Bugfixes

Features

Bugfixes

Features

Bugfixes

Features

Bugfixes

Bugfixes

Features

Bugfixes

Features

Bugfixes

Known issues
https://github.com/molgenis/molgenis/issues?utf8=✓&q=label%3A1.11.0

Bug fixes

• #3712 Static content migration 1.8.x to 1.9.0 incorrect

Bug fixes

• #3866 Missing AttributeMapping.sourceAttribute migration step
• #3683 Migrate MappingProject.owner
• #3685 Menu migration encoding errors
• #???? Missing foreign key migration in convert names
• #3869 entities_attributes foreign key fix

Features

M3741 As dataexplorer user I would like to load more rows
M3677 As a biobankconnect user I would like to change the 'key words' on the mapping screen so the suggested attributes can be updated at real time
M3699 As GAF list plugin user I want to configure settings in plugin
M3764 As a BiobankConnect (MappingService) developer, I would like to wrap up the auto-algorithm generator
M3698 As annotator user I want to configure annotator settings in UI

Bugfixes

Fix #3827 Exception creating entity with mref attr that refren…
Fix #3831 Mapping service error
Fix #3828 Commandline annotator gives unhelpful error message when VCF validation cannot be run
Fix #3786 Filtering in the DataExplorer on date / timestamp fails
Fix #3675 Error when typing something in the search bar of the settings plugin
Fix #3785 Pager and rows-per-page pulldown don't play nice together
Fix #3802 Exac location does not get migrated
Remove entity locking
Fix #3784 Error evaluating visibleExpressions in the form editor
Fix #3764 TransactionLogService throws duplicate key exception
Fix #3746 'Validation failed' message doesn't disappear when you close an invalid conditional question
Fix #3763 fitconLocation migration fails and blows up the migration
Fix #3738 After deleting one entity row from a repository within a transaction, the repository comes up as completely empty for the rest of the transaction
Fix #3747 In the "Single Mapping project overview" add source does not work
Fix #3756 build->built in the footer
Fix #3737 Infinite transaction loop
Fix #3663 Importing two questionnaires after each other results in a dead data-explorer
Fix #3686 Annotators refuse to run for EMX files with string type ALT attributes
Fix #3705 VCF import slow
Fix #3218 Not able to map MREF attributes to MREF attributes in the mapping service with the help of the Map tab
Fix streams not being closed in a finally block. Use Java IO standard for file writing
Fix #3560 Wrong alignment of header/values in dataexplorer
Fix #3637 Clicking the 'map'-tab gives an error when no xref attribute has been selected yet
Fix #3413 Expanding a categorical in an mref breaks that column
Fix #3661 Remove date button in the date input component is not working.
Fix #3599 Annotating as a normal user will result in no permission on attributes and entities. Using the copy function will fail on no write permissions for packages
Fix Scanners and FileWriters using default encoding
Fix #3678 Model registry is broken when there are boolean attributes in an entity within a selected model
Fix #3645 GoNL annotator annotates with a random match from the GoNL source and Fix #3674 GoNL annotator throws UnknownAttributeException for AF column
Fix #3655: The SnpEff annotator contains a field that fails with large inserts or deletes
Fix #3671 The VCF writer writes newlines in VCF metadata for long descriptions
Fix #3650 MultiAllelicResultFilter remembers results from previous attribute
Fix #3665 Entity with extends and id attribute has no id attribute
Fix #3654 Errors&StackTraces when a query on the resource fails
Fix #3647: If you have an mref with missing values in one of the refe…
Fix #3643 VCF writer should place GT field first when writing samples
Fix #3626 migration fails
Fix #2768: When CHROM / POS columns are hidden and you click a geneti…
Fix #3596 GenomeBrowser das track load error IE11
Fix #3625 Clinvar annotator gives Message:null
Fix #3516 Questionnaire does not submit
Fix #3594 Data explorer download files no extensions (Firefox)
Fix #3351 VCF import with large deletion/insertion fails
Fix #3596: GenomeBrowser doesn't work properly with MOLGENIS hosted t…
Fix #3462 React error changing data set after selecting invalid data set
Fix #3587 Settings panel can't be reopened after cancel/close
Fix #3589 Settings plugin edit form when user can only read settings
Fix #3600: Using an int as an identifier for entities used as ref entities, i.e. target entities for mrefs, xrefs etc.. will cause the DOM to crash if you click the mref link in the dataexplorer
Fix #3551 Annotating with two annotators shows only one annotator's data unless you create a copy
Fix #3585 OntologyTermRepository returns almost all ontology terms if the search term is a pure number
Fix Findbugs error: relying on default encoding
Fix #3572 Form validation errors displayed wrong location

Breaking changes

MolgenisSettings have been removed, create your own settings entity instead.

Known issues

https://github.com/molgenis/molgenis/issues?utf8=✓&q=label%3A1.10.0+

Features

M3454 JavaScript and JavaScript (Magma) script runners
M3677 Remove unused code
M3727 require default description for the vcf writer
M3495 create a new annotator framework
M3455 Complex unit conversion
M3710 questionnaire improvements
M3676 add a next uncurated button
M3455 Automatic unit conversion in mappings
M2286 Settings management for plugins and app (improved migration)
M2286 Settings management for plugins and app
M3561 As Genome Browser user i want the browser viewer to adjust when…

New annotators: 1000G, SnpEff, DANN, ExAC
Privacy friendly Google Analytics

Bugfixes

Fix #3534 MapEntity hashcode ignores values
Fix #3561 galaxyURL is a URL which behaves badly when equals() and hashCode() are called
Fix #3368 Importing an entity with the same name but different casing will result in a locked importer
Fix #3549 Fix the unit test in molgenis-js module
Fix #3542 genomebrowser does not show if the CHROM and/or POS field a…
Fix #3546: If you have invalid code in you freemarker the dataexplorer…
Fix #3544 remove the old method consumeCaptcha and replaced it with validateCaptch
Fix #3481 IE8 alert not displayed in IE8
Fix #3083 "Sign in" button is not working correctly
Fix #3492 Default R roc script does not run on MOLGENIS VM
Fix #3463 Static content WYSIWYG editing broken
Fix #3500 (defaultValue can be > 255 characters so should be stored in TEXT not STRING)
Fix #3453 Compounds were still affected by the bug
Fix #3439 Annotators command-line missing value not according VCF specification
Fix #1810 EMX misses DefaultValue
Fix #3458 Annotators strip VCF flag fields
Fix #3453 Visible expressions in forms do not submit hidden values
Fix #3487 OntologyTermRepository.getChildren low performance
Fix #3298 AttributeMetaDataRepository now uses UuidGenerator
Fix #3376 Incorrect validation error when inserting invalid enum
Fix #3427 Molgenis01 is crashing after nightly deploy
Fix #3270 Mapping service expects mapping service to be in main menu
Fix #3254 When logged out, clicking the "entity report" will lead to a login dialog with a spinner on top
Fix #3233 Mapping result "Error details" button does nothing
Fix #3038 AttributeMapping must be < 255 characters
Fix #3415 App restart fails for entity with many mrefs
Fix #3359 Mismatch in LoggingEvent identifier of elastic is not used by elastic as an id
Fix #3346 IE9 complains about console not being defined... until it is...
Fix #3290 Cannot create TypeTest entity [master]
Fix #3293 Error annotating vcf with 'copy before annotating' option
Fix #3324 Deleting an entity in the dataexplorer will throw an error
Fix #3306 GAF list is broken due to the new limits of valid attributes names
Fix #3320 Uploaded logo displayed in original size
Fix #3317 MappingProjectMetaData.owner xref MolgenisUser instead of string
Fix #3236 Mapping Results: Shouldn't allow mapping if the result is of type String or decimal
Fix #3231 An attribute, in the attributes table of the attribute mapping page, are not shown correctly!
Fix #3313 IN/SEARCH query fails for FILE data type
Fix #3310 FUZZY_MATCH query fails for FILE/CATEGORICAL/CATEGORICAL_MREF
Fix #3301 Entity.getLabelValue throws RuntimeException for SCRIPT
Fix #3288 VCF import: entity name with underscore not allowed
Fix #3654 Errors&StackTraces when a query on the resource fails
Fix #3643 VCF writer should place GT field first when writing samples
Fix #3647 If you have an mref with missing values in one of the referenced entities, the table shifts the values
Fix #2768 When CHROM / POS columns are hidden and you click a genetic...
Fix #3625 Clinvar annotator gives Message:null
Fix #3626 Migration 1.8.2 --> 1.9.0 failure
Fix #3551 Annotating with two annotators shows only one annotator's data unless you create a copy
Fix #3462 React error changing data set after selecting invalid data set
Fix #3587 Settings panel can't be reopened after cancel/close
Fix #3600 Using an int as an identifier for entities used as ref…
Fix #3671 The VCF writer writes newlines in VCF metadata for long descriptions

Bug fixes

• Fixed #3415 App restart fails for entity with many mrefs

Bug fixes

• Fixed questionnaire module not being able to load
• Fixed other apps not starting due to missing spring beans

Features

• Reintroduced the catalogue plugin due to popular demand

Migration

• When migrating from older versions the catalogue can be added to the menu through the menu manager

Features

• Questionnaire plugin
• New data table design
• New mapping service design
• Dev: Annotator framework updated to allow quick and easy annotator creation
• Specify backend to store data in EMX upload format

Bugfixes

#3293 Error annotating vcf with 'copy before annotating' option (master)
#3320 Uploaded logo displayed in original size
#3317 MappingProjectMetaData.owner xref MolgenisUser instead of string
#3324 Deleting an entity in the dataexplorer will throw an error
#3306 GAF list is broken due to the new limits of valid attributes names
#3290 Cannot create TypeTest entity
#3236 Mapping Results: Shouldn't allow mapping if the result is of type String or decimal
#3231 An attribute, in the attributes table of the attribute mapping page, are not shown correctly!
#3332 Tag wizard shows strange succes message when finished data-mapper enhancement
#3321 molgenis.org does not log the standard INFO to catalina.out bug release test v15.07
#3313 IN/SEARCH query fails for FILE data type bug data-elasticsearch
#3310 FUZZY_MATCH query fails for FILE/CATEGORICAL/CATEGORICAL_MREF bug data-elasticsearch
#3301 Entity.getLabelValue throws RuntimeException for SCRIPT bug data
#3289 Wrong dataexplorer filter representation bug release test v15.07
#3288 VCF import: entity name with underscore not allowed bug data-vcf
#3282 dragging a menu item does not work. drags entire menu bug release test v15.07
#3279 dataexplorer: forms should be saved and give a 'saved' message bug dataexplorer release test v15.07
#3275 Annotators HGNC-Symbol is not a valid name bug data-annotators
#3267 Testing of mysql fails on windows 8/8.1
#3265 'endPostable already set' on installing molgenis on windows 7/8.1
#3262 Model registry is broken: HTTP Status 500 - Request processing failed; bug model-registry
#3244 Palga zoekterm select not usable bug
#3236 Mapping Results: Shouldn't allow mapping if the result is of type String or decimal data-mapper
#3235 SQL error: "Out of sort memory" when trying to reindex DICOM model bug data-elasticsearch data-mysql
#3232 Mapping results: Mapping should also work for categoricals with String IDs bug data-mapper
#3231 An attribute, in the attributes table of the attribute mapping page, are not shown correctly! bug data-mapper
#3224 Annotators fail to run more than one annotator bug data-annotators
#3219 Fix screen text overflow in the result table bug data-mapper
#3210 Javascript error in dataexplorer bug dataexplorer
#3186 Data explorer search term with space error bug dataexplorer
#3183 UML diagram not scrollable in Chrome bug model-registry priority: first
#3178 Permission manager setting permission broken bug security
#3169 Found entities are not shown in the dataexplorer bug dataexplorer
#3164 bbmri-nl-final.xlsx import fails bug data-importer
#3161 Max file upload size cannot exceed 2047 (mb) bug data-importer priority: first
#3160 Substring search broken? bug data question
#3156 Restarting after dropping the index only breaks the app bug priority: first
#3155 StackOverflowError when selecting 'packages', 'entities' and 'attributes' in Data Explorer bug data-rest dataexplorer
#3152 WAR breaks the server because it cannot find org/apache/commons/logging/LogFactory bug
#3145 Adding an entity for TypeTest in the new linked-in data table does not work bug dataexplorer priority: first
#3131 Document the way users can activate the dev profile.
#3128 Filter wizard tabs are broken bug dataexplorer
#3125 Filter wizard shows filters for hidden attributes bug dataexplorer
#3116 Migration from 1.5 to 1.7 tries to alter table for abstract entities bug data-mysql migrate
#3109 If session times out during import, the importer logs that as cause for import failure bug data-importer priority: first
#3105 Switching themes does not show expected theme bug
#3104 Tag Wizard: Run the Automatic Tagging multiple times and it will add the same tags multiple times browser: chrome bug data-mapper priority: first
#3099 MappingService: after running the automatic tagging service trying to edit results in error (Mappings for the project) browser: chrome bug data-mapper priority: first
#3095 Mref select2 pulldown gets the striping wrong bug dataexplorer priority: next
#3092 MappingService: it is possible to save when no source attribute is selected browser: chrome bug data-mapper priority: first
#3074 Hyperlink validator reports MalformedUrl validation error as invalid length bug data-validation priority: next
#3068 A REST API request with a logged out token gives error message in HTML instead of JSON bug data-rest priority: next
#3062 when I am on a very slow connection I don't see that MOLGENIS is working to talk to backend
#3061 User editor shows "big fixme: password type" bug core priority: first
#3060 Integer validation broken after clearing the field. bug priority: next
#3043 EMX nillable MREF validation broken bug data-importer priority: first
#3020 Data mapper does not show the auto-generated algorithms until you refresh. bug data-mapper priority: next
#3009 Chosing non-existing css file breaks MOLGENIS bug core-ui priority: next
#2917 Elasticsearch index not recreated on restart bug data-elasticsearch release test v15.05
#2609 User with READ permission on dataexplorer can edit entities bug dataexplorer priority: first
#2528 Importing VCF allows NaN as a valid Float value, but data explorer hangs on it bug data-importer dataexplorer priority: first
#2031 Rest API doesn't allow update of MREF attribute in MySQL repository bug data-rest priority: next
#1698 xrefmref select incorrectly uses lookup attributes when no unique attributes are available bug data-mysql priority: first
#1458 Option to download the values for the categorical values instead of the name dataexplorer enhancement priority: next
#3346 IE9 complains about console not being defined... until it is...

Breaking changes

• The EMX format is now subject to new formatting rules. For a complete list of rule changes see the molgenis github wiki

Maintenance release for Palga

Bugfixes since 1.4.3:

#3257 Unicode escape the Searching...
#3244 Palga zoekterm select not usable
#3173 Stream small files, store large files on disk
#3161 Max file upload size cannot exceed 2GB

Bugfixes since 1.4.2:

#2594 Replace escapeXml with escapeHtml4 to keep javascript in home content working. Fix JS in certain browsers crashing because function was specified within an if statement.
#2592 Fix for editor not understanding HTML named entities like ≤
#2579 Use createEntityQuery instead of auto returning the state query. The entity query might be translated in case of chr:pos format
#2577 Now check on attribute filter change if the genome browser is active or not. If not, don't try to set viewStart etc..
#2559 Runtime property enables/disables genome browser

Changes since v15.05

Features
#3006 Trac story 3473 Change True False labels into Yes No
#3001 Automatically generate mapping algorithms in the mapping service
#2996 Update annotators and create some new "genetic" entity-reports
#2998 Bootstrap theme selector + css fixes
Col7a1 specific tables and views
Update README.md

Bugfixes
#2916 Tag wizard tries to combine tags it finds into one big tag
#2935 Forms: error selecting categoricals with int ids
#2989 Use InnoDB
#2978 Fix metadata delete
#2981 Fix migration step 8 falling over table/column names with special characters
#2935: Fix error when selecting categoricals that have int as identifier
#2970: Fixed MySQL tests not applying identifier attributes correctly
#2891: StackOverflowError when selecting entities or attributes in Data Explorer
#2918: Key columns still stored as TEXT in MySQL when superclass is StringField
#3105: Switching themes does not show expected theme
#3101: Aggregateable attribute of type [BOOL] cannot be nillable

Bugfixes

• Fixed #3023 Mapping mref attribute to itself fails
• Fixed #3026 Mapping dates are not working correctly
• Fixed #3028 Mapping service breaks when an entity is removed

Features

• New forms based on reactjs
• New attribute features 'visibleExpression' and 'validationExpression'
• MySQL backend now supports more string attributes and xref/mrefs
• New datatype 'CATEGORICAL_MREF'
• New 'packages' tab in the importer
• M3 tagging enhancements
• Dataset delete: Select between data or data and metadata
• EMX format now uses fully qualified entity and packagenames

Bugfixes

• Entity delete does not delete references from entities_attributes table #2958
• Forms: nillable compound attributes are not hidden #2930
• Pathways applied to VCF not coloring gene #2912
• Default entity report error for user with explorer view permissions #2910
• Catalogue 'selectedEntityName' is undefined if dropdown empty #2908
• Entity Delete button not properly positioned #2889
• Importing data is not transactional #2873
• Deleting a dataset in the data explorer is not transactional #2872
• In the data explorer deleting a reference tabel will throw an error and only delete the index #2871
• EMX NullPointer on parsing meta data #2867
• Entity range validation broken in case of only min or max #2865
• Form decimal/int/long validation incorrect behavior #2863
• importer shows error when switching groups at report/permissions page #2862
• filter "from --> to" does not except "from 1 to 1" and results on 1<=x #2846
• REST login not working for non-admin users #2800

Breaking changes

• In the EMX format you must now use the fully qualified names for entities and packages

Bugfixes

molgenis-lifelines: #135: Entity form search broken
#2477: Search on lifelines catalog not working properly

Features

• #2551 map xref values in the Mapping service
• #2557 Enable uploading of OWL files using the standard importer
• #2465 Biobankconnect Mapping Service
• #2553 New pathways module
• #2701 Implement automatic migration from molgenis 1.4.3 to 1.5
• #2489 Improved annotator UI
• #2622 Added SNPEff as an annotator
• #2664 Add cookies message
• #2450 Change css styling at run-time
• #2483 Computed attributes
• #2556 Uuid string AutoID. Specify idAttribute: 'AUTO' in the attributes tab of the emx file for auto id's.
• #2487 GAF list tweaks
• #2563 New meta data api
• #2511 Importer: upload options now expanded by default.
• #2567 Updated dependency on Genotype-IO to newest version
• #2708 Rename Piwik RTP to body and Google Analytics to header
• #2561 Updated README for java8 + eclipse juno

Bugfixes

• Fixed #2734 Spaces, dots and other special characters in entity names cause the data explorer to no longer show tables
• Fixed #2736 Creating a redirect plugin in the menumanager with a URL does not work
• Fixed #2765 Importer permissions panel Save button does not look like a button
• Fixed #2756 Using multiple annotators will result in an error
• Fixed #2762 OMIM HPO annotator broken
• Fixed #2596 "No suitable importer found" when uploading .tsv files
• Fixed #2738 If a user has "count" permissions on a plugin, it is shown in the menu but gives 403 on click
• Fixed #2759 R Script cannot connect to Molgenis API
• Fixed #2755 In IE9 all content under the table is increasingly pushed down on hover of an x/mref
• Fixed #2740 Pathways plugin does not show uploaded VCF
• Fixed #2706 Max input length is not validated in forms
• Fixed #2735 The model registry Tree view does not show details after using the print option in the UML view
• Fixed #2758 Large ontology import is excruciatingly slow
• Fixed #2752 While the Importer is asynchronous importing, going to the data explorer will throw an error
• Fixed #2613 Missing refEntity while uploading, even though refEntity metadata is present
• Fixed #1979 Rows with only null values are less high than normal rows.
• Fixed #2749 As a User I cannot upload files if I only have import plugin permission
• Fixed #2769 Migration does not update menu
• Fixed #2751 Editable data explorer broken in IE9 for primitive types
• Fixed #2739 Merging 2 datasets with the name of an existing entity will overwrite this entity
• Fixed #2761 Entity report for OntologyTerm creates error.
• Fixed #2744 model registry does not work for normal user
• Fixed #2800 REST login not working for non-admin users
• Fixed #2628 Merge Genomic Data doesn't merge genomic data
• Fixed #2659 When updating an xref or mref entity the referencing entities do not change
• Fixed #2607 DataExplorer entity undefined error in case of no permitted entities
• Fixed #2721 When user is trying to sign up and the email is not sent, then some info of the user gets into the database.
• Fixed #2546 Unable to view dataexplorer with "view" permissions if "editable dataexplorer" is true
• Fixed #2716 VCF info compound data is missing
• Fixed #2713 annotating destroys entitymetadata
• Fixed #2711 show "home" instead of logo if "home" has been specified.
• Fixed #2709 REST API create/update from form ignores multi-value params
• Fixed #2710 Fix findbugs warning
• Fixed #2707 REST API expose lookup attributes and enum options
• Fixed #2699 REST entity meta: add writable property
• Fixed #2695 Attribute with auto=true broken for DATE and DATE_TIME data types
• Fixed #2687 Inconsistent encoding in the REST controller
• Fixed #2693 Updating read-only entities fails for categorical/xref
• Fixed #2685 Annotators fail with a nullpointer exception.
• Fixed #2684 show "home" instead of logo if no logo has been specified + default logo in populator
• Fixed #2683 A fix for a bug found by molgenis-reports
• Fixed #2602 StackOverflowError when adding MetaData to an Entity with self-reference
• Fixed #2679 Eclipse build errors for AutoValue classes
• Fixed #2674 Eclipse overwrites filtered resources with incorrectly filtered resources
• Fixed #2667 ${maven.build.timestamp} in MOLGENIS footer
• Fixed #2680 fix data too long for column in importer
• Fixed #2661 MREFs between the same entity do not get properly imported.
• Fixed #2675 fix error in "NONE" check on setting permissions on imported entities
• Fixed #2673 fix saving permission=none at import
• Fixed #2671 Expandable ref entities in data explorer attribute tree
• Fixed #2670 Range query operator
• Fixed #2669 Fix ontology and ontology-core unit tests on windows
• Fixed #2582 attribute metadata order gets shuffled when the metadata repositories get reindexed
• Fixed #2645 MySQL MREFs lose values when the combined ID strings are > 1024 characters
• Fixed #2668 Introduce CATEGORICAL_MREF datatype M3193
• Fixed #2665 HtmlField has enum type TEXT instead of HTML
• Fixed #2662 As 5GPM I want to upload data and automatically add permissions for my group so we can work together
• Fixed #2660 No WRITE permission on entity when importing VCF as normal user
• Fixed #2657 Annotators throw nullpointer exception
• Fixed #2619 "Unknown entity exist" when merging data with name field left empty
• Fixed #2608 Annotate button enabled in case no annotators available
• Fixed #2656 XSLT transform Phenotype DB data type xml into EMX excel sheets.
• Fixed #2651 Add instructions to configure eclipse's annotation processing to synchronize with maven builds.
• Fixed #2646 Hidden attributes not hidden in data explorer and entity view
• Fixed #2648 Clean up addAttribute methods in MySqlRepository. Add compound attribute example to the TypeTest entity.
• Fixed #2640 Rest API does not expose auto attribute
• Fixed #2641 Rest API does not expose non-visible attributes
• Fixed #2638 JPA entity meta data misses enum options
• Fixed #2565 Changing existing attributes is not currently supported when updating a dataset.
• Fixed #2616 When mapping xref attributes, the test method reports 0 valid entries even though the actual mapping works fine.
• Fixed #2610 Filterwizard shows wrong fields for COMPOUND attribute
• Fixed #2409 Entity report does not support compound attributes
• Fixed #2630 Fix bug for adding compound attributes, created util class for annotators, eclipse formatted all annotatos
• Fixed #2626 fix findbugs warnings and fix imports for snpEffAnnotator
• Fixed #2621 "Repository is null" when trying to merge genomic data
• Fixed #2617 Automatic reindexing fails
• Fixed #2625 Add missing resources for unit tests
• Fixed #2620 fix vcf issue + merge some annotator code from branch "annotator-unit-test"
• Fixed #2581 Cannot import separate EMX data file
• Fixed #2604 Fix annotators for the new Data-API + add username to logging and progress indication in logging
• Fixed #2601 MySQL entity with xref attribute to JPA entity not working
• Fixed #2598 Fix findbugs warnings
• Fixed #2593 Fix JS in certain browsers crashing because function was specified within an if statement
• Fixed #2591 Fix for editor not understanding HTML named entities like ≤
• Fixed #2589 Fix JPA canImport method
• Fixed #2585 Implement molgenis autoid for JPA so we can upload JPA entities
• Fixed #2580 Removed searchTerm from dataexplorercontroller + ftl. Now return createEntityQuery instead of force return the statequery
• Fixed #2549 Molgenis R API does not work over https
• Fixed #2571 VCF import is slowed down to about 150 a minute after the new data api
• Fixed #2566 "Unknown mref value for attribute SAMPLES" when uploading big vcf
• Fixed #2568 Fix reindexing
• Fixed #2555 Change generated ID encoding to prevent casing problems
• Fixed #2543 MyDasServerConfig is not detected on startup, breaking the genome browser
• Fixed #2538 Added FreemarkerTemplate to the molgenis_ui.xml
• Fixed #2533 3rd party dependencies use Log4j instead of Logback
• Fixed #2527 Unique id generator
• Fixed #2524 Dropdown search returns unexpected matches
• Fixed #2521 Indexer doesn't have to ngram analyze nested docs
• Fixed #1550 GenomeBrowser makes the browser crash
• Fixed #2351 Elasticsearch all shards failed error
• Fixed #2515 fixed test input file for attribute mapping
• Fixed #2513 OMX2EMX converter fails to convert features belonging to multiple protocols
• Fixed #2505 Added a check to the dataexplorer.js to see if chromosomeAttribute and posAttribute are undefined
• Fixed #2455 A deleted entity is not removed from the menu
• Fixed #2490 All menu-items from the same plugin are active
• Fixed #2481 Batched annotators improve performance
• Fixed #2445 new relations for UML imports
• Fixed #2458 Don't URL escape the URL bit of a menu item.
• Fixed #2469 DependencyResolver did not check CompoundAttributes, resulting in "NULL" refEntities in the attributes table.
• Fixed #2460 Added standalone runnable JAR creation of CmdLineAnnotator to Maven build
• Fixed #2453 dataset is now called entity in the dataexplorer url
• Fixed #2448 Import validator improvement
• Fixed #2427 Deleting VCF data set does not remove references

Migration

Now happens automatically.