Attachment is missing',
           type: 'Other',
           url: uri,
+          source: 'unknown',
           size: 0,
           sizeString: null
         })

lib/views/addToCollection.js

@@ -3,6 +3,7 @@ const pug = require('pug')
 const config = require('../config')
 const sparql = require('../sparql/sparql')
 const getOwnedBy = require('../query/ownedBy')
+const getUrisFromReq = require('../getUrisFromReq')
 
 module.exports = function (req, res) {
   req.setTimeout(0) // no timeout
@@ -18,11 +19,16 @@ module.exports = function (req, res) {
       }
     }
 
+    const { uri } = getUrisFromReq(req, res)
+
     return sparql.queryJson(collectionQuery, req.user.graphUri).then((collections) => {
-      collections.map((result) => {
+      collections = collections.filter((result) => {
+        return result.subject !== uri
+      }).map((result) => {
         result.uri = result.subject
         result.name = result.name ? result.name : result.uri.toString()
         delete result.subject
+        return result
       })
       collections.sort(sortByNames)
 
@@ -64,6 +70,20 @@ module.exports = function (req, res) {
       memberUri = memberUri.replace('/user/', config.get('databasePrefix') + 'user/')
     }
 
+    if (memberUri === uri) {
+      if (!req.accepts('text/html')) {
+        return res.status(400).type('text/plain').send('Cannot make a collection a member of itself')
+      } else {
+        const locals = {
+          config: config.get(),
+          section: 'errors',
+          user: req.user,
+          errors: [ 'Cannot make a collection a member of itself' ]
+        }
+        return res.status(400).send(pug.renderFile('templates/views/errors/errors.jade', locals))
+      }
+    }
+
     var templateParams = {
       uri: uri,
       memberUri: memberUri

lib/views/submit.js

@@ -467,8 +467,8 @@ async function handleSubmission (req, res, submission) {
 
   await sparql.uploadFile(submissionData.createdBy.graphUri, resultFilename, 'application/rdf+xml')
 
-  let baseURI = config.get('databasePrefix') + 'user/' + encodeURIComponent(submissionData.createdBy.username) + '/' + submissionData.collectionId
-  let collectionURI = baseURI + '/' + submissionData.collectionId + '_collection/' + submissionData.version
+  let baseURI = config.get('databasePrefix') + 'user/' + encodeURIComponent(submissionData.createdBy.username) + '/' + submissionData.collectionId.replace('_collection', '')
+  let collectionURI = baseURI + '/' + submissionData.collectionId + '/' + submissionData.version
 
   let sourceQuery = loadTemplate('sparql/GetAttachmentSourceFromTopLevel.sparql', { uri: collectionURI })
 
@@ -504,7 +504,6 @@ async function handleSubmission (req, res, submission) {
 
       return
     }
-
     let attachmentUri = await attachments.addAttachmentToTopLevel(
       submissionData.createdBy.graphUri,
       baseURI,
@@ -513,7 +512,7 @@ async function handleSubmission (req, res, submission) {
       hash,
       size,
       attachmentFiles[originalFilename] || mime,
-      submissionData.createdBy.username)
+      submissionData.createdBy.username, null)
 
     console.log(attachmentUri)
 

sparql/AttachUrl.sparql

@@ -5,6 +5,8 @@ PREFIX sbol: <http://sbols.org/v2#>
 INSERT {
     <$topLevel> sbol:attachment <$uri> .
 
+    <$collectionUri> sbol:member <$uri> .
+
     <$uri> a sbol:Attachment ;
         dcterms:title "$name" ;
         sbol:displayId "$displayId" ;

templates/mixins/attachments.jade

@@ -20,7 +20,7 @@ mixin attachments(url, attachments, canEdit)
                             if attachment.sizeString
                                 | #{attachment.sizeString}
                         td
-                            a(href=attachment.url + '/download')
+                            a(href=attachment.source)
                                 button.btn.btn-primary
                                     span.fa.fa-download
                                     |  Download
@@ -38,6 +38,9 @@ mixin attachments(url, attachments, canEdit)
                                     span.btn.btn-primary
                                         | Select file(s)…
                                         input(type="file",name="file",style="display: none;",multiple,form="sbh-attachment-upload")
+                            div.row(style="margin-top: 10px")
+                                div.col-md-6
+                                    input.form-control(type="text", name="id", placeholder="Name", form="sbh-attachment-upload")
                         td(colspan=2)
                             button.btn.btn-success(type='submit',style='width:100%;',form="sbh-attachment-upload") Attach
                     div.row

tests/previousresults/getrequest_user-:userId-:collectionId-:displayId_docker.html

@@ -526,6 +526,11 @@ <h4 class="panel-title">
                </span>
               </label>
              </div>
+             <div class="row" style="margin-top: 10px">
+              <div class="col-md-6">
+               <input class="form-control" form="sbh-attachment-upload" name="id" placeholder="Name" type="text"/>
+              </div>
+             </div>
             </td>
             <td colspan="2">
              <button class="btn btn-success" form="sbh-attachment-upload" style="width:100%" type="submit">