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release-notes-1.5.0.html
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Release Notes - SEEK - Version 1.5.0
<h2> New Feature
</h2>
<ul>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1408'>OPSK-1408</a>] - Add DataFile button on Assay page, also Add Model
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1451'>OPSK-1451</a>] - Button to request to join a project
</li>
</ul>
<h2> Improvement
</h2>
<ul>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1277'>OPSK-1277</a>] - Update to JERM 2 ontology
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1296'>OPSK-1296</a>] - Allow sample attributes to follow an identification scheme
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1302'>OPSK-1302</a>] - Make sure JSON keys use a consistent format
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1303'>OPSK-1303</a>] - Use a consistent format for IDs
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1309'>OPSK-1309</a>] - Consider hiding id attributes
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1316'>OPSK-1316</a>] - Check/refactor Ability class
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1336'>OPSK-1336</a>] - Fix how versions of data files are serialized
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1337'>OPSK-1337</a>] - Fix how tags are serialized
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1338'>OPSK-1338</a>] - Make sure "links" and "type" match and lead to a valid URL
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1357'>OPSK-1357</a>] - Always use purl.bioontology for NCBI URI's for organism and strain
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1403'>OPSK-1403</a>] - Change filtering in association view to filter by sub-strings
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1405'>OPSK-1405</a>] - Get proper errors out of JSON validation
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1413'>OPSK-1413</a>] - Add versions attribute to versioned assets
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1414'>OPSK-1414</a>] - Add a UUID to organism
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1416'>OPSK-1416</a>] - Move the content blobs out of relationships and show as part of the attributes
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1417'>OPSK-1417</a>] - Include links for listed versions
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1418'>OPSK-1418</a>] - Model format, type, and environment should just be shown as text
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1424'>OPSK-1424</a>] - Combine JSON schemas into one file
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1425'>OPSK-1425</a>] - Add title and href to elements of resource index lists
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1426'>OPSK-1426</a>] - Prevent samples and sample types JSON output
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1432'>OPSK-1432</a>] - Change rest test case code for error codes
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1436'>OPSK-1436</a>] - Order resource lists
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1439'>OPSK-1439</a>] - content testing for maximal objects
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1440'>OPSK-1440</a>] - content testing for minimal objects
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1446'>OPSK-1446</a>] - change 'tags' to 'funding_code' in programme_serializer
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1450'>OPSK-1450</a>] - Improve look of project positions on person show page
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1458'>OPSK-1458</a>] - show whether items have snapshots in resource list view
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1460'>OPSK-1460</a>] - Enforce singleton relationships
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1461'>OPSK-1461</a>] - Make orcid more prominent and appear on the resource list items
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1478'>OPSK-1478</a>] - Make DOI creation more apparent
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1500'>OPSK-1500</a>] - Exception emails aren't always being sent
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1536'>OPSK-1536</a>] - Add new units ng, µg/ml, mg/ml, µg/µl, CFU
</li>
</ul>
<h2> Bug
</h2>
<ul>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-807'>OPSK-807</a>] - Research Object has problems
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1194'>OPSK-1194</a>] - name recognition does not properly work
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1231'>OPSK-1231</a>] - Include CM (centimetre) in the list of units
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1234'>OPSK-1234</a>] - Some issues on the ISA graph when things have multiple parents
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1284'>OPSK-1284</a>] - Check and update File.open().read cases
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1304'>OPSK-1304</a>] - Orcid id missing from person details
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1305'>OPSK-1305</a>] - email address being exposed in JSON
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1306'>OPSK-1306</a>] - JSON should not include extra unless asked
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1310'>OPSK-1310</a>] - Attributes called id are not allowed
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1311'>OPSK-1311</a>] - Suggested assay/tech type isn't selected when editing an assay
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1339'>OPSK-1339</a>] - Fix id of content_blob when presenting different versions
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1340'>OPSK-1340</a>] - hidden and total counts in XML does not match html count
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1349'>OPSK-1349</a>] - Getting /programmes does not work if programmes disabled
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1375'>OPSK-1375</a>] - Clear our the sharing_scope=2 when asset is updated by a manager
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1389'>OPSK-1389</a>] - Content Blobs aren't resolvable, just results in a download
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1390'>OPSK-1390</a>] - Publication authors are shown for publication JSON
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1393'>OPSK-1393</a>] - statistics wrong/ assay type
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1397'>OPSK-1397</a>] - Related assets is wrong for programme
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1399'>OPSK-1399</a>] - Problem reading and displaying JSON text file with new lines and readlines
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1402'>OPSK-1402</a>] - RDF doesn't sychronise properly when the type changes
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1407'>OPSK-1407</a>] - Institutions are only partially correct correctly in the rdf
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1415'>OPSK-1415</a>] - undefined method `rdf_repository_configured?' for Event
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1419'>OPSK-1419</a>] - remove workgroups from person JSON representation
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1421'>OPSK-1421</a>] - Only show the version dropdown selection if logged into SEEK
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1423'>OPSK-1423</a>] - Correct JSON for get assay
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1429'>OPSK-1429</a>] - Organism does not show correct relationships to strains
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1431'>OPSK-1431</a>] - Hide strain behind NotImplemented
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1435'>OPSK-1435</a>] - Changing a suggested type should update all associated assays
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1438'>OPSK-1438</a>] - JSON must include version number
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1449'>OPSK-1449</a>] - Error when filtering people by discipline
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1452'>OPSK-1452</a>] - Should notify user by email when they are added to a project
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1454'>OPSK-1454</a>] - Project json schema ignored addition of "programmes"
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1457'>OPSK-1457</a>] - Clean out Specimens from ResourcePublishLog
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1462'>OPSK-1462</a>] - Citation box doesn't appear for Assets with a DOI
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1464'>OPSK-1464</a>] - RO internal paths can exceed Windows MAX_PATH length
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1466'>OPSK-1466</a>] - Fix DOI in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1467'>OPSK-1467</a>] - Gatekeeper email incorrectly sent
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1488'>OPSK-1488</a>] - email checksum in JSON has email attribute name
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1492'>OPSK-1492</a>] - Error when getting Storage stats on the fairdomhub
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1509'>OPSK-1509</a>] - DOI isn't displayed quite right for publication
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1511'>OPSK-1511</a>] - Missing project error, when creating a publication
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1512'>OPSK-1512</a>] - Check & remove strains and samples from relationships of readAPI objects
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1514'>OPSK-1514</a>] - Non-visible samples are listed for sample type
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1515'>OPSK-1515</a>] - Samples and strains are listed in the results of search JSON
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1518'>OPSK-1518</a>] - Make snapshot prevention reason more obvious
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1529'>OPSK-1529</a>] - Fix subscription job delay
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1530'>OPSK-1530</a>] - Snapshotting an assay with samples in it causes an error
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1537'>OPSK-1537</a>] - nil error for rdf generation when the ncbi id is nil (or incorrect)
</li>
</ul>
<h2> Task
</h2>
<ul>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1307'>OPSK-1307</a>] - Document API on SwaggerHub
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1308'>OPSK-1308</a>] - Check return codes are correct
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1312'>OPSK-1312</a>] - Update JERM ontology to JERM2
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1313'>OPSK-1313</a>] - Update ontology uri's for JERM2
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1319'>OPSK-1319</a>] - Update RDF for JERM2
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1343'>OPSK-1343</a>] - Make plain JSON acceptable to the API
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1348'>OPSK-1348</a>] - Fix getting of many projects
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1369'>OPSK-1369</a>] - Include search in the JSON API
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1396'>OPSK-1396</a>] - Move schemas to somewhere better
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1398'>OPSK-1398</a>] - RDF doesn't appear in public graph after data file is made public
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1411'>OPSK-1411</a>] - JSON schemas for indexing
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1412'>OPSK-1412</a>] - JSON schemas for show/get
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1437'>OPSK-1437</a>] - upgrade task to strip trailing spaces from weblinks
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1444'>OPSK-1444</a>] - Document search API
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1480'>OPSK-1480</a>] - Set up sparql endpoint for fairdomhub
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1489'>OPSK-1489</a>] - Publishing should clear the policy sharing scope
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1493'>OPSK-1493</a>] - Clean out dangling policies
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1494'>OPSK-1494</a>] - Clean out policies set to sharing scope ALL_USERS
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1528'>OPSK-1528</a>] - Docker Mysql container for docker compose needs to be UTF-8
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1535'>OPSK-1535</a>] - Document the request to join a project
</li>
</ul>
<h2> Sub-task
</h2>
<ul>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1320'>OPSK-1320</a>] - Check over current mappings
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1321'>OPSK-1321</a>] - Update RDF for validation and construction data
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1322'>OPSK-1322</a>] - Check for mssing bi-directional statements
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1323'>OPSK-1323</a>] - Include jerm:title and jerm:description terms
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1324'>OPSK-1324</a>] - Describe Programmes in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1325'>OPSK-1325</a>] - Describe assay hasInput and hasOutput in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1326'>OPSK-1326</a>] - Describe Assay hasPart <Asset> in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1327'>OPSK-1327</a>] - Include Assay isAssociatedWith <Sop> in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1330'>OPSK-1330</a>] - Include SEEKID for relevant classes in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1331'>OPSK-1331</a>] - Include Person isAssociatedWith <Project> in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1332'>OPSK-1332</a>] - Add Project WEBLINK <uri> in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1333'>OPSK-1333</a>] - Include Strain is_investigated_by in RDF
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1334'>OPSK-1334</a>] - Make sure the Assay is the appropriate class, according to whether it is Experimental or Modelling
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1361'>OPSK-1361</a>] - Change behaviour to allow simulation data to be flagged as such when uploaded
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1385'>OPSK-1385</a>] - Fix SEEK_ID to only be shown for appropriate types
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1391'>OPSK-1391</a>] - Update terms following ontology refactoring
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1392'>OPSK-1392</a>] - Check and update modelling_analysis and experimental_assay tech types
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1505'>OPSK-1505</a>] - Maximal object JSON API content testing for ISA
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1506'>OPSK-1506</a>] - Maximal object JSON API content testing for Yellow pages
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1507'>OPSK-1507</a>] - Maximal object JSON API content testing for Assets
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1508'>OPSK-1508</a>] - Maximal object JSON API content testing for Activities
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1531'>OPSK-1531</a>] - Check DOI search indexing still works
</li>
</ul>
<h2> Issue
</h2>
<ul>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1362'>OPSK-1362</a>] - problem with view content at presentation
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1400'>OPSK-1400</a>] - Change empty string output to null
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1434'>OPSK-1434</a>] - Associate data files filter shows duplicates
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1441'>OPSK-1441</a>] - Check cache expiration is working
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1442'>OPSK-1442</a>] - Tagging autocompleter displays "[object Object]" when there are no matches
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1459'>OPSK-1459</a>] - Split factories up
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1468'>OPSK-1468</a>] - "Show more" not working for some nodes in ISA graph
</li>
<li>[<a href='https://jira-bsse.ethz.ch/browse/OPSK-1510'>OPSK-1510</a>] - Nil error when getting bio reference for a pre-print
</li>
</ul>