MOLGENIS v1.9.0

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
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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