Release Notes - Sysmo DB - Version 0.18 - HTML format

Bug

  • [SYSMO-826] - Events selection box (in this case on presentation form) always includes all events from all projects
  • [SYSMO-1192] - If model has single viewable file, it doesn't have a View Content button
  • [SYSMO-1230] - is_published? needs fixing
  • [SYSMO-1231] - can_delete? called on each model and the value stored in autholookup tables are not synchronized
  • [SYSMO-1239] - sharing status of public item needs to be checked through can_download for downloadable assets
  • [SYSMO-1240] - remove the is_entirely_private? check on summarize_permissions
  • [SYSMO-1264] - Need to handle updating the rdf when an item changes to private to public - or vice versa
  • [SYSMO-1265] - When you request RDF through content negotitation (or .rdf at the end) a cache of the rdf file isn't stored
  • [SYSMO-1266] - clicking the view all link, whilst logged out, requests a password
  • [SYSMO-1268] - Removing a favourite logs you out
  • [SYSMO-1269] - Dragging a favourite on front page becomes invisible
  • [SYSMO-1271] - Associate Sample box doesn't have a preview
  • [SYSMO-1272] - can not upload a help image
  • [SYSMO-1281] - Chrome warns insecure content on https://testing.sysmo-db.org/models/17/simulate?version=1
  • [SYSMO-1283] - Cannot create a new ReindexingJob if a failed one exists
  • [SYSMO-1284] - Projects latest are not ordered correctly
  • [SYSMO-1285] - Setting the "latest" list length in the admin setting has no effect
  • [SYSMO-1286] - Organism#visualise needs a new layout
  • [SYSMO-1287] - "destroy specimen" specimen unit test fails when run on its own
  • [SYSMO-1295] - content_blob_test gets deleted
  • [SYSMO-1300] - The previous model filename does not display correctly when uploading new version for the model imported from biomodel database
  • [SYSMO-1303] - Find related data/model seems to work not correctly?
  • [SYSMO-1304] - Receive message 'New assay_type was created but its parent window was closed.' even it is created from admin page
  • [SYSMO-1306] - Error when updating home page settings
  • [SYSMO-1307] - A duplicate delayed job for subscription daily emails has appeared
  • [SYSMO-1313] - Home page description text disappeared after update
  • [SYSMO-1315] - Error when matching data for models
  • [SYSMO-1316] - Upgrade issue - problem with queue missing in DB
  • [SYSMO-1317] - init.d scripts fail with bundler
  • [SYSMO-1318] - Organism visualization should use the secure link to keg ncbi browser
  • [SYSMO-1319] - Fetching rdf gives a undefined class/module CSV::Cell error
  • [SYSMO-1320] - nil resources in RDF aren't described correctly
  • [SYSMO-1321] - revert_fixtures_identify used in rake task stops working
  • [SYSMO-1323] - Sample #assets incorrect
  • [SYSMO-1331] - Mysql2::Error: Illegal mix of collations (latin1_swedish_ci,IMPLICIT) and (utf8_general_ci,COERCIBLE)
  • [SYSMO-1340] - Selecting Invalid Users/Profile from the admin stats show the wrong view
  • [SYSMO-1344] - Graphs do not appear for matching data
  • [SYSMO-1348] - Return to search link is misplaced in Admin page
  • [SYSMO-1351] - The URL to the Help attachments has changed

Improvement

  • [SYSMO-1261] - Separate the generated .pdf and .txt files from the main content-blob assets
  • [SYSMO-1276] - Put back the header on pages (other than front page which already has it) but smaller
  • [SYSMO-1292] - Rename 'Publish all your assets' to 'Publish your assets'
  • [SYSMO-1293] - In the publishing process, if it is not the final step, should rename the button 'Submit' by 'Next'
  • [SYSMO-1296] - When viewing inline document content, should open it in a new tab
  • [SYSMO-1310] - for batch publishing, send only one email to the gatekeepers containing all the request approval items
  • [SYSMO-1314] - Review guide text for publishing wizard
  • [SYSMO-1325] - Make the edit description box larger for Project
  • [SYSMO-1334] - should show a warning message instead of throwing an error when can not remove a workgroup
  • [SYSMO-1367] - Reintroduce caching of front page activity items

New Feature

Refinement

  • [SYSMO-1175] - remove 'Back to model' from jws onestop page
  • [SYSMO-1289] - Make the file storage location configurable
  • [SYSMO-1290] - Internationalize configurable strings
  • [SYSMO-1309] - Extend rdf listener hook to push rdf to virtuoso
  • [SYSMO-1346] - Remove the move to presentations button
  • [SYSMO-1355] - Remove the ability to add or edit assay or technology types
  • [SYSMO-1374] - check if the 'git' package is needed for installing seek on ubuntu 10.04/12.04, or only git-core needed

Task

  • [SYSMO-1221] - Publishing
  • [SYSMO-1252] - make sycamore open in a new tab to avoid the page out of seek domain
  • [SYSMO-1311] - Upgrade and Installation guide needs updating to reflect change of rubygems, ruby1.9 and database utf-8
  • [SYSMO-1312] - Thorough testing of fresh installation, and upgrading from 0.17.x
  • [SYSMO-1349] - Refresh bundled Help docs with those from live server

Sub-task

  • [SYSMO-1222] - get the old publishing page up and running again
  • [SYSMO-1223] - add one click publishing with a button, that mimicks manually setting the sharing permissions
  • [SYSMO-1224] - Prevent published items being unpublished or deleted
  • [SYSMO-1225] - Batch publishing
  • [SYSMO-1226] - send an email to the person who submit publishing request, to let them know the final decision of the gatekeepers
  • [SYSMO-1235] - Should log whether a gatekeeper request for publishing was accepted or approved, along with when and why
  • [SYSMO-1328] - replace rake task sunspot:solr:reindex by seek:reindex_all in the guides
  • [SYSMO-1329] - Check libxml2-dev is needed to be installed or just libxml++2.6-dev
  • [SYSMO-1335] - update the guides to install libreoffice 3.5, as it fixes some converting problems and improves the speed.
  • [SYSMO-1337] - changing adapter in database.yml to mysql2
  • [SYSMO-1338] - need to run db:migrate before seek:upgrade, otherwise seek:repopulate_auth_lookup_tables will throw error
  • [SYSMO-1342] - upgrade to ruby 1.9.3 by RVM
  • [SYSMO-1343] - install ruby 1.9.3 from scratch, without ruby 1.8 available

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