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@fdlk fdlk released this 10 Sep 12:51
· 1 commit to 7.0 since this release
7.0.0-RELEASE
39cd8ae

Documentation

Updated documentation is available here.

Features

  • Dynamic decorators.
  • EntityType permissions can now be set in bulk by handing out permissions to the package they are in.
  • EntityTypes can now be row level secured in the permission manager. This replaces the Owned entity.
  • Using the includeCategories flag in a REST query will now add categorical options to the api/v2 attribute metadata response for CATEGORICAL and CATEGORICAL_MREF attributes.
  • Mapping service now supports algorithms which want to use values from a referenced entity besides ID values
  • Made changes to make searching and filtering in MOLGENIS case-IN-sensitive. Changes are reflected in the following modules:
    • XREF / MREF filters in the data explorer
      • Searching and filtering is now performed via a SEARCH query instead of a LIKE query.
    • Search in settings screen
  • M5663 As data owner I want to check package permissions when creating packages or entitytypes
  • Users cannot be deleted anymore, only disabled.
  • Disabled users cannot authenticate nor be used to create an authentication token
  • Upgraded the App store, now called the App manager.
    • New UI written in Vue
    • New backend
    • New app zip specifications
      • Apps are now described by a config.json file
    • Added app search functionality
  • Increased performance by implementing different strategy for evaluating javascript validation expressions
  • M5796 As dev/ops I want to be able to configure MOLGENIS using only environment variables
    • store version in database instead of mutating molgenis-server.properties
    • set default application data root to 'user.home/.molgenis'
    • generate random one-time use password for admin
  • Added group API which makes it possible to add a Group with default Roles, Permissions and Package in one simple step.
  • M5811 - Add Security Manager to MOLGENIS. You can manage groups and role memberships in groups. When you create a group, a folder is created implicitly. Members can be MANAGER, EDITOR or VIEWER in this folder-context.
  • Data explorer delete button for those who have the proper permission
  • M5980 Questionnaire PDF download: optionally include logo, introduction text and pagenumbers
  • Importer now has an option to ignore metadata changes when importing EMX

Fixes

  • Fix #7542 #7665 #7666 Python tests and documentation fixes
  • Fix #7611 EMX import with tags fails when ignoring metadata
  • Fix #7615 Deleting all row-level secured data does not delete all data
  • Fix #7631 #6930 Deleting 'cascade delete' entity type does not perform cascade delete
  • Fix #7588 Editor/viewer cannot view reports in the view tab
  • Fix #7543 Vue style plugins are broken when using a 'top'
  • Fix #7374 Vulnerability in math.js used in MagmaScript
  • Fix #7184 When I upload dataset with wrong mref value I get wrong error message
  • Fix #6969 label must be specified when id is hidden
  • Fix #7247 lookup attributes must be visible
  • Fix #7183 CSV read exception on #values mismatch with #headers
  • Fix #6906 Importing an entitytype with several columns with the same name, import without errors
  • Fix #6792 When adding a new setting, using it after restart will add a comma to all inputs
  • Fix #6729 When adding a compound attribute to a system entity the attribute is added twice
  • Fix #7254 Cannot update attributes for an abstract entity that is extended by concrete entity
  • Fix "Dataexplorer should be usable without permission on genomebrowser config entities"
  • Fix #7280 Importing multiple attributes with the same name doesn't throw an error
  • Fix #7297 One-to-many with integer ids retrieval
  • Fix #7178 Navigator results might not be up-to-date
  • Fix #7302 Search all plugin missing results
  • Fix #6945 NPE importing EMX with abtract entity type data
  • Fix #7131 Unclear error importing an EMX file twice in ADD mode
  • Fix #7336 REST API v2 unknown error instead of not found message
  • Fix #7169 When having jobs running as superuser and my account is set to inactive, my jobs still run
  • Fix #2691 Infinite EMX import for EMX with deep nested formulas
  • Fix #7341 Excel repository assumes case insensitive headers
  • Fix #292 Change default FreeMarker number formatting
  • Fix #7365 Range type mismatch unclear error
  • Fix #7199 Mapping service: do not map to target expressed attribute
  • Fix #7335 Metadata manager: error creating file attribute
  • EMX metadata parser: validate that compound parent is not itself
  • Fix #7379 Import wizard package assignment broken
  • Fix #7438: 2FA pincode entry does not acquire focus
  • Fix #6418 As data manager user I require that 'label' attribute cannot be nillable
  • Fix #7248 Label attribute can be hidden
  • Fix #7360 Entities without labels cannot be saved in the metadata manager
  • Fix #7455 Can't delete entity with id containing special chars
  • Fix #7474 Metadata manager one-to-many attribute creation not possible
  • Fix #7440 Invalid range in input in questionnaire results in loss of progress
  • Fix #7415 My generated algorithm in mapping service starts with tabs
  • Fix #7416 Large text indexing results in exception
  • Fix #7496 Mapping service attribute search results incorrect count/results
  • Fix #7498 Mappings between molgenis 6 and 7 not compatible
  • Fix #7545: SearchAll does not show thrown exceptions
  • Fix #7558: Test Questionnaire EMX file is not properly localized
  • Fix #7536: Cannot select label in compound
  • Fix broken styling for login modal in Vue menu
  • Fix #7585 Quick data import fails on dates
  • Fix #7666 Python test script UploadZipAndDeleteList.py is broken (this time also for python 3)

Changes

  • Removed hierarchical permissions from permission manager controller plugin
  • Permissions not accessible through data explorer plugin or REST API
  • Remove ontology manager plugin
  • Remove gavin and annotators

#7239 Elasticsearch config changes

  • Reduce Elasticsearch index size by a factor of ten
  • Increase Elasticsearch indexing speed (Travis integration tests finish in 28.5 instead of 40.5 min)
  • Split on case transitions: search query 'ontology' matches 'ontologyTerm'
  • Split on letter-number transitions: search query 'sample' matches' 'sample123'
  • ASCII folding: search query 'role' matches 'rôle', 'strasse' matches 'Straße'
  • Ngram tokenization changes: like query 'ring' doesn't match 'String', 'stri' does match 'String'

Breaking changes

  • Tomcat 8.5.x required instead of 7.x
  • Drop-in upgrade not possible: use a clean install
  • Numbers in freemarker are now by default "computer language" (https://freemarker.apache.org/docs/ref_builtins_number.html#ref_builtin_c)
  • Upgraded mathjs from 2.1.1 to 4.3.0
  • Entities must have a visible label attribute (this may be the id attribute if no label attribute is present)
  • Only superusers can use the mapping service
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