Bugfixes

• Fixed #2612 Content created in the home page editor as admin is now correctly escaped and unescaped.

Features

• Admins can now specify if the genomebrowser should be active or not

Bugfixes

• Fixed #2533 3rd party dependencies use Log4j instead of Logback
• Fixed #2524 Dropdown search returns unexpected matches
• Fixed #2521 Indexer doesn't have to ngram analyze nested docs
• Fixed #2351 Elasticsearch all shards failed error
• Fixed #2478 Reindexing fails when an entity has multiple references to the same categorical
• Fixed #2490 All menu items from the same plugin are active
• Fixed #2541 Searching for chr:pos-pos or chr:pos in the dataexplorer throws errors
• Fixed #2543 MyDasServerConfig is not detected on startup, breaking the genome browser

Migration

• Remove /.molgenis/data/elasticsearch before starting your application

Bug fixes

• Fix #2458 Don't URL escape the URL bit of a menu item
• Fix #2462 Importer silently ignores missing refEntity on Categoricals
• Fix #2508 Change EMX importer registration order to allow other importers to register before this importer

Features

• Manage MOLGENIS footer text through UI
• R API: support sorting
• Data explorer: add rows in edit mode
• Data explorer: delete data sets
• Data explorer: bookmark state of current entity, search query and selected module
• Data explorer annotator: copy before annotating
• Automatically recreate index if not exists on application startup

Bug fixes

• Fixed #1971 Even on highest resolution, data explorer has vertical scrollbar
• Fixed #1986 IE8 warning bar behind top menu
• Fixed #2004 Forgot password should force a change of password at the first login
• Fixed #2033 Entity form saves false boolean properties as NULL values.
• Fixed #2148 Model registry details view unknown model warnings on reload
• Fixed #2211 Data explorer data select layout issues
• Fixed #2225 Data explorer IE9 JavaScript error
• Fixed #2245 Attribute update can results in incorrect index update
• Fixed #2247 Query with operator NOT not working
• Fixed #2255 Default Entity reports not working for some entities
• Fixed #2256 Case sensitive search not working in xref/mref search control
• Fixed #2275 Data explorer text filters only match exact text
• Fixed #2314 Static content plugins save button disabled
• Fixed #2326 Query with multiple NOT clauses not working
• Fixed #2342 Importer fails on empty but defined row in the excel sheet
• Fixed #2346 Disease Matcher disease filter does not respect data item filters
• Fixed #2354 XREF or MREF columns in the download as CSV are incorrect
• Fixed #2371 Select2 do not close dropdown on select
• Fixed #2381 Various data explorer CADD annotator problems
• Fixed #2382 Various data explorer disease matcher problems
• Fixed #2383 DataExplorer entity dropdown is not hidden
• Fixed #2387 DataExplorer filter errors
• Fixed #2392 Sample refs not clickable in imported VCF in data explorer
• Fixed #2396 'Run annotation' button should be disabled if no annotators available
• Fixed #2398 Error run annotator with 'Copy before annotating'
• Fixed #2400 GAF list validation errors are html encoded
• Fixed #2401 'lookup attribute is not defined' when importng vcf with samples
• Fixed #2403 Merge plugin error
• Fixed #2405 Error creating menu with strange chars
• Fixed #2406 Error after adding a redirect plugin to the menu and restarting the server
• Fixed #2416 Editable DataExplorer error updating #CHROM attr
• Fixed #2417 Error Editable DataExplorer add new ES entity
• Fixed #2424 Genome browser not working on IE9
• Fixed #2428 Custom views missing js dependency
• Fixed #2432 Minified resources are re-minified

Breaking changes

• MOLGENIS requires Java 8 to build and run
• Genome browser does not work on IE9

Migrating from MOLGENIS 1.3.0 to 1.4.0

• Create table in MySQL:

CREATE TABLE `entities_tags` (
  `fullName` varchar(255) NOT NULL,
  `tags` varchar(255) NOT NULL,
  KEY `fullName` (`fullName`),
  KEY `tags` (`tags`),
  CONSTRAINT `entities_tags_ibfk_1` FOREIGN KEY (`fullName`) REFERENCES `entities` (`fullName`) ON DELETE CASCADE,
  CONSTRAINT `entities_tags_ibfk_2` FOREIGN KEY (`tags`) REFERENCES `tags` (`identifier`) ON DELETE CASCADE
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin;

• Remove <home_dir>/.molgenis/data/elasticsearch
• Start application, go to Admin --> Menu Manager and delete Ontology and Custom Views menus
• Hide dataexplorer dropdown using query string parameter hideselect=true instead of RuntimeProperty for menu items
• Initialize dataexplorer with query= instead of searchTerm

Use iframe uploader to upload study file in order item form. Fixes https://github.com/molgenis/molgenis-lifelines/issues/128
Language corrections in messages to user
Removing in Submit Study Request modal does not work #2318
Show Group in Submission details modal.
Show group in Submit Study Request as well.
Add group column to export
CatalogManager: Activate and Deactivate methods are made synchronized
Fix: filter draft study definitions from order list
Change unique validation message into a more user friendly message
Replace the symbol point '.' with space ' '. That causes in some situations messages with double points. Example: "message one.." "message two."
Add middle name to account related emails
Require MolgenisUser first and last name
html and js escaping (prevent xss exploits)
Show external item id in study manager
Specify measurement with observation
Specify measurement for items in order
Trac issue #2973 As LifeLines datamanager I want to publish unavailable items in the catalogue
Withdraw study definitions
Trac issue #1981 As LifeLines datamanager I want to update study definition title
Trac issue #2994 As LifeLines datamanager I want to search on study definition date
M2974 As LifeLines datamanager I want researchers to only order groups of items (wip)
M2974 order catalog item groups instead of individual items (WIP)
#1784 Edit mode of rest api is broken
#1782 User manager is broken
#1796 Send user to home page when session has expired

Molgenis 1.3.0 release

• Replace MOLGENIS security framework with Spring security framework
• Genome browser plugin
• Biobankconnect plugins
• User manager plugin
• Permission manager plugin
• Data set deleter plugin
• Add data aggregates to data explorer plugin

2013-08-21 Before hackaton