Release Notes - Sysmo DB - Version 0.20 - HTML format


  • [SYSMO-1435] - undefined method `can_see_hidden_item?' for #<Sop::Version:0x007f0028477320>
  • [SYSMO-1442] - When disassociating people from projects, it should also remove the project subscriptions
  • [SYSMO-1454] - the row index display wrongly for some sheets
  • [SYSMO-1461] - famfamfam_silk/page_add.png is missing from compiled images
  • [SYSMO-1462] - can download the whole model package, but can not download individual file, or view the content
  • [SYSMO-1467] - Biological problem addressed: /assay_types? appears on assay page
  • [SYSMO-1468] - investigation and study still appear on study/assay page, even they are hidden
  • [SYSMO-1469] - the isa graph disappears if zoom in/out on FF and Chrome and IE on Window
  • [SYSMO-1471] - Bug with list item avatar images being regenerated
  • [SYSMO-1472] - Fix the font-awsome css to be seperate from cytoscape
  • [SYSMO-1474] - Update to use cytoscape 2.0.3 in a clean state
  • [SYSMO-1478] - some publication author names are wrong displayed
  • [SYSMO-1483] - Error when exploring spreadsheet via pagination
  • [SYSMO-1484] - Error when trying to create a new study based on an existing one
  • [SYSMO-1485] - The announcements box on the test server is empty?
  • [SYSMO-1494] - Allow administrator to view the asset report for other projects.
  • [SYSMO-1495] - No indication there are more items in the list
  • [SYSMO-1496] - Enhanced asset reporting
  • [SYSMO-1497] - SopSpecimens are not correctly being cleaned up
  • [SYSMO-1499] - Problem with email settings with a long password
  • [SYSMO-1504] - Biomodels link is incorrect
  • [SYSMO-1505] - Incorrect BioModels results if publication is a DOI
  • [SYSMO-1506] - Problem during sign-up if full details aren't given
  • [SYSMO-1507] - Required fields in the profile creation page need to labeled as such
  • [SYSMO-1508] - Text replacement for Investigation wrong on activity stream
  • [SYSMO-1510] - experimental assay types appear for modelling analysis
  • [SYSMO-1512] - Periodic error when trying to render an exception
  • [SYSMO-1516] - list of presentations for people only filters by the uploader
  • [SYSMO-1517] - missing html_safe for specimen creators
  • [SYSMO-1520] - 'save as annotation' appears on the plotting graph of downloadable item
  • [SYSMO-1523] - expected related ISA's aren't returned when searching for a person
  • [SYSMO-1524] - Unable to determine strain when linking to assay
  • [SYSMO-1525] - Assay / new_object_based_on_existing_one should require a login
  • [SYSMO-1526] - XML Schema and XML needs updating for BioPortal
  • [SYSMO-1529] - when you log out a / gets put on the end of the path
  • [SYSMO-1530] - comparing model versions should not be available for non-downloadable models


  • [SYSMO-1359] - Update SEEK to make use of the asset pipelining
  • [SYSMO-1424] - Authors associated with a publication should also have edit rights
  • [SYSMO-1449] - pagination for excel content
  • [SYSMO-1486] - Increase the sheet explorer size limit
  • [SYSMO-1490] - Navigation problems in SEEk if using back button of the browser
  • [SYSMO-1498] - Upgrade to latest version of sunspot solr
  • [SYSMO-1500] - Check and override the default number of results for sunspot
  • [SYSMO-1501] - Include institution address in search indexing
  • [SYSMO-1519] - Add some guidance text for tagging


  • [SYSMO-1432] - Double check the use of html_safe and h() to check for potential XSS or overzealous escaping
  • [SYSMO-1459] - Is the pubmed_query_tool gem still needed?

New Feature

  • [SYSMO-1450] - Read the ontology terms for assay/technology types directly from the ontology
  • [SYSMO-1476] - Integrate BiVeS to support the comparison between SBML versions


  • [SYSMO-1477] - Clarify the new file when uploading new model file version
  • [SYSMO-1522] - Update BioPortal plugin to use new API
  • [SYSMO-1552] - Remove Find related models button


  • [SYSMO-1455] - add a upgrade task to clear avatars, model_images, image_assets under filestore/tmp
  • [SYSMO-1466] - automatically choose ruby version and gemset when cd to the seek repo
  • [SYSMO-1503] - Update documentation for install and upgrade for asset pipelining
  • [SYSMO-1513] - Hide the treatments from data file view
  • [SYSMO-1514] - Collapse some boxes on profile page by default
  • [SYSMO-1521] - Visualise ontology term of an organism: the window is very small in Firefox and can not be expanded


  • [SYSMO-1451] - Fix for fontawesome-webfont.ttf
  • [SYSMO-1456] - Multiple duplicate avatars are appearing on the Person#edit page

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