Release Notes - SEEK - Version 1.6.0

New Feature

[OPSK-1272] - Project-specific configuration
[OPSK-1371] - Implement sample metadata extraction for NeLS files
[OPSK-1475] - Update Sample templates to use new metadata sheet
[OPSK-1476] - Update to workflow when uploading a data file, along with RightField metadata extraction
[OPSK-1549] - New asset type document
[OPSK-1735] - Docker support for running under a sub uri

Improvement

[OPSK-284] - Improve upload workflow
[OPSK-1147] - Document experimentalists
[OPSK-1496] - Setup the ActiveJob queue adaptor to use delayed job
[OPSK-1516] - SOLR not running causes 500
[OPSK-1543] - Remove biovel-related + workflows code
[OPSK-1564] - Indicate to user that they can't see any NeLS projects
[OPSK-1565] - Hide irrelevant info from NeLS DataFile show page
[OPSK-1576] - "Upload and Save" button is misleading when registering links to remote things
[OPSK-1593] - Remove Forum code
[OPSK-1626] - institution attributes should include country code
[OPSK-1629] - Remove acts_as_trashable
[OPSK-1637] - Include soffice in the application status info
[OPSK-1667] - Project title - if it is long no line break in sharing view
[OPSK-1677] - Show project roles on profile page
[OPSK-1691] - Alter NeLS data registration workflow to better mesh with the new data file upload process
[OPSK-1695] - Fix response for .rdf for those that dont' support it
[OPSK-1698] - Update spreadsheet extractor gem & jar files
[OPSK-1713] - Make download button easier to find
[OPSK-1714] - Re-word data file metadata modal title text
[OPSK-1716] - Make the JVM memory for spreadsheets configurable
[OPSK-1720] - In data file wizard - make the home button jump to start
[OPSK-1731] - Obfuscate displayed email in dropdown lists

Task

[OPSK-1347] - Ensure assay ID is passed through all NeLS requests
[OPSK-1351] - CU for Investigation
[OPSK-1352] - CU for Study
[OPSK-1353] - CU for Assay
[OPSK-1354] - Large file uploading support
[OPSK-1356] - CU for DataFile
[OPSK-1363] - CU for Programme
[OPSK-1364] - CU for Project
[OPSK-1365] - CU for Institution
[OPSK-1366] - CU for People
[OPSK-1367] - CU for Events
[OPSK-1370] - Make the URL field of NeLS data immutable
[OPSK-1377] - CU for organism
[OPSK-1379] - CU for model
[OPSK-1380] - CU for presentation
[OPSK-1381] - CU for Sop
[OPSK-1382] - CU for strain
[OPSK-1386] - Error on registering NeLS data loses form info
[OPSK-1410] - Automatically associate samples with assay
[OPSK-1422] - Breadcrumbs
[OPSK-1447] - Make relationships more meaningful
[OPSK-1472] - Integration tests demostrating creating ISA elements through the write API
[OPSK-1473] - Revisit and update DOI creation code, particular in relation to versioned assets
[OPSK-1479] - Integration tests demostrating creating Yellow Pages elements through the write API
[OPSK-1526] - update rubyzip gem
[OPSK-1559] - Define permissions through API
[OPSK-1560] - Be able to define relationships through the API
[OPSK-1569] - Check that items can only be associated with projects a person is a member of
[OPSK-1570] - Duplicate organisms on fairdomhub
[OPSK-1575] - Remove paperclip dependency
[OPSK-1578] - Convert the yellow pages testing framework to the json.erb framework
[OPSK-1580] - 3.4.2
[OPSK-1581] - 3.4.4
[OPSK-1592] - 4.0.0
[OPSK-1606] - Write JSON Schema description for CUD
[OPSK-1607] - Document CUD in Swagger(Hub)
[OPSK-1651] - Allow NeLS project configuration through UI if admin
[OPSK-1654] - Add or revise Max relationships in json api integration tests for yellow pages
[OPSK-1655] - add max patch - yellow pages
[OPSK-1669] - Complete Swagger Hub
[OPSK-1671] - Ensure Swagger does not have write execution
[OPSK-1690] - Increase session store timeout & make configurable
[OPSK-1703] - Write examples
[OPSK-1710] - Ensure errors are in definitions.json

Sub-task

[OPSK-1481] - Route and action to simply upload data file and store
[OPSK-1482] - Framework and mechanism for multiple steps,and maintaining state between them
[OPSK-1483] - Split the current form across the steps
[OPSK-1484] - Submit and create the data file entry
[OPSK-1485] - Extract RightField properties and populate forms
[OPSK-1486] - Step to create assay
[OPSK-1524] - Write CUD of investigation
[OPSK-1554] - Investigate best practice for file upload
[OPSK-1555] - Implement file upload
[OPSK-1556] - Register the metadata for the file
[OPSK-1558] - Update data file metadata
[OPSK-1566] - Make sure content blob linked to data file is the one uploaded
[OPSK-1568] - Check and ensure the activity logs are recorded for the created data file
[OPSK-1572] - Track and clean up dangling content blobs
[OPSK-1574] - Deleting content blobs should also clean up associated files
[OPSK-1597] - Write CUD for study
[OPSK-1598] - Test CUD of investigation
[OPSK-1599] - Test CUD of study
[OPSK-1600] - Write CUD of assay
[OPSK-1601] - Test CUD of assay
[OPSK-1602] - Pull out test commonality
[OPSK-1603] - Add max test for investigation
[OPSK-1604] - Add max test for study
[OPSK-1605] - Add max test for assay
[OPSK-1610] - Person min json.erb
[OPSK-1611] - Programme min json.erb
[OPSK-1612] - Project min json.erb
[OPSK-1613] - institution min json.erb
[OPSK-1614] - institution max json.erb
[OPSK-1615] - Person max json.erb
[OPSK-1616] - Project max json.erb
[OPSK-1617] - Programme max json.erb
[OPSK-1619] - Add read error states
[OPSK-1620] - Add create calls
[OPSK-1621] - Add create error states
[OPSK-1622] - Add update calls
[OPSK-1623] - Add update error states
[OPSK-1624] - Add delete calls
[OPSK-1625] - Add delete error states
[OPSK-1627] - Polish UI, add additional step necessary
[OPSK-1628] - Finalize first version of template
[OPSK-1632] - Separate upload and extraction steps
[OPSK-1633] - Ensure that associated study and/or assay is editable
[OPSK-1634] - Add ability to select the SOP when creating the assay, and also from the template
[OPSK-1639] - refactor api_test_helper before continuing with other objects
[OPSK-1653] - Add (or revise) max relationships
[OPSK-1659] - Assay permissions ?
[OPSK-1660] - Add FAIRDOM and RightField logos to the metadata sheet
[OPSK-1663] - Ambiguity issue when extracting from RDF
[OPSK-1664] - Display validation errors for Assay
[OPSK-1687] - Show warnings about extracted information
[OPSK-1688] - Display steps and progress at the top of the wizard
[OPSK-1699] - Permissions preview popup does not appear
[OPSK-1702] - Write Search example
[OPSK-1704] - Write search for specific kind example
[OPSK-1705] - Write creation of one of the Yellow Pages example
[OPSK-1706] - Write creation of an ISA structure example
[OPSK-1707] - Write creation of a remote data file example
[OPSK-1708] - Write creation of a local data file example
[OPSK-1709] - Write linkage within ISA example

Bug

[OPSK-1290] - Change content blob URL field type to be TEXT
[OPSK-1358] - Docs need to say how to upload a new version
[OPSK-1427] - NeLS location info does not work in production mode
[OPSK-1430] - Favourites cache is not expired when favourites are added/removed
[OPSK-1541] - GET people is paginated
[OPSK-1552] - Project admin can delete people
[OPSK-1553] - Remove subscriptions associated with Specimens
[OPSK-1563] - Error when exporting to Zenodo
[OPSK-1573] - Checkbox misaligned on "published_related_items" page
[OPSK-1577] - ContentBlob json rest test disabled
[OPSK-1618] - Make sure attr_encrypted key is 32 bytes
[OPSK-1638] - Ability to link publication to presentation appears to be missing
[OPSK-1641] - remove tags from max Investigation, max Study JSON-API (read) tests
[OPSK-1650] - Make NeLS endpoints configurable
[OPSK-1652] - Project settings using global defaults
[OPSK-1656] - on publication page creator's picture shown 2 times
[OPSK-1665] - Model added via link, with make a copy, not directly viewable or simulatable
[OPSK-1668] - Checksums not calculated for remote content, even after fetching
[OPSK-1680] - Study Experimentalist field is String and too short
[OPSK-1681] - Make publication formats fail more gracefully
[OPSK-1682] - SEEK ignores remote content filename in response headers
[OPSK-1683] - SEEK ignores original filename parameter when posting remote content through the API
[OPSK-1686] - People not associated with a project are not listed
[OPSK-1689] - Lack of error email reporting (on test server)
[OPSK-1701] - Remote content for content blob not validated
[OPSK-1712] - definitions.json has api_version ref
[OPSK-1715] - Settings with hash values do not have consistent keys
[OPSK-1717] - programmePost and programmePatch are wrong
[OPSK-1718] - No setting for the default index listing for Programme
[OPSK-1719] - Add Data file, from Assay doesn't work properly
[OPSK-1721] - Error generating RDF for template based data files
[OPSK-1726] - API allows tags to be specified for ISA
[OPSK-1732] - License links to opendefinition are broken
[OPSK-1733] - Update publication_author when deleting a Person
[OPSK-1734] - Avoid having to select terms and conditions when setting up new instance

Issue

[OPSK-1448] - Investigate SEEK sample link validation
[OPSK-1453] - Allow samples linking to missing samples to be registered
[OPSK-1495] - Add more info to sample resource list item
[OPSK-1642] - 2 pictures of the same person on publication page
[OPSK-1648] - Study capitalization reset on assay show page