Release Notes - SEEK - Version 1.5.0

New Feature

[OPSK-1408] - Add DataFile button on Assay page, also Add Model
[OPSK-1451] - Button to request to join a project

Improvement

[OPSK-1277] - Update to JERM 2 ontology
[OPSK-1296] - Allow sample attributes to follow an identification scheme
[OPSK-1302] - Make sure JSON keys use a consistent format
[OPSK-1303] - Use a consistent format for IDs
[OPSK-1309] - Consider hiding id attributes
[OPSK-1316] - Check/refactor Ability class
[OPSK-1336] - Fix how versions of data files are serialized
[OPSK-1337] - Fix how tags are serialized
[OPSK-1338] - Make sure "links" and "type" match and lead to a valid URL
[OPSK-1357] - Always use purl.bioontology for NCBI URI's for organism and strain
[OPSK-1403] - Change filtering in association view to filter by sub-strings
[OPSK-1405] - Get proper errors out of JSON validation
[OPSK-1413] - Add versions attribute to versioned assets
[OPSK-1414] - Add a UUID to organism
[OPSK-1416] - Move the content blobs out of relationships and show as part of the attributes
[OPSK-1417] - Include links for listed versions
[OPSK-1418] - Model format, type, and environment should just be shown as text
[OPSK-1424] - Combine JSON schemas into one file
[OPSK-1425] - Add title and href to elements of resource index lists
[OPSK-1426] - Prevent samples and sample types JSON output
[OPSK-1432] - Change rest test case code for error codes
[OPSK-1436] - Order resource lists
[OPSK-1439] - content testing for maximal objects
[OPSK-1440] - content testing for minimal objects
[OPSK-1446] - change 'tags' to 'funding_code' in programme_serializer
[OPSK-1450] - Improve look of project positions on person show page
[OPSK-1458] - show whether items have snapshots in resource list view
[OPSK-1460] - Enforce singleton relationships
[OPSK-1461] - Make orcid more prominent and appear on the resource list items
[OPSK-1478] - Make DOI creation more apparent
[OPSK-1500] - Exception emails aren't always being sent
[OPSK-1536] - Add new units ng, µg/ml, mg/ml, µg/µl, CFU

Bug

[OPSK-807] - Research Object has problems
[OPSK-1194] - name recognition does not properly work
[OPSK-1231] - Include CM (centimetre) in the list of units
[OPSK-1234] - Some issues on the ISA graph when things have multiple parents
[OPSK-1284] - Check and update File.open().read cases
[OPSK-1304] - Orcid id missing from person details
[OPSK-1305] - email address being exposed in JSON
[OPSK-1306] - JSON should not include extra unless asked
[OPSK-1310] - Attributes called id are not allowed
[OPSK-1311] - Suggested assay/tech type isn't selected when editing an assay
[OPSK-1339] - Fix id of content_blob when presenting different versions
[OPSK-1340] - hidden and total counts in XML does not match html count
[OPSK-1349] - Getting /programmes does not work if programmes disabled
[OPSK-1375] - Clear our the sharing_scope=2 when asset is updated by a manager
[OPSK-1389] - Content Blobs aren't resolvable, just results in a download
[OPSK-1390] - Publication authors are shown for publication JSON
[OPSK-1393] - statistics wrong/ assay type
[OPSK-1397] - Related assets is wrong for programme
[OPSK-1399] - Problem reading and displaying JSON text file with new lines and readlines
[OPSK-1402] - RDF doesn't sychronise properly when the type changes
[OPSK-1407] - Institutions are only partially correct correctly in the rdf
[OPSK-1415] - undefined method `rdf_repository_configured?' for Event
[OPSK-1419] - remove workgroups from person JSON representation
[OPSK-1421] - Only show the version dropdown selection if logged into SEEK
[OPSK-1423] - Correct JSON for get assay
[OPSK-1429] - Organism does not show correct relationships to strains
[OPSK-1431] - Hide strain behind NotImplemented
[OPSK-1435] - Changing a suggested type should update all associated assays
[OPSK-1438] - JSON must include version number
[OPSK-1449] - Error when filtering people by discipline
[OPSK-1452] - Should notify user by email when they are added to a project
[OPSK-1454] - Project json schema ignored addition of "programmes"
[OPSK-1457] - Clean out Specimens from ResourcePublishLog
[OPSK-1462] - Citation box doesn't appear for Assets with a DOI
[OPSK-1464] - RO internal paths can exceed Windows MAX_PATH length
[OPSK-1466] - Fix DOI in RDF
[OPSK-1467] - Gatekeeper email incorrectly sent
[OPSK-1488] - email checksum in JSON has email attribute name
[OPSK-1492] - Error when getting Storage stats on the fairdomhub
[OPSK-1509] - DOI isn't displayed quite right for publication
[OPSK-1511] - Missing project error, when creating a publication
[OPSK-1512] - Check & remove strains and samples from relationships of readAPI objects
[OPSK-1514] - Non-visible samples are listed for sample type
[OPSK-1515] - Samples and strains are listed in the results of search JSON
[OPSK-1518] - Make snapshot prevention reason more obvious
[OPSK-1529] - Fix subscription job delay
[OPSK-1530] - Snapshotting an assay with samples in it causes an error
[OPSK-1537] - nil error for rdf generation when the ncbi id is nil (or incorrect)

Task

[OPSK-1307] - Document API on SwaggerHub
[OPSK-1308] - Check return codes are correct
[OPSK-1312] - Update JERM ontology to JERM2
[OPSK-1313] - Update ontology uri's for JERM2
[OPSK-1319] - Update RDF for JERM2
[OPSK-1343] - Make plain JSON acceptable to the API
[OPSK-1348] - Fix getting of many projects
[OPSK-1369] - Include search in the JSON API
[OPSK-1396] - Move schemas to somewhere better
[OPSK-1398] - RDF doesn't appear in public graph after data file is made public
[OPSK-1411] - JSON schemas for indexing
[OPSK-1412] - JSON schemas for show/get
[OPSK-1437] - upgrade task to strip trailing spaces from weblinks
[OPSK-1444] - Document search API
[OPSK-1480] - Set up sparql endpoint for fairdomhub
[OPSK-1489] - Publishing should clear the policy sharing scope
[OPSK-1493] - Clean out dangling policies
[OPSK-1494] - Clean out policies set to sharing scope ALL_USERS
[OPSK-1528] - Docker Mysql container for docker compose needs to be UTF-8
[OPSK-1535] - Document the request to join a project

Sub-task

[OPSK-1320] - Check over current mappings
[OPSK-1321] - Update RDF for validation and construction data
[OPSK-1322] - Check for mssing bi-directional statements
[OPSK-1323] - Include jerm:title and jerm:description terms
[OPSK-1324] - Describe Programmes in RDF
[OPSK-1325] - Describe assay hasInput and hasOutput in RDF
[OPSK-1326] - Describe Assay hasPart <Asset> in RDF
[OPSK-1327] - Include Assay isAssociatedWith <Sop> in RDF
[OPSK-1330] - Include SEEKID for relevant classes in RDF
[OPSK-1331] - Include Person isAssociatedWith <Project> in RDF
[OPSK-1332] - Add Project WEBLINK <uri> in RDF
[OPSK-1333] - Include Strain is_investigated_by in RDF
[OPSK-1334] - Make sure the Assay is the appropriate class, according to whether it is Experimental or Modelling
[OPSK-1361] - Change behaviour to allow simulation data to be flagged as such when uploaded
[OPSK-1385] - Fix SEEK_ID to only be shown for appropriate types
[OPSK-1391] - Update terms following ontology refactoring
[OPSK-1392] - Check and update modelling_analysis and experimental_assay tech types
[OPSK-1505] - Maximal object JSON API content testing for ISA
[OPSK-1506] - Maximal object JSON API content testing for Yellow pages
[OPSK-1507] - Maximal object JSON API content testing for Assets
[OPSK-1508] - Maximal object JSON API content testing for Activities
[OPSK-1531] - Check DOI search indexing still works

Issue

[OPSK-1362] - problem with view content at presentation
[OPSK-1400] - Change empty string output to null
[OPSK-1434] - Associate data files filter shows duplicates
[OPSK-1441] - Check cache expiration is working
[OPSK-1442] - Tagging autocompleter displays "[object Object]" when there are no matches
[OPSK-1459] - Split factories up
[OPSK-1468] - "Show more" not working for some nodes in ISA graph
[OPSK-1510] - Nil error when getting bio reference for a pre-print